Human L1 Transposition Dynamics Unraveled with Functional Data Analysis
Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been stu...
Gespeichert in:
| Veröffentlicht in: | Molecular biology and evolution Jg. 37; H. 12; S. 3576 - 3600 |
|---|---|
| Hauptverfasser: | , , , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
United States
Oxford University Press
16.12.2020
|
| Schlagworte: | |
| ISSN: | 0737-4038, 1537-1719, 1537-1719 |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| Abstract | Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. To fill this gap, we investigated three genome-wide data sets of L1s that integrated at different evolutionary times: 17,037 de novo L1s (from an L1 insertion cell-line experiment conducted in-house), and 1,212 polymorphic and 1,205 human-specific L1s (from public databases). We characterized 49 genomic features—proxying chromatin accessibility, transcriptional activity, replication, recombination, etc.—in the ±50 kb flanks of these elements. These features were contrasted between the three L1 data sets and L1-free regions using state-of-the-art Functional Data Analysis statistical methods, which treat high-resolution data as mathematical functions. Our results indicate that de novo, polymorphic, and human-specific L1s are surrounded by different genomic features acting at specific locations and scales. This led to an integrative model of L1 transposition, according to which L1s preferentially integrate into open-chromatin regions enriched in non-B DNA motifs, whereas they are fixed in regions largely free of purifying selection—depleted of genes and noncoding most conserved elements. Intriguingly, our results suggest that L1 insertions modify local genomic landscape by extending CpG methylation and increasing mononucleotide microsatellite density. Altogether, our findings substantially facilitate understanding of L1 integration and fixation preferences, pave the way for uncovering their role in aging and cancer, and inform their use as mutagenesis tools in genetic studies. |
|---|---|
| AbstractList | Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. To fill this gap, we investigated three genome-wide data sets of L1s that integrated at different evolutionary times: 17,037 de novo L1s (from an L1 insertion cell-line experiment conducted in-house), and 1,212 polymorphic and 1,205 human-specific L1s (from public databases). We characterized 49 genomic features-proxying chromatin accessibility, transcriptional activity, replication, recombination, etc.-in the ±50 kb flanks of these elements. These features were contrasted between the three L1 data sets and L1-free regions using state-of-the-art Functional Data Analysis statistical methods, which treat high-resolution data as mathematical functions. Our results indicate that de novo, polymorphic, and human-specific L1s are surrounded by different genomic features acting at specific locations and scales. This led to an integrative model of L1 transposition, according to which L1s preferentially integrate into open-chromatin regions enriched in non-B DNA motifs, whereas they are fixed in regions largely free of purifying selection-depleted of genes and noncoding most conserved elements. Intriguingly, our results suggest that L1 insertions modify local genomic landscape by extending CpG methylation and increasing mononucleotide microsatellite density. Altogether, our findings substantially facilitate understanding of L1 integration and fixation preferences, pave the way for uncovering their role in aging and cancer, and inform their use as mutagenesis tools in genetic studies. Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. To fill this gap, we investigated three genome-wide data sets of L1s that integrated at different evolutionary times: 17,037 de novo L1s (from an L1 insertion cell-line experiment conducted in-house), and 1,212 polymorphic and 1,205 human-specific L1s (from public databases). We characterized 49 genomic features-proxying chromatin accessibility, transcriptional activity, replication, recombination, etc.-in the ±50 kb flanks of these elements. These features were contrasted between the three L1 data sets and L1-free regions using state-of-the-art Functional Data Analysis statistical methods, which treat high-resolution data as mathematical functions. Our results indicate that de novo, polymorphic, and human-specific L1s are surrounded by different genomic features acting at specific locations and scales. This led to an integrative model of L1 transposition, according to which L1s preferentially integrate into open-chromatin regions enriched in non-B DNA motifs, whereas they are fixed in regions largely free of purifying selection-depleted of genes and noncoding most conserved elements. Intriguingly, our results suggest that L1 insertions modify local genomic landscape by extending CpG methylation and increasing mononucleotide microsatellite density. Altogether, our findings substantially facilitate understanding of L1 integration and fixation preferences, pave the way for uncovering their role in aging and cancer, and inform their use as mutagenesis tools in genetic studies.Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. To fill this gap, we investigated three genome-wide data sets of L1s that integrated at different evolutionary times: 17,037 de novo L1s (from an L1 insertion cell-line experiment conducted in-house), and 1,212 polymorphic and 1,205 human-specific L1s (from public databases). We characterized 49 genomic features-proxying chromatin accessibility, transcriptional activity, replication, recombination, etc.-in the ±50 kb flanks of these elements. These features were contrasted between the three L1 data sets and L1-free regions using state-of-the-art Functional Data Analysis statistical methods, which treat high-resolution data as mathematical functions. Our results indicate that de novo, polymorphic, and human-specific L1s are surrounded by different genomic features acting at specific locations and scales. This led to an integrative model of L1 transposition, according to which L1s preferentially integrate into open-chromatin regions enriched in non-B DNA motifs, whereas they are fixed in regions largely free of purifying selection-depleted of genes and noncoding most conserved elements. Intriguingly, our results suggest that L1 insertions modify local genomic landscape by extending CpG methylation and increasing mononucleotide microsatellite density. Altogether, our findings substantially facilitate understanding of L1 integration and fixation preferences, pave the way for uncovering their role in aging and cancer, and inform their use as mutagenesis tools in genetic studies. |
| Author | Chiaromonte, Francesca Makova, Kateryna D Qi, Zongtai Chen, Di Cremona, Marzia A Mitra, Robi D |
| AuthorAffiliation | 2 Department of Statistics, The Pennsylvania State University , University Park, PA 3 Department of Operations and Decision Systems, Université Laval , Québec, Canada 1 Intercollege Graduate Degree Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, PA 4 Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis, MO 5 EMbeDS, Sant’Anna School of Advanced Studies , Pisa, Italy 6 The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University , University Park, PA 7 Department of Biology, The Pennsylvania State University , University Park, PA |
| AuthorAffiliation_xml | – name: 4 Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis, MO – name: 1 Intercollege Graduate Degree Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, PA – name: 2 Department of Statistics, The Pennsylvania State University , University Park, PA – name: 3 Department of Operations and Decision Systems, Université Laval , Québec, Canada – name: 7 Department of Biology, The Pennsylvania State University , University Park, PA – name: 6 The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University , University Park, PA – name: 5 EMbeDS, Sant’Anna School of Advanced Studies , Pisa, Italy |
| Author_xml | – sequence: 1 givenname: Di surname: Chen fullname: Chen, Di organization: Intercollege Graduate Degree Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA – sequence: 2 givenname: Marzia A surname: Cremona fullname: Cremona, Marzia A organization: Department of Statistics, The Pennsylvania State University, University Park, PA – sequence: 3 givenname: Zongtai surname: Qi fullname: Qi, Zongtai organization: Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO – sequence: 4 givenname: Robi D surname: Mitra fullname: Mitra, Robi D organization: Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO – sequence: 5 givenname: Francesca surname: Chiaromonte fullname: Chiaromonte, Francesca email: fxc11@psu.edu organization: Department of Statistics, The Pennsylvania State University, University Park, PA – sequence: 6 givenname: Kateryna D orcidid: 0000-0002-6212-9526 surname: Makova fullname: Makova, Kateryna D email: kdm16@psu.edu organization: The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32722770$$D View this record in MEDLINE/PubMed |
| BookMark | eNqFkc1r3DAQxUVJaTZprzkWQy7NYRONJVvWJRDyWVjoZXsWY1lOFGxpK9lb9r-PzG5CEggBgQb0e6OZ9w7InvPOEHIE9BSoZGe972qzPusjIkj-hcygYGIOAuQemVGRak5ZtU8OYnykFDgvy29kn-Uiz4WgM3J7N_bosgVky4Aurny0g_Uuu9o47K2O2V8XcG0602T_7fCQ3YxOTwB22RUOmF2kahNt_E6-tthF82N3H5LlzfXy8m6--HP7-_JiMde8yIc5cFForHUpG9GWNdWtlg2rkANWtQSKFXBZirptGeSGQ1VXDRRNIcu2FIKxQ3K-bbsa69402rghYKdWwfYYNsqjVW9fnH1Q936thOAsndTg165B8P9GEwfV26hN16Ezfowq53nFoYRqQo_foY9-DGnfqFgyOJcC6ET9fD3RyyjPFifgdAvo4GMMpn1BgKopQ7XNUO0yTAL-TqDtgJPpaSPbfSw72cr8uPrsiyfKO7Ii |
| CitedBy_id | crossref_primary_10_1016_j_tig_2022_11_005 crossref_primary_10_3390_genes12060918 crossref_primary_10_1007_s11222_024_10537_y |
| Cites_doi | 10.1074/jbc.M117.802074 10.1371/journal.pgen.1004395 10.1038/s41576-019-0165-8 10.1371/journal.pgen.1002154 10.1101/gr.161760.113 10.1016/0092-8674(82)90194-5 10.1093/nar/gks955 10.1073/pnas.152346799 10.1016/j.mad.2010.03.008 10.1016/j.cell.2007.05.009 10.1038/nrg3296 10.1093/nar/gkg296 10.1016/S0168-9525(97)01181-5 10.1093/nar/gkx1020 10.1093/nar/gkt1117 10.1038/s41598-019-47002-0 10.1111/j.1467-9868.2007.00627.x 10.1016/j.molcel.2019.02.036 10.1016/j.cell.2008.09.022 10.1038/nsmb786 10.1038/nature10531 10.1101/gr.205701 10.1101/gr.8.2.100 10.1046/j.1365-294X.2002.01643.x 10.1038/35057062 10.1093/nar/gky610 10.1016/j.cell.2011.08.016 10.1101/gad.277863.116 10.1074/jbc.M201032200 10.1126/science.aah3378 10.1016/j.cell.2011.11.058 10.1073/pnas.80.7.1816 10.1101/gr.388902 10.1016/j.csda.2015.08.020 10.1093/gbe/evx206 10.1101/gr.247965.118 10.1038/nature08514 10.1017/S0016672303006268 10.1101/gr.2326704 10.1038/nn.2959 10.1371/journal.pgen.1004531 10.1038/nrg2905 10.1038/35080577 10.1016/S0092-8674(00)81998-4 10.1038/nature02536 10.1101/gr.099655.109 10.1126/science.1186366 10.1128/MCB.26.5.1865-1878.2006 10.1111/biom.12476 10.1186/gb-2008-9-9-r137 10.1186/1471-2164-6-108 10.1093/nar/gky379 10.1007/s00018-009-0131-2 10.1002/bies.950160306 10.1016/j.ceb.2018.01.004 10.1101/gr.136184.111 10.3390/cells6020015 10.1101/gr.122937.111 10.1126/science.aac7247 10.1101/gad.1803909 10.1093/nar/gkw925 10.1371/journal.pgen.1008036 10.1186/1742-4690-10-156 10.1186/1759-8753-5-14 10.1371/journal.pgen.1002236 10.1002/humu.20307 10.1038/nrg3080 10.1371/journal.pgen.1000071 10.1016/S0092-8674(00)81997-2 10.1080/15592294.2019.1621140 10.1016/j.csda.2014.04.015 10.1038/nsmb.2339 10.1038/nrg3663 10.1126/science.1098119 10.1002/0471250953.bi1112s47 10.1371/journal.pgen.1002371 10.1186/gb-2010-11-8-r86 10.1093/oxfordjournals.molbev.a026372 10.1126/science.1117196 10.1073/pnas.0308084100 10.1016/j.cell.2006.12.048 10.1177/1471082X16681317 10.1111/j.1467-9868.2005.00532.x 10.1155/JBB/2006/75327 10.1016/j.cell.2019.02.050 10.1038/nsmb.1594 10.1038/ncomms5767 10.3390/genes10060419 10.1093/nar/gkh103 10.1093/molbev/mss202 10.1038/nrg.2016.139 10.1101/gr.099044.109 10.1016/j.gene.2006.09.033 10.3390/v9030057 10.1371/journal.pgen.1008291 10.1038/ng0597-6 10.1126/science.1225057 10.1101/gr.241257.118 10.1146/annurev-genet-110711-155621 10.1038/nature09525 10.1146/annurev.genet.35.102401.091032 10.7554/eLife.13926 10.1016/S0014-5793(98)01338-6 10.1073/pnas.0603334103 10.1002/evan.20283 10.1093/gbe/evw264 10.1016/S0378-1119(00)00434-0 10.1038/nmeth.1332 10.1093/gbe/evw224 10.1371/journal.pgen.1002842 10.1073/pnas.0509315102 10.1371/journal.pone.0045519 10.1101/gr.187989.114 10.1038/nature11247 10.1371/journal.pgen.1008043 10.1038/ng1990 10.7554/eLife.30058 10.1038/nrg3117 10.1371/journal.pcbi.0030254 10.1093/nar/gkm1105 10.1146/annurev.genet.42.110807.091549 10.1038/nature13985 10.1038/nrg2640 10.1093/oxfordjournals.molbev.a003893 10.1371/journal.pcbi.1004956 10.1146/annurev-genom-090413-025437 10.1073/pnas.0605300103 10.1101/gad.266098.115 10.1016/bs.ircmb.2016.08.002 10.1186/gm97 10.1016/j.ajhg.2012.10.018 10.1016/j.cell.2011.04.024 10.1093/bioinformatics/btz045 10.1186/1756-8935-7-33 10.1073/pnas.94.5.1872 10.1002/bies.200800219 10.1126/science.2981116 10.1038/nmeth.1828 10.1093/bioinformatics/bty090 10.1038/nsmb.3367 10.1101/gr.185132.114 10.1038/nrg.2017.7 10.1371/journal.pgen.1002384 10.1101/gr.282402 10.1186/1471-2164-15-1032 10.1016/S0888-7543(03)00105-8 10.1002/sim.1068 10.1016/S0959-437X(99)00031-3 10.1021/bi981858s 10.1073/pnas.0611223104 10.1038/s41598-019-45839-z 10.1053/j.seminhematol.2013.03.030 10.1101/gr.219022.116 10.3390/v9060131 10.1186/gb-2011-12-12-236 10.2741/e537 10.1186/1759-8753-2-2 10.1146/annurev-genom-082509-141802 10.2741/3990 10.1186/1759-8753-4-10 10.1038/ng0598-19 10.1038/nprot.2012.101 10.1093/gigascience/gix066 10.1093/nar/gkl027 10.18637/jss.v042.i07 10.1093/bioinformatics/btr026 10.1016/j.gene.2006.07.040 10.1038/ng.213 10.1038/nbt.3598 10.1534/genetics.115.180968 10.1093/nar/gkq1170 10.1038/nmeth.1313 10.1101/gr.4001406 10.1101/gr.229102 10.1038/nature25179 10.1101/gr.114777.110 10.1016/j.gde.2004.08.008 |
| ContentType | Journal Article |
| Copyright | The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. |
| Copyright_xml | – notice: The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2020 – notice: The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. |
| DBID | AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7QG 7QP 7QR 7SN 7SS 7TK 7TM 7TO 7U9 7X7 7XB 88A 88E 8AO 8FD 8FE 8FH 8FI 8FJ 8FK 8G5 ABUWG AEUYN AFKRA AZQEC BBNVY BENPR BHPHI C1K CCPQU DWQXO FR3 FYUFA GHDGH GNUQQ GUQSH H94 HCIFZ K9. LK8 M0S M1P M2O M7N M7P MBDVC P64 PHGZM PHGZT PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS Q9U RC3 7X8 5PM |
| DOI | 10.1093/molbev/msaa194 |
| DatabaseName | CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Central (Corporate) Animal Behavior Abstracts Calcium & Calcified Tissue Abstracts Chemoreception Abstracts Ecology Abstracts Entomology Abstracts (Full archive) Neurosciences Abstracts Nucleic Acids Abstracts Oncogenes and Growth Factors Abstracts Virology and AIDS Abstracts Health & Medical Collection ProQuest Central (purchase pre-March 2016) Biology Database (Alumni Edition) Medical Database (Alumni Edition) ProQuest Pharma Collection Technology Research Database ProQuest SciTech Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) Research Library (Alumni Edition) ProQuest Central (Alumni) ProQuest One Sustainability (subscription) ProQuest Central UK/Ireland ProQuest Central Essentials Biological Science Collection ProQuest Central Natural Science Collection Environmental Sciences and Pollution Management ProQuest One Community College ProQuest Central Engineering Research Database Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student Research Library Prep AIDS and Cancer Research Abstracts SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) Biological Sciences Health & Medical Collection (Alumni Edition) PML(ProQuest Medical Library) Research Library Algology Mycology and Protozoology Abstracts (Microbiology C) Biological Science Database Research Library (Corporate) Biotechnology and BioEngineering Abstracts ProQuest Central Premium ProQuest One Academic (New) ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China ProQuest Central Basic Genetics Abstracts MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Research Library Prep ProQuest Central Student Oncogenes and Growth Factors Abstracts ProQuest Central Essentials Nucleic Acids Abstracts SciTech Premium Collection ProQuest Central China Environmental Sciences and Pollution Management ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Natural Science Collection Health & Medical Research Collection Biological Science Collection Chemoreception Abstracts ProQuest Central (New) ProQuest Medical Library (Alumni) Virology and AIDS Abstracts ProQuest Biological Science Collection ProQuest One Academic Eastern Edition ProQuest Hospital Collection Health Research Premium Collection (Alumni) Biological Science Database Ecology Abstracts Neurosciences Abstracts ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering Abstracts Entomology Abstracts ProQuest Health & Medical Complete ProQuest One Academic UKI Edition Engineering Research Database ProQuest One Academic Calcium & Calcified Tissue Abstracts ProQuest One Academic (New) Technology Research Database ProQuest One Academic Middle East (New) ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) ProQuest One Community College ProQuest One Health & Nursing Research Library (Alumni Edition) ProQuest Natural Science Collection ProQuest Pharma Collection ProQuest Biology Journals (Alumni Edition) ProQuest Central ProQuest Health & Medical Research Collection Genetics Abstracts Health and Medicine Complete (Alumni Edition) ProQuest Central Korea Algology Mycology and Protozoology Abstracts (Microbiology C) AIDS and Cancer Research Abstracts ProQuest Research Library ProQuest Central Basic ProQuest SciTech Collection ProQuest Medical Library Animal Behavior Abstracts ProQuest Central (Alumni) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE Research Library Prep CrossRef MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: BENPR name: ProQuest Central url: https://www.proquest.com/central sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1537-1719 |
| EndPage | 3600 |
| ExternalDocumentID | PMC7743743 32722770 10_1093_molbev_msaa194 10.1093/molbev/msaa194 |
| Genre | Research Support, U.S. Gov't, Non-P.H.S Comparative Study Research Support, Non-U.S. Gov't Journal Article Research Support, N.I.H., Extramural |
| GrantInformation_xml | – fundername: NIGMS NIH HHS grantid: R01 GM123203 – fundername: NIMH NIH HHS grantid: RF1 MH117070 – fundername: ; ; grantid: RF1 MH117070; R01GM123203 |
| GroupedDBID | --- -E4 -~X .2P .GJ .I3 .ZR 0R~ 18M 1TH 29M 2WC 4.4 48X 53G 5VS 5WA 70D 7X7 88E 8AO 8FI 8FJ 8G5 AAFWJ AAIJN AAIMJ AAJKP AAJQQ AAMDB AAMVS AAOGV AAPNW AAPQZ AAPXW AAUQX AAVAP AAVLN ABEJV ABEUO ABGNP ABIXL ABKDP ABLJU ABNKS ABPTD ABQLI ABSMQ ABUFD ABUWG ABXVV ABZBJ ACGFO ACGFS ACIPB ACIWK ACNCT ACPRK ACUTO ACYTK ADBBV ADEYI ADEZT ADFTL ADGZP ADHKW ADHZD ADOCK ADRTK ADXHL ADYVW ADZTZ ADZXQ AECKG AEGPL AEJOX AEKKA AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEUYN AEWNT AFFHD AFFNX AFIYH AFKRA AFOFC AFPKN AFRAH AGINJ AGKEF AGSYK AHMBA AHXPO AIAGR AIJHB AJEUX AKHUL AKWXX ALMA_UNASSIGNED_HOLDINGS ALTZX ALUQC AMNDL APIBT APWMN ARIXL ASAOO ATDFG AXUDD AYOIW AZQEC AZVOD BAWUL BAYMD BBNVY BENPR BEYMZ BHONS BHPHI BQDIO BQUQU BSWAC BTQHN BTRTY BVRKM C1A CAG CCPQU CDBKE COF CS3 CXTWN CZ4 DAKXR DFGAJ DIK DILTD DU5 DWQXO D~K E3Z EBS EE~ EJD EMOBN F5P F9B FHSFR FLIZI FOTVD FYUFA GAUVT GJXCC GNUQQ GROUPED_DOAJ GUQSH GX1 H13 H5~ HAR HCIFZ HH5 HMCUK HW0 HZ~ IAO IGS IHR IOX ITC J21 KOP KQ8 KSI M-Z M1P M2O M7P MBTAY ML0 MVM N9A NGC NLBLG NMDNZ NOYVH NTWIH NU- O0~ O9- OAWHX ODMLO OJQWA OK1 OVD O~Y P2P PAFKI PEELM PHGZM PHGZT PJZUB PPXIY PQGLB PQQKQ PSQYO Q1. Q5Y RD5 RNI ROL ROZ RPM RUSNO RW1 RXO RZO TEORI TJP TJX TLC TN5 TOX TR2 UKHRP W8F WOQ X7H XSW YAYTL YHZ YKOAZ YXANX ZCA ZCG ZKX ZXP ZY4 ~02 ~91 AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7QG 7QP 7QR 7SN 7SS 7TK 7TM 7TO 7U9 7XB 88A 8FD 8FE 8FH 8FK C1K FR3 H94 K9. LK8 M7N MBDVC P64 PKEHL PQEST PQUKI PRINS Q9U RC3 7X8 5PM |
| ID | FETCH-LOGICAL-c452t-1475cabc69d7f6b0cfc9d38a41a8b910a814967bff312e418b8d15d596f67733 |
| IEDL.DBID | M7P |
| ISICitedReferencesCount | 4 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000606021400013&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 0737-4038 1537-1719 |
| IngestDate | Tue Nov 04 01:47:31 EST 2025 Thu Oct 02 07:03:38 EDT 2025 Mon Oct 06 17:54:04 EDT 2025 Mon Jul 21 06:02:46 EDT 2025 Sat Nov 29 05:53:06 EST 2025 Tue Nov 18 22:09:53 EST 2025 Tue Nov 25 06:14:01 EST 2025 |
| IsDoiOpenAccess | false |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 12 |
| Keywords | transposition fixation integration LINE-1 transposable elements |
| Language | English |
| License | This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c452t-1475cabc69d7f6b0cfc9d38a41a8b910a814967bff312e418b8d15d596f67733 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Article-2 ObjectType-Feature-1 content type line 23 Di Chen and Marzia A. Cremona contributed equally to this work. |
| ORCID | 0000-0002-6212-9526 |
| OpenAccessLink | https://www.ncbi.nlm.nih.gov/pmc/articles/7743743 |
| PMID | 32722770 |
| PQID | 3171297103 |
| PQPubID | 36253 |
| PageCount | 25 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_7743743 proquest_miscellaneous_2428416183 proquest_journals_3171297103 pubmed_primary_32722770 crossref_primary_10_1093_molbev_msaa194 crossref_citationtrail_10_1093_molbev_msaa194 oup_primary_10_1093_molbev_msaa194 |
| PublicationCentury | 2000 |
| PublicationDate | 2020-12-16 |
| PublicationDateYYYYMMDD | 2020-12-16 |
| PublicationDate_xml | – month: 12 year: 2020 text: 2020-12-16 day: 16 |
| PublicationDecade | 2020 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States – name: Oxford |
| PublicationTitle | Molecular biology and evolution |
| PublicationTitleAlternate | Mol Biol Evol |
| PublicationYear | 2020 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| References | Liu (2020121613440458100_msaa194-B95) 2018; 553 Payer (2020121613440458100_msaa194-B121) 2019; 20 Scott (2020121613440458100_msaa194-B142) 2017; 9 Pini (2020121613440458100_msaa194-B126) 2016; 72 Ward (2020121613440458100_msaa194-B169) 2012; 337 (2020121613440458100_msaa194-B45); 5128 Ghirlando (2020121613440458100_msaa194-B52) 2016; 30 Treangen (2020121613440458100_msaa194-B160) 2011; 13 Sahakyan (2020121613440458100_msaa194-B139) 2017; 24 Han (2020121613440458100_msaa194-B60) 2004; 429 Cheng (2020121613440458100_msaa194-B29) 2014; 515 Horvath (2020121613440458100_msaa194-B63) 2017; 9 Beck (2020121613440458100_msaa194-B10) 2011; 12 Yu (2020121613440458100_msaa194-B177) 2017; 6 Huang (2020121613440458100_msaa194-B65) 2017; 328 Wallrath (2020121613440458100_msaa194-B167) 1994; 16 Petri (2020121613440458100_msaa194-B124) 2019; 15 Rodriguez (2020121613440458100_msaa194-B136) 2008; 36 Zhou (2020121613440458100_msaa194-B185) 2011; 12 Jurka (2020121613440458100_msaa194-B70) 2004; 101 Molaro (2020121613440458100_msaa194-B107) 2011; 146 Ramsay (2020121613440458100_msaa194-B129) 2007 Sultana (2020121613440458100_msaa194-B156) 2017; 18 Gu (2020121613440458100_msaa194-B58) 2000; 259 Guiblet (2020121613440458100_msaa194-B59) 2018; 28 Konkel (2020121613440458100_msaa194-B82) 2007; 390 Singer (2020121613440458100_msaa194-B146) 1982; 28 Zhang (2020121613440458100_msaa194-B181) 2014; 24 Penzkofer (2020121613440458100_msaa194-B123) 2017; 45 Schmidt (2020121613440458100_msaa194-B140) 2012; 148 Lander (2020121613440458100_msaa194-B86) 2001; 409 Lowe (2020121613440458100_msaa194-B96) 2007; 104 Elbarbary (2020121613440458100_msaa194-B41) 2016; 351 Rebollo (2020121613440458100_msaa194-B132) 2012; 46 Flasch (2020121613440458100_msaa194-B49) 2019; 177 Mooijman (2020121613440458100_msaa194-B108) 2016; 34 Sun (2020121613440458100_msaa194-B157) 2015; 21 Eyre-Walker (2020121613440458100_msaa194-B44) 2001; 2 Rosser (2020121613440458100_msaa194-B137) 2012; E4 Yoder (2020121613440458100_msaa194-B176) 1997; 13 Venkatesan (2020121613440458100_msaa194-B163) 2017; 6 Medstrand (2020121613440458100_msaa194-B101) 2002; 12 Kazazian (2020121613440458100_msaa194-B73) 1998; 19 Calado (2020121613440458100_msaa194-B25) 2013; 50 Mita (2020121613440458100_msaa194-B106) 2018; 7 Croll (2020121613440458100_msaa194-B36) 2015; 201 An (2020121613440458100_msaa194-B3) 2011; 2 Hesselberth (2020121613440458100_msaa194-B62) 2009; 6 Casper (2020121613440458100_msaa194-B27) 2018; 46 Karolchik (2020121613440458100_msaa194-B72) 2004; 32(Database issue Lin (2020121613440458100_msaa194-B91) 2014; 5 Meier (2020121613440458100_msaa194-B102) 2008; 70 Wimmer (2020121613440458100_msaa194-B171) 2011; 7 Besnard (2020121613440458100_msaa194-B15) 2012; 19 Kejnovský (2020121613440458100_msaa194-B74) 2013; 8 Meyers (2020121613440458100_msaa194-B104) 2006 Deininger (2020121613440458100_msaa194-B38) 2002; 12 Ryba (2020121613440458100_msaa194-B138) 2010; 20 Goecks (2020121613440458100_msaa194-B53) 2010; 11 Quinlan (2020121613440458100_msaa194-B128) 2014; 47 Szulwach (2020121613440458100_msaa194-B159) 2011; 14 Landt (2020121613440458100_msaa194-B87) 2012; 22 Myers (2020121613440458100_msaa194-B112) 2005; 310 Straussman (2020121613440458100_msaa194-B154) 2009; 16 Feng (2020121613440458100_msaa194-B46) 2012; 7 An (2020121613440458100_msaa194-B4) 2006; 103 Afgan (2020121613440458100_msaa194-B1) 2018; 46 Richardson (2020121613440458100_msaa194-B133) 2017; 27 Lees-Murdock (2020121613440458100_msaa194-B89) 2003; 82 Myers (2020121613440458100_msaa194-B113) 2008; 40 Silva (2020121613440458100_msaa194-B144) 2003; 82 Stewart (2020121613440458100_msaa194-B152) 2011; 7 Grandi (2020121613440458100_msaa194-B56) 2015; 25 Binz (2020121613440458100_msaa194-B16) 2019; 9 Yang (2020121613440458100_msaa194-B174) 2014; 10 Morrissey (2020121613440458100_msaa194-B110) 2013 Sultana (2020121613440458100_msaa194-B155) 2019; 74 (2020121613440458100_msaa194-B42) 2012; 489 St. Laurent (2020121613440458100_msaa194-B153) 2010; 131 Matassi (2020121613440458100_msaa194-B98) 1998; 439 Kelkar (2020121613440458100_msaa194-B75) 2011; 21 Bejerano (2020121613440458100_msaa194-B12) 2004; 304 Gates (2020121613440458100_msaa194-B51) 2017; 292 Cordaux (2020121613440458100_msaa194-B32) 2009; 10 Kines (2020121613440458100_msaa194-B79) 2012; 17 Pedram (2020121613440458100_msaa194-B122) 2006; 26 Usset (2020121613440458100_msaa194-B162) 2016; 94 Matsui (2020121613440458100_msaa194-B99) 2014; 78 Khan (2020121613440458100_msaa194-B77) 2005; 16 Greven (2020121613440458100_msaa194-B57) 2017; 17 Rio (2020121613440458100_msaa194-B134) 1985; 227 Zhao (2020121613440458100_msaa194-B184) 2010; 67 Ewing (2020121613440458100_msaa194-B43) 2011; 21 Krueger (2020121613440458100_msaa194-B84) 2012; 9 Lexa (2020121613440458100_msaa194-B90) 2014; 15 Song (2020121613440458100_msaa194-B149) 2007; 390 Wang (2020121613440458100_msaa194-B168) 2006; 27 Duret (2020121613440458100_msaa194-B40) 2008; 4 Jjingo (2020121613440458100_msaa194-B67) 2014; 5 Rivera-Mulia (2020121613440458100_msaa194-B135) 2015; 25 Yuan (2020121613440458100_msaa194-B178) 2006; 68 Chuong (2020121613440458100_msaa194-B30) 2017; 18 Fu (2020121613440458100_msaa194-B50) 2018; 52 Graham (2020121613440458100_msaa194-B55) 2006; 2006 Philippe (2020121613440458100_msaa194-B125) 2016; 5 Kano (2020121613440458100_msaa194-B71) 2009; 23 Boeke (2020121613440458100_msaa194-B18) 1997; 16 Rangasamy (2020121613440458100_msaa194-B130) 2004; 11 Ratcliffe (2020121613440458100_msaa194-B131) 2002; 21 Baillie (2020121613440458100_msaa194-B7) 2011; 479 Zhang (2020121613440458100_msaa194-B182) 2008; 9 Miki (2020121613440458100_msaa194-B105) 1992; 52 Boissinot (2020121613440458100_msaa194-B22) 2001; 18 2020121613440458100_msaa194-B244063892 Weber (2020121613440458100_msaa194-B170) 2007; 39 Sinden (2020121613440458100_msaa194-B145) 2012 Lindič (2020121613440458100_msaa194-B92) 2013; 10 Moran (2020121613440458100_msaa194-B109) 1996; 87 Xie (2020121613440458100_msaa194-B173) 2013; 4 Campos-Sánchez (2020121613440458100_msaa194-B26) 2016; 12 Zemach (2020121613440458100_msaa194-B180) 2010; 328 Zhao (2020121613440458100_msaa194-B183) 2019; 15 Branco (2020121613440458100_msaa194-B24) 2012; 13 Bochman (2020121613440458100_msaa194-B17) 2012; 13 Zaratiegui (2020121613440458100_msaa194-B179) 2017; 9 Feusier (2020121613440458100_msaa194-B48) 2019; 29 Smit (2020121613440458100_msaa194-B147) 1999; 9 Kent (2020121613440458100_msaa194-B76) 2002; 12 Mahtani (2020121613440458100_msaa194-B97) 1998; 8 McLaughlin (2020121613440458100_msaa194-B100) 2014; 10 Meyer (2020121613440458100_msaa194-B103) 2016; 8 Nishida (2020121613440458100_msaa194-B114) 2005; 6 Ostertag (2020121613440458100_msaa194-B118) 2001; 11 Muotri (2020121613440458100_msaa194-B111) 2005; 102 Jurka (2020121613440458100_msaa194-B68) 1997; 94 Kim (2020121613440458100_msaa194-B78) 2007; 128 Lister (2020121613440458100_msaa194-B93) 2009; 462 Deininger (2020121613440458100_msaa194-B37) 2011; 12 Belancio (2020121613440458100_msaa194-B13) 2009; 1 Li (2020121613440458100_msaa194-B94) 2002; 11 Cremona (2020121613440458100_msaa194-B35) 2019; 35 Szulwach (2020121613440458100_msaa194-B158) 2011; 7 Bourgeois (2020121613440458100_msaa194-B23) 2019; 10 Jurka (2020121613440458100_msaa194-B69) 2004; 14 Hou (2020121613440458100_msaa194-B64) 2019; 14 Cer (2020121613440458100_msaa194-B60903427) 2011; 39 Kvikstad (2020121613440458100_msaa194-B85) 2010; 20 Ostertag (2020121613440458100_msaa194-B119) 2001; 35 Beauregard (2020121613440458100_msaa194-B9) 2008; 42 Noshay (2020121613440458100_msaa194-B115) 2019; 15 Wagstaff (2020121613440458100_msaa194-B165) 2012; 8 de Koning (2020121613440458100_msaa194-B39) 2011; 7 Vinogradov (2020121613440458100_msaa194-B164) 2003; 31 Amemiya (2020121613440458100_msaa194-B2) 2019; 9 Boissinot (2020121613440458100_msaa194-B19) 2004; 14 Ovchinnikov (2020121613440458100_msaa194-B120) 2002; 99 Soriano (2020121613440458100_msaa194-B150) 1983; 80 Boissinot (2020121613440458100_msaa194-B21) 2006; 103 Ong (2020121613440458100_msaa194-B117) 2014; 15 He (2020121613440458100_msaa194-B61) 2015; 16 Wylie (2020121613440458100_msaa194-B172) 2016; 30 Smit (2020121613440458100_msaa194-B148) 2015 Konkel (2020121613440458100_msaa194-B81) 2010; 19 Lee (2020121613440458100_msaa194-B88) 2014; 42 Tsompana (2020121613440458100_msaa194-B161) 2014; 7 Cer (2020121613440458100_msaa194-B28) 2013; 41 Cohen (2020121613440458100_msaa194-B31) 2011; 145 Yehuda (2020121613440458100_msaa194-B175) 2018; 46 Bedrosian (2020121613440458100_msaa194-B11) 2018; 359 Asthana (2020121613440458100_msaa194-B6) 2007; 3 Goodier (2020121613440458100_msaa194-B54) 2008; 135 Kong (2020121613440458100_msaa194-B80) 2010; 467 Sotero-Caio (2020121613440458100_msaa194-B151) 2017; 9 Belancio (2020121613440458100_msaa194-B14) 2006; 34 Schmieder (2020121613440458100_msaa194-B141) 2011; 27 Wagstaff (2020121613440458100_msaa194-B166) 2013; 30 Ivics (2020121613440458100_msaa194-B66) 2009; 6 Feng (2020121613440458100_msaa194-B47) 1996; 87 Plohl (2020121613440458100_msaa194-B127) 2002; 277 Koren (2020121613440458100_msaa194-B83) 2012; 91 Sekhon (2020121613440458100_msaa194-B143) 2011; 42 Barski (2020121613440458100_msaa194-B8) 2007; 129 Boissinot (2020121613440458100_msaa194-B20) 2000; 17 Cost (2020121613440458100_msaa194-B33) 1998; 37 Cremona (2020121613440458100_msaa194-B34) 2018; 34 (2020121613440458100_msaa194-B242) 2020 Oliver (2020121613440458100_msaa194-B116) 2009; 31 |
| References_xml | – volume: 292 start-page: 14456 issue: 35 year: 2017 ident: 2020121613440458100_msaa194-B51 article-title: Acetylation on histone H3 lysine 9 mediates a switch from transcription initiation to elongation publication-title: J Biol Chem doi: 10.1074/jbc.M117.802074 – volume: 10 start-page: e1004395 issue: 6 year: 2014 ident: 2020121613440458100_msaa194-B174 article-title: Reviving the dead: history and reactivation of an extinct L1 publication-title: PLoS Genet doi: 10.1371/journal.pgen.1004395 – volume: 20 start-page: 760 issue: 12 year: 2019 ident: 2020121613440458100_msaa194-B121 article-title: Transposable elements in human genetic disease publication-title: Nat Rev Genet doi: 10.1038/s41576-019-0165-8 – volume: 7 start-page: e1002154 issue: 6 year: 2011 ident: 2020121613440458100_msaa194-B158 article-title: Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002154 – volume: 24 start-page: 989 issue: 6 year: 2014 ident: 2020121613440458100_msaa194-B181 article-title: Epistasis analysis for quantitative traits by functional regression model publication-title: Genome Res doi: 10.1101/gr.161760.113 – volume: 28 start-page: 433 issue: 3 year: 1982 ident: 2020121613440458100_msaa194-B146 article-title: SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes publication-title: Cell doi: 10.1016/0092-8674(82)90194-5 – volume: 41 start-page: 94 year: 2013 ident: 2020121613440458100_msaa194-B28 article-title: Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools publication-title: Nucleic Acids Res doi: 10.1093/nar/gks955 – volume: 99 start-page: 10522 issue: 16 year: 2002 ident: 2020121613440458100_msaa194-B120 article-title: Tracing the LINEs of human evolution publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.152346799 – volume: 131 start-page: 299 issue: 5 year: 2010 ident: 2020121613440458100_msaa194-B153 article-title: A LINE-1 component to human aging: do LINE elements exact a longevity cost for evolutionary advantage? publication-title: Mech Ageing Dev doi: 10.1016/j.mad.2010.03.008 – volume: 129 start-page: 823 issue: 4 year: 2007 ident: 2020121613440458100_msaa194-B8 article-title: High-resolution profiling of histone methylations in the human genome publication-title: Cell doi: 10.1016/j.cell.2007.05.009 – volume: 13 start-page: 770 issue: 11 year: 2012 ident: 2020121613440458100_msaa194-B17 article-title: DNA secondary structures: stability and function of G-quadruplex structures publication-title: Nat Rev Genet doi: 10.1038/nrg3296 – volume: 31 start-page: 1838 issue: 7 year: 2003 ident: 2020121613440458100_msaa194-B164 article-title: DNA helix: the importance of being GC-rich publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg296 – volume: 13 start-page: 335 issue: 8 year: 1997 ident: 2020121613440458100_msaa194-B176 article-title: Cytosine methylation and the ecology of intragenomic parasites publication-title: Trends Genet doi: 10.1016/S0168-9525(97)01181-5 – volume: 46 start-page: D762 issue: D1 year: 2018 ident: 2020121613440458100_msaa194-B27 article-title: The UCSC Genome Browser database: 2018 update publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx1020 – volume: 42 start-page: 1733 issue: 3 year: 2014 ident: 2020121613440458100_msaa194-B88 article-title: Telomere extension by telomerase and ALT generates variant repeats by mechanistically distinct processes publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt1117 – volume: 9 start-page: 1 issue: 1 year: 2019 ident: 2020121613440458100_msaa194-B16 article-title: Identification of novel breakpoints for locus-and region-specific translocations in 293 cells by molecular cytogenetics before and after irradiation publication-title: Sci Rep doi: 10.1038/s41598-019-47002-0 – volume: 70 start-page: 53 issue: 1 year: 2008 ident: 2020121613440458100_msaa194-B102 article-title: The group lasso for logistic regression publication-title: J R Stat Soc Ser B Stat Methodol doi: 10.1111/j.1467-9868.2007.00627.x – volume: 74 start-page: 555 issue: 3 year: 2019 ident: 2020121613440458100_msaa194-B155 article-title: The landscape of L1 retrotransposons in the human genome is shaped by pre-insertion sequence biases and post-insertion selection publication-title: Mol Cell doi: 10.1016/j.molcel.2019.02.036 – volume: 135 start-page: 23 issue: 1 year: 2008 ident: 2020121613440458100_msaa194-B54 article-title: Retrotransposons revisited: the restraint and rehabilitation of parasites publication-title: Cell doi: 10.1016/j.cell.2008.09.022 – volume-title: Functional data analysis: methods and case studie year: 2007 ident: 2020121613440458100_msaa194-B129 – volume: 11 start-page: 650 issue: 7 year: 2004 ident: 2020121613440458100_msaa194-B130 article-title: RNA interference demonstrates a novel role for H2A.Z in chromosome segregation publication-title: Nat Struct Mol Biol doi: 10.1038/nsmb786 – volume: 479 start-page: 534 issue: 7374 year: 2011 ident: 2020121613440458100_msaa194-B7 article-title: Somatic retrotransposition alters the genetic landscape of the human brain publication-title: Nature doi: 10.1038/nature10531 – volume: 11 start-page: 2059 issue: 12 year: 2001 ident: 2020121613440458100_msaa194-B118 article-title: Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition publication-title: Genome Res doi: 10.1101/gr.205701 – volume: 8 start-page: 100 issue: 2 year: 1998 ident: 2020121613440458100_msaa194-B97 article-title: Physical and genetic mapping of the human X chromosome centromere: repression of recombination publication-title: Genome Res doi: 10.1101/gr.8.2.100 – ident: 2020121613440458100_msaa194-B244063892 – volume: 11 start-page: 2453 issue: 12 year: 2002 ident: 2020121613440458100_msaa194-B94 article-title: Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review publication-title: Mol Ecol doi: 10.1046/j.1365-294X.2002.01643.x – volume: 409 start-page: 860 issue: 6822 year: 2001 ident: 2020121613440458100_msaa194-B86 article-title: Initial sequencing and analysis of the human genome publication-title: Nature doi: 10.1038/35057062 – volume: 46 start-page: 8299 issue: 16 year: 2018 ident: 2020121613440458100_msaa194-B175 article-title: Germline DNA replication timing shapes mammalian genome composition publication-title: Nucleic Acids Res doi: 10.1093/nar/gky610 – volume: 146 start-page: 1029 issue: 6 year: 2011 ident: 2020121613440458100_msaa194-B107 article-title: Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates publication-title: Cell doi: 10.1016/j.cell.2011.08.016 – volume: 30 start-page: 881 issue: 8 year: 2016 ident: 2020121613440458100_msaa194-B52 article-title: CTCF: making the right connections publication-title: Genes Dev doi: 10.1101/gad.277863.116 – volume: 277 start-page: 19839 issue: 22 year: 2002 ident: 2020121613440458100_msaa194-B127 article-title: Telomeric localization of the vertebrate-type hexamer repeat, (TTAGGG)n, in the wedgeshell clam Donax trunculus and other marine invertebrate genomes publication-title: J Biol Chem doi: 10.1074/jbc.M201032200 – volume: 359 start-page: 1395 issue: 6382 year: 2018 ident: 2020121613440458100_msaa194-B11 article-title: Early life experience drives structural variation of neural genomes in mice publication-title: Science doi: 10.1126/science.aah3378 – volume: 148 start-page: 335 issue: 1–2 year: 2012 ident: 2020121613440458100_msaa194-B140 article-title: Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages publication-title: Cell doi: 10.1016/j.cell.2011.11.058 – volume: 80 start-page: 1816 issue: 7 year: 1983 ident: 2020121613440458100_msaa194-B150 article-title: The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.80.7.1816 – volume: 12 start-page: 1483 issue: 10 year: 2002 ident: 2020121613440458100_msaa194-B101 article-title: Retroelement distributions in the human genome: variations associated with age and proximity to genes publication-title: Genome Res doi: 10.1101/gr.388902 – volume: 94 start-page: 317 year: 2016 ident: 2020121613440458100_msaa194-B162 article-title: Interaction models for functional regression publication-title: Comput Stat Data Anal doi: 10.1016/j.csda.2015.08.020 – volume: 9 start-page: 2911 issue: 10 year: 2017 ident: 2020121613440458100_msaa194-B63 article-title: The role of small RNA-based epigenetic silencing for purifying selection on transposable elements in Capsella grandiflora publication-title: Genome Biol Evol doi: 10.1093/gbe/evx206 – volume: 29 start-page: 1567 issue: 10 year: 2019 ident: 2020121613440458100_msaa194-B48 article-title: Pedigree-based estimation of human mobile element retrotransposition rates publication-title: Genome Res doi: 10.1101/gr.247965.118 – volume: 462 start-page: 315 issue: 7271 year: 2009 ident: 2020121613440458100_msaa194-B93 article-title: Human DNA methylomes at base resolution show widespread epigenomic differences publication-title: Nature doi: 10.1038/nature08514 – volume: 82 start-page: 1 issue: 1 year: 2003 ident: 2020121613440458100_msaa194-B144 article-title: Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes publication-title: Genet Res doi: 10.1017/S0016672303006268 – volume: 14 start-page: 1221 issue: 7 year: 2004 ident: 2020121613440458100_msaa194-B19 article-title: The insertional history of an active family of L1 retrotransposons in humans publication-title: Genome Res doi: 10.1101/gr.2326704 – volume: 14 start-page: 1607 issue: 12 year: 2011 ident: 2020121613440458100_msaa194-B159 article-title: 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging publication-title: Nat Neurosci doi: 10.1038/nn.2959 – volume: 10 start-page: e1004531 issue: 9 year: 2014 ident: 2020121613440458100_msaa194-B100 article-title: Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency publication-title: PLoS Genet doi: 10.1371/journal.pgen.1004531 – volume: 12 start-page: 7 issue: 1 year: 2011 ident: 2020121613440458100_msaa194-B185 article-title: Charting histone modifications and the functional organization of mammalian genomes publication-title: Nat Rev Genet doi: 10.1038/nrg2905 – volume: 2 start-page: 549 issue: 7 year: 2001 ident: 2020121613440458100_msaa194-B44 article-title: The evolution of isochores publication-title: Nat Rev Genet doi: 10.1038/35080577 – volume: 87 start-page: 917 issue: 5 year: 1996 ident: 2020121613440458100_msaa194-B109 article-title: High frequency retrotransposition in cultured mammalian cells publication-title: Cell doi: 10.1016/S0092-8674(00)81998-4 – volume: 429 start-page: 268 issue: 6989 year: 2004 ident: 2020121613440458100_msaa194-B60 article-title: Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes publication-title: Nature doi: 10.1038/nature02536 – volume: 20 start-page: 761 issue: 6 year: 2010 ident: 2020121613440458100_msaa194-B138 article-title: Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types publication-title: Genome Res doi: 10.1101/gr.099655.109 – volume: 328 start-page: 916 issue: 5980 year: 2010 ident: 2020121613440458100_msaa194-B180 article-title: Genome-wide evolutionary analysis of eukaryotic DNA methylation publication-title: Science doi: 10.1126/science.1186366 – volume: 26 start-page: 1865 issue: 5 year: 2006 ident: 2020121613440458100_msaa194-B122 article-title: Telomere Position Effect and silencing of transgenes near telomeres in the mouse publication-title: MCB doi: 10.1128/MCB.26.5.1865-1878.2006 – volume: 21 start-page: 955 year: 2015 ident: 2020121613440458100_msaa194-B157 article-title: Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators publication-title: Mol Vis – volume: 72 start-page: 835 issue: 3 year: 2016 ident: 2020121613440458100_msaa194-B126 article-title: The interval testing procedure: a general framework for inference in functional data analysis publication-title: Biometrics doi: 10.1111/biom.12476 – volume: 9 start-page: R137 issue: 9 year: 2008 ident: 2020121613440458100_msaa194-B182 article-title: Model-based analysis of ChIP-Seq (MACS) publication-title: Genome Biol doi: 10.1186/gb-2008-9-9-r137 – volume: 6 start-page: 108 issue: 1 year: 2005 ident: 2020121613440458100_msaa194-B114 article-title: Comparative analysis of expression of histone H2a genes in mouse publication-title: BMC Genomics doi: 10.1186/1471-2164-6-108 – volume: 46 start-page: W537 issue: W1 year: 2018 ident: 2020121613440458100_msaa194-B1 article-title: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update publication-title: Nucleic Acids Res doi: 10.1093/nar/gky379 – volume: 67 start-page: 43 issue: 1 year: 2010 ident: 2020121613440458100_msaa194-B184 article-title: Non-B DNA structure-induced genetic instability and evolution publication-title: Cell Mol Life Sci doi: 10.1007/s00018-009-0131-2 – volume: 16 start-page: 165 issue: 3 year: 1994 ident: 2020121613440458100_msaa194-B167 article-title: Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures publication-title: BioEssays doi: 10.1002/bies.950160306 – volume: 52 start-page: 43 year: 2018 ident: 2020121613440458100_msaa194-B50 article-title: Replication timing and nuclear structure publication-title: Curr Opin Cell Biol doi: 10.1016/j.ceb.2018.01.004 – volume: 22 start-page: 1813 issue: 9 year: 2012 ident: 2020121613440458100_msaa194-B87 article-title: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia publication-title: Genome Res doi: 10.1101/gr.136184.111 – volume: 6 start-page: 15 issue: 2 year: 2017 ident: 2020121613440458100_msaa194-B163 article-title: Telomere biology—insights into an intriguing phenomenon publication-title: Cells doi: 10.3390/cells6020015 – volume: 21 start-page: 2038 issue: 12 year: 2011 ident: 2020121613440458100_msaa194-B75 article-title: A matter of life or death: how microsatellites emerge in and vanish from the human genome publication-title: Genome Res doi: 10.1101/gr.122937.111 – volume: 351 start-page: aac7247 issue: 6274 year: 2016 ident: 2020121613440458100_msaa194-B41 article-title: Retrotransposons as regulators of gene expression publication-title: Science doi: 10.1126/science.aac7247 – volume: 23 start-page: 1303 issue: 11 year: 2009 ident: 2020121613440458100_msaa194-B71 article-title: L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism publication-title: Genes Dev doi: 10.1101/gad.1803909 – volume: 45 start-page: D68 issue: D1 year: 2017 ident: 2020121613440458100_msaa194-B123 article-title: L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw925 – volume: 15 start-page: e1008036 issue: 3 year: 2019 ident: 2020121613440458100_msaa194-B124 article-title: LINE-2 transposable elements are a source of functional human microRNAs and target sites publication-title: PLoS Genet doi: 10.1371/journal.pgen.1008036 – volume: 10 start-page: 156 issue: 1 year: 2013 ident: 2020121613440458100_msaa194-B92 article-title: Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins publication-title: Retrovirology doi: 10.1186/1742-4690-10-156 – volume: 5 start-page: 14 issue: 1 year: 2014 ident: 2020121613440458100_msaa194-B67 article-title: Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression publication-title: Mobile DNA doi: 10.1186/1759-8753-5-14 – volume: 7 start-page: e1002236 issue: 8 year: 2011 ident: 2020121613440458100_msaa194-B152 article-title: A comprehensive map of mobile element insertion polymorphisms in humans publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002236 – volume: 27 start-page: 323 issue: 4 year: 2006 ident: 2020121613440458100_msaa194-B168 article-title: dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans publication-title: Hum Mutat doi: 10.1002/humu.20307 – volume: 13 start-page: 7 issue: 1 year: 2012 ident: 2020121613440458100_msaa194-B24 article-title: Uncovering the role of 5-hydroxymethylcytosine in the epigenome publication-title: Nat Rev Genet doi: 10.1038/nrg3080 – volume: 4 start-page: e1000071 issue: 5 year: 2008 ident: 2020121613440458100_msaa194-B40 article-title: The impact of recombination on nucleotide substitutions in the human genome publication-title: PLoS Genet doi: 10.1371/journal.pgen.1000071 – volume: 87 start-page: 905 issue: 5 year: 1996 ident: 2020121613440458100_msaa194-B47 article-title: Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition publication-title: Cell doi: 10.1016/S0092-8674(00)81997-2 – volume: 14 start-page: 894 issue: 9 year: 2019 ident: 2020121613440458100_msaa194-B64 article-title: Integrative characterization of G-quadruplexes in the three-dimensional chromatin structure publication-title: Epigenetics doi: 10.1080/15592294.2019.1621140 – volume: 78 start-page: 176 year: 2014 ident: 2020121613440458100_msaa194-B99 article-title: Variable and boundary selection for functional data via multiclass logistic regression modeling publication-title: Comput Stat Data Anal doi: 10.1016/j.csda.2014.04.015 – year: 2013 ident: 2020121613440458100_msaa194-B110 – volume: 19 start-page: 837 issue: 8 year: 2012 ident: 2020121613440458100_msaa194-B15 article-title: Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs publication-title: Nat Struct Mol Biol doi: 10.1038/nsmb.2339 – volume: 15 start-page: 234 issue: 4 year: 2014 ident: 2020121613440458100_msaa194-B117 article-title: CTCF: an architectural protein bridging genome topology and function publication-title: Nat Rev Genet doi: 10.1038/nrg3663 – volume: 304 start-page: 1321 issue: 5675 year: 2004 ident: 2020121613440458100_msaa194-B12 article-title: Ultraconserved elements in the human genome publication-title: Science doi: 10.1126/science.1098119 – volume: 47 start-page: 11.12.1 issue: 1 year: 2014 ident: 2020121613440458100_msaa194-B128 article-title: BEDTools: the Swiss-army tool for genome feature analysis publication-title: Curr Protoc Bioinform doi: 10.1002/0471250953.bi1112s47 – volume: 7 start-page: e1002371 issue: 11 year: 2011 ident: 2020121613440458100_msaa194-B171 article-title: The NF1 gene contains hotspots for L1 endonuclease-dependent de novo insertion publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002371 – volume: 11 start-page: R86 issue: 8 year: 2010 ident: 2020121613440458100_msaa194-B53 article-title: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences publication-title: Genome Biol doi: 10.1186/gb-2010-11-8-r86 – volume: 17 start-page: 915 issue: 6 year: 2000 ident: 2020121613440458100_msaa194-B20 article-title: L1 (LINE-1) retrotransposon evolution and amplification in recent human history publication-title: Mol Biol Evol doi: 10.1093/oxfordjournals.molbev.a026372 – volume-title: DNA structure and function year: 2012 ident: 2020121613440458100_msaa194-B145 – volume: 310 start-page: 321 issue: 5746 year: 2005 ident: 2020121613440458100_msaa194-B112 article-title: A fine-scale map of recombination rates and hotspots across the human genome publication-title: Science doi: 10.1126/science.1117196 – volume: 101 start-page: 1268 issue: 5 year: 2004 ident: 2020121613440458100_msaa194-B70 article-title: Duplication, coclustering, and selection of human Alu retrotransposons publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0308084100 – volume: 128 start-page: 1231 issue: 6 year: 2007 ident: 2020121613440458100_msaa194-B78 article-title: Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome publication-title: Cell doi: 10.1016/j.cell.2006.12.048 – volume: 17 start-page: 1 issue: 1–2 year: 2017 ident: 2020121613440458100_msaa194-B57 article-title: A general framework for functional regression modelling publication-title: Stat Model doi: 10.1177/1471082X16681317 – volume: 52 start-page: 643 year: 1992 ident: 2020121613440458100_msaa194-B105 article-title: Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer publication-title: Cancer Res – volume: 68 start-page: 49 issue: 1 year: 2006 ident: 2020121613440458100_msaa194-B178 article-title: Model selection and estimation in regression with grouped variables publication-title: J R Stat Soc B doi: 10.1111/j.1467-9868.2005.00532.x – volume: 2006 start-page: 1 year: 2006 ident: 2020121613440458100_msaa194-B55 article-title: The genomic distribution of L1 elements: the role of insertion bias and natural selection publication-title: J Biomed Biotechnol doi: 10.1155/JBB/2006/75327 – volume: 177 start-page: 837 issue: 4 year: 2019 ident: 2020121613440458100_msaa194-B49 article-title: Genome-wide de novo L1 retrotransposition connects endonuclease activity with replication publication-title: Cell doi: 10.1016/j.cell.2019.02.050 – volume: 16 start-page: 564 issue: 5 year: 2009 ident: 2020121613440458100_msaa194-B154 article-title: Developmental programming of {CpG} island methylation profiles in the human genome publication-title: Nat Struct Mol Biol doi: 10.1038/nsmb.1594 – volume: 5 start-page: 4767 year: 2014 ident: 2020121613440458100_msaa194-B91 article-title: Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations publication-title: Nat Commun doi: 10.1038/ncomms5767 – volume: 10 start-page: 419 issue: 6 year: 2019 ident: 2020121613440458100_msaa194-B23 article-title: On the population dynamics of junk: a review on the population genomics of transposable elements publication-title: Genes doi: 10.3390/genes10060419 – volume: 32(Database issue start-page: D493 year: 2004 ident: 2020121613440458100_msaa194-B72 article-title: The UCSC Table Browser data retrieval tool publication-title: Nucleic Acids Res doi: 10.1093/nar/gkh103 – volume: 30 start-page: 88 issue: 1 year: 2013 ident: 2020121613440458100_msaa194-B166 article-title: Molecular reconstruction of extinct LINE-1 elements and their interaction with nonautonomous elements publication-title: Mol Biol Evol doi: 10.1093/molbev/mss202 – volume: 18 start-page: 71 issue: 2 year: 2017 ident: 2020121613440458100_msaa194-B30 article-title: Regulatory activities of transposable elements: from conflicts to benefits publication-title: Nat Rev Genet doi: 10.1038/nrg.2016.139 – volume: 20 start-page: 600 issue: 5 year: 2010 ident: 2020121613440458100_msaa194-B85 article-title: The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important publication-title: Genome Res doi: 10.1101/gr.099044.109 – volume: 390 start-page: 206 issue: 1–2 year: 2007 ident: 2020121613440458100_msaa194-B149 article-title: Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination publication-title: Gene doi: 10.1016/j.gene.2006.09.033 – volume: 9 start-page: 57 issue: 3 year: 2017 ident: 2020121613440458100_msaa194-B179 article-title: Cross-regulation between transposable elements and host DNA replication publication-title: Viruses doi: 10.3390/v9030057 – volume: 15 start-page: e1008291 issue: 9 year: 2019 ident: 2020121613440458100_msaa194-B115 article-title: Monitoring the interplay between transposable element families and DNA methylation in maize publication-title: PLoS Genet doi: 10.1371/journal.pgen.1008291 – volume: 16 start-page: 6 issue: 1 year: 1997 ident: 2020121613440458100_msaa194-B18 article-title: LINEs and Alus—the polyA connection publication-title: Nat Genet doi: 10.1038/ng0597-6 – volume: 337 start-page: 1675 issue: 6102 year: 2012 ident: 2020121613440458100_msaa194-B169 article-title: Evidence of abundant purifying selection in humans for recently acquired regulatory functions publication-title: Science doi: 10.1126/science.1225057 – volume: 28 start-page: 1767 issue: 12 year: 2018 ident: 2020121613440458100_msaa194-B59 article-title: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate publication-title: Genome Res doi: 10.1101/gr.241257.118 – volume: 46 start-page: 21 issue: 1 year: 2012 ident: 2020121613440458100_msaa194-B132 article-title: Transposable elements: an abundant and natural source of regulatory sequences for host genes publication-title: Annu Rev Genet doi: 10.1146/annurev-genet-110711-155621 – volume: 467 start-page: 1099 issue: 7319 year: 2010 ident: 2020121613440458100_msaa194-B80 article-title: Fine-scale recombination rate differences between sexes, populations and individuals publication-title: Nature doi: 10.1038/nature09525 – volume: 35 start-page: 501 issue: 1 year: 2001 ident: 2020121613440458100_msaa194-B119 article-title: Biology of mammalian L1 retrotransposons publication-title: Annu Rev Genet doi: 10.1146/annurev.genet.35.102401.091032 – volume: 5 start-page: 1 year: 2016 ident: 2020121613440458100_msaa194-B125 article-title: Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci publication-title: eLife doi: 10.7554/eLife.13926 – volume: 439 start-page: 63 issue: 1–2 year: 1998 ident: 2020121613440458100_msaa194-B98 article-title: Distribution of the mammalian-wide interspersed repeats (MIRs) in the isochores of the human genome publication-title: FEBS Lett doi: 10.1016/S0014-5793(98)01338-6 – volume: 103 start-page: 9590 issue: 25 year: 2006 ident: 2020121613440458100_msaa194-B21 article-title: Fitness cost of LINE-1 (L1) activity in humans publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0603334103 – volume: 19 start-page: 236 issue: 6 year: 2010 ident: 2020121613440458100_msaa194-B81 article-title: LINEs and SINEs of primate evolution publication-title: Evol Anthropol doi: 10.1002/evan.20283 – volume: 9 start-page: 161 issue: 1 year: 2017 ident: 2020121613440458100_msaa194-B151 article-title: Evolution and diversity of transposable elements in vertebrate genomes publication-title: Genome Biol Evol doi: 10.1093/gbe/evw264 – volume: 259 start-page: 81 issue: 1–2 year: 2000 ident: 2020121613440458100_msaa194-B58 article-title: Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence publication-title: Gene doi: 10.1016/S0378-1119(00)00434-0 – volume: 6 start-page: 415 issue: 6 year: 2009 ident: 2020121613440458100_msaa194-B66 article-title: Transposon-mediated genome manipulation in vertebrates publication-title: Nat Methods doi: 10.1038/nmeth.1332 – volume: 8 start-page: 3209 issue: 10 year: 2016 ident: 2020121613440458100_msaa194-B103 article-title: The flow of the gibbon LAVA element is facilitated by the LINE-1 retrotransposition machinery publication-title: Genome Biol Evol doi: 10.1093/gbe/evw224 – volume: 8 start-page: e1002842 issue: 8 year: 2012 ident: 2020121613440458100_msaa194-B165 article-title: Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002842 – volume: 102 start-page: 18644 issue: 51 year: 2005 ident: 2020121613440458100_msaa194-B111 article-title: Development of functional human embryonic stem cell-derived neurons in mouse brain publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0509315102 – volume: 8 start-page: e45519 issue: 1 year: 2013 ident: 2020121613440458100_msaa194-B74 article-title: Expansion of microsatellites on evolutionary young Y chromosome publication-title: PLoS One doi: 10.1371/journal.pone.0045519 – volume: 25 start-page: 1091 issue: 8 year: 2015 ident: 2020121613440458100_msaa194-B135 article-title: Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells publication-title: Genome Res doi: 10.1101/gr.187989.114 – volume: 489 start-page: 57 year: 2012 ident: 2020121613440458100_msaa194-B42 article-title: An integrated encyclopedia of DNA elements in the human genome publication-title: Nature doi: 10.1038/nature11247 – volume: 15 start-page: e1008043 issue: 4 year: 2019 ident: 2020121613440458100_msaa194-B183 article-title: Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals publication-title: PLoS Genet doi: 10.1371/journal.pgen.1008043 – volume: 39 start-page: 457 issue: 4 year: 2007 ident: 2020121613440458100_msaa194-B170 article-title: Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome publication-title: Nat Genet doi: 10.1038/ng1990 – volume: 7 start-page: e30058 year: 2018 ident: 2020121613440458100_msaa194-B106 article-title: LINE-1 protein localization and functional dynamics during the cell cycle publication-title: eLife doi: 10.7554/eLife.30058 – volume: 13 start-page: 36 issue: 1 year: 2011 ident: 2020121613440458100_msaa194-B160 article-title: Repetitive DNA and next-generation sequencing: computational challenges and solutions publication-title: Nat Rev Genet doi: 10.1038/nrg3117 – volume: 3 start-page: e254 issue: 12 year: 2007 ident: 2020121613440458100_msaa194-B6 article-title: Analysis of Sequence Conservation at Nucleotide Resolution publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.0030254 – volume: 5128 issue: 4 ident: 2020121613440458100_msaa194-B45 article-title: Oviedo de la Fuente M. 2012. Statistical Computing in Functional Data Analysis: The R Package Fda.usc. J Stat Softw – volume: 36 start-page: 770 issue: 3 year: 2008 ident: 2020121613440458100_msaa194-B136 article-title: Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells publication-title: Nucleic Acids Res doi: 10.1093/nar/gkm1105 – volume: 42 start-page: 587 issue: 1 year: 2008 ident: 2020121613440458100_msaa194-B9 article-title: The take and give between retrotransposable elements and their hosts publication-title: Annu Rev Genet doi: 10.1146/annurev.genet.42.110807.091549 – volume: 515 start-page: 371 year: 2014 ident: 2020121613440458100_msaa194-B29 article-title: Principles of regulatory information conservation between mouse and human publication-title: Nature doi: 10.1038/nature13985 – volume: 10 start-page: 691 issue: 10 year: 2009 ident: 2020121613440458100_msaa194-B32 article-title: The impact of retrotransposons on human genome evolution publication-title: Nat Rev Genet doi: 10.1038/nrg2640 – volume: 18 start-page: 926 issue: 6 year: 2001 ident: 2020121613440458100_msaa194-B22 article-title: Selection against deleterious LINE-1-containing loci in the human lineage publication-title: Mol Biol Evol doi: 10.1093/oxfordjournals.molbev.a003893 – volume: 12 start-page: 1 year: 2016 ident: 2020121613440458100_msaa194-B26 article-title: Integration and fixation preferences of human and mouse endogenous retroviruses uncovered with functional data analysis publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1004956 – volume: 16 start-page: 55 issue: 1 year: 2015 ident: 2020121613440458100_msaa194-B61 article-title: Non-CG methylation in the human genome publication-title: Annu Rev Genomics Hum Genet doi: 10.1146/annurev-genom-090413-025437 – volume: 103 start-page: 18662 issue: 49 year: 2006 ident: 2020121613440458100_msaa194-B4 article-title: Active retrotransposition by a synthetic L1 element in mice publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0605300103 – volume: 30 start-page: 64 issue: 1 year: 2016 ident: 2020121613440458100_msaa194-B172 article-title: p53 genes function to restrain mobile elements publication-title: Genes Dev doi: 10.1101/gad.266098.115 – volume: 328 start-page: 25 year: 2017 ident: 2020121613440458100_msaa194-B65 article-title: Epigenetic control of gene expression in maize publication-title: Int Rev Cell Mol Biol doi: 10.1016/bs.ircmb.2016.08.002 – volume: 1 start-page: 97 issue: 10 year: 2009 ident: 2020121613440458100_msaa194-B13 article-title: LINE dancing in the human genome: transposable elements and disease publication-title: Genome Med doi: 10.1186/gm97 – volume: 91 start-page: 1033 issue: 6 year: 2012 ident: 2020121613440458100_msaa194-B83 article-title: Differential relationship of DNA replication timing to different forms of human mutation and variation publication-title: Am J Hum Genet doi: 10.1016/j.ajhg.2012.10.018 – volume: 145 start-page: 773 issue: 5 year: 2011 ident: 2020121613440458100_msaa194-B31 article-title: Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection publication-title: Cell doi: 10.1016/j.cell.2011.04.024 – volume: 35 start-page: 3211 issue: 17 year: 2019 ident: 2020121613440458100_msaa194-B35 article-title: Functional data analysis for computational biology publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz045 – volume: 7 start-page: 33 issue: 1 year: 2014 ident: 2020121613440458100_msaa194-B161 article-title: Chromatin accessibility: a window into the genome publication-title: Epigenet Chromatin doi: 10.1186/1756-8935-7-33 – volume: 94 start-page: 1872 issue: 5 year: 1997 ident: 2020121613440458100_msaa194-B68 article-title: Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.94.5.1872 – volume: 31 start-page: 703 issue: 7 year: 2009 ident: 2020121613440458100_msaa194-B116 article-title: Transposable elements: powerful facilitators of evolution publication-title: BioEssays doi: 10.1002/bies.200800219 – volume: 227 start-page: 23 issue: 4682 year: 1985 ident: 2020121613440458100_msaa194-B134 article-title: A mammalian host-vector system that regulates expression and amplification of transfected genes by temperature induction publication-title: Science doi: 10.1126/science.2981116 – volume: 9 start-page: 145 issue: 2 year: 2012 ident: 2020121613440458100_msaa194-B84 article-title: DNA methylome analysis using short bisulfite sequencing data publication-title: Nat Methods doi: 10.1038/nmeth.1828 – volume: 34 start-page: 2289 issue: 13 year: 2018 ident: 2020121613440458100_msaa194-B34 article-title: IWTomics: testing high-resolution sequence-based “Omics” data at multiple locations and scales publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty090 – volume: 24 start-page: 243 issue: 3 year: 2017 ident: 2020121613440458100_msaa194-B139 article-title: G-quadruplex structures within the 3′UTR of LINE-1 elements stimulate retrotransposition publication-title: Nat Struct Mol Biol doi: 10.1038/nsmb.3367 – volume: 25 start-page: 1135 issue: 8 year: 2015 ident: 2020121613440458100_msaa194-B56 article-title: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites publication-title: Genome Res doi: 10.1101/gr.185132.114 – volume: 18 start-page: 292 issue: 5 year: 2017 ident: 2020121613440458100_msaa194-B156 article-title: Integration site selection by retroviruses and transposable elements in eukaryotes publication-title: Nat Rev Genet doi: 10.1038/nrg.2017.7 – volume: 7 start-page: e1002384 issue: 12 year: 2011 ident: 2020121613440458100_msaa194-B39 article-title: Repetitive elements may comprise over two-thirds of the human genome publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002384 – volume: 12 start-page: 1455 issue: 10 year: 2002 ident: 2020121613440458100_msaa194-B38 article-title: Mammalian retroelements publication-title: Genome Res doi: 10.1101/gr.282402 – volume: 15 start-page: 1032 issue: 1 year: 2014 ident: 2020121613440458100_msaa194-B90 article-title: Guanine quadruplexes are formed by specific regions of human transposable elements publication-title: BMC Genomics doi: 10.1186/1471-2164-15-1032 – volume: 82 start-page: 230 issue: 2 year: 2003 ident: 2020121613440458100_msaa194-B89 article-title: Methylation dynamics of repetitive DNA elements in the mouse germ cell lineage publication-title: Genomics doi: 10.1016/S0888-7543(03)00105-8 – start-page: 370 volume-title: Encyclopedia of molecular cell biology and molecular medicine year: 2006 ident: 2020121613440458100_msaa194-B104 – volume: 21 start-page: 1115 issue: 8 year: 2002 ident: 2020121613440458100_msaa194-B131 article-title: Functional data analysis with application to periodically stimulated foetal heart rate data. II: Functional Logistic Regression publication-title: Stat Med doi: 10.1002/sim.1068 – year: 2020 ident: 2020121613440458100_msaa194-B242 – volume: 9 start-page: 657 issue: 6 year: 1999 ident: 2020121613440458100_msaa194-B147 article-title: Interspersed repeats and other mementos of transposable elements in mammalian genomes publication-title: Curr Opin Genet Dev doi: 10.1016/S0959-437X(99)00031-3 – volume: 37 start-page: 18081 issue: 51 year: 1998 ident: 2020121613440458100_msaa194-B33 article-title: Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure publication-title: Biochemistry doi: 10.1021/bi981858s – volume: 104 start-page: 8005 issue: 19 year: 2007 ident: 2020121613440458100_msaa194-B96 article-title: Thousands of human mobile element fragments undergo strong purifying selection near developmental genes publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0611223104 – volume: 9 start-page: 9354 issue: 1 year: 2019 ident: 2020121613440458100_msaa194-B2 article-title: The ENCODE blacklist: identification of problematic regions of the genome publication-title: Sci Rep doi: 10.1038/s41598-019-45839-z – volume: 50 start-page: 165 issue: 2 year: 2013 ident: 2020121613440458100_msaa194-B25 article-title: Telomere dynamics in mice and humans publication-title: Semin Hematol doi: 10.1053/j.seminhematol.2013.03.030 – volume: 27 start-page: 1395 issue: 8 year: 2017 ident: 2020121613440458100_msaa194-B133 article-title: Heritable L1 retrotransposition in the mouse primordial germline and early embryo publication-title: Genome Res doi: 10.1101/gr.219022.116 – volume: 9 start-page: 131 issue: 6 year: 2017 ident: 2020121613440458100_msaa194-B142 article-title: The role of somatic L1 retrotransposition in human cancers publication-title: Viruses doi: 10.3390/v9060131 – volume: 12 start-page: 236 issue: 12 year: 2011 ident: 2020121613440458100_msaa194-B37 article-title: Alu elements: know the SINEs publication-title: Genome Biol doi: 10.1186/gb-2011-12-12-236 – volume: E4 start-page: 2203 issue: 6 year: 2012 ident: 2020121613440458100_msaa194-B137 article-title: L1 expression and regulation in humans and rodents publication-title: Front Biosci doi: 10.2741/e537 – volume: 2 start-page: 2 issue: 1 year: 2011 ident: 2020121613440458100_msaa194-B3 article-title: Characterization of a synthetic human LINE-1 retrotransposon ORFeus-Hs publication-title: Mobile DNA doi: 10.1186/1759-8753-2-2 – volume: 12 start-page: 187 issue: 1 year: 2011 ident: 2020121613440458100_msaa194-B10 article-title: LINE-1 elements in structural variation and disease publication-title: Annu Rev Genomics Hum Genet doi: 10.1146/annurev-genom-082509-141802 – volume: 17 start-page: 1329 issue: 1 year: 2012 ident: 2020121613440458100_msaa194-B79 article-title: Expressing genes do not forget their LINEs: transposable elements and gene expression publication-title: Front Biosci doi: 10.2741/3990 – volume: 4 start-page: 10 issue: 1 year: 2013 ident: 2020121613440458100_msaa194-B173 article-title: Cell division promotes efficient retrotransposition in a stable L1 reporter cell line publication-title: Mobile DNA doi: 10.1186/1759-8753-4-10 – volume: 19 start-page: 19 issue: 1 year: 1998 ident: 2020121613440458100_msaa194-B73 article-title: The impact of L1 retrotransposons on the human genome publication-title: Nat Genet doi: 10.1038/ng0598-19 – volume: 7 start-page: 1728 issue: 9 year: 2012 ident: 2020121613440458100_msaa194-B46 article-title: Identifying ChIP-seq enrichment using MACS publication-title: Nat Protoc doi: 10.1038/nprot.2012.101 – volume: 6 start-page: 1 issue: 9 year: 2017 ident: 2020121613440458100_msaa194-B177 article-title: Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection publication-title: GigaScience doi: 10.1093/gigascience/gix066 – volume: 34 start-page: 1512 issue: 5 year: 2006 ident: 2020121613440458100_msaa194-B14 article-title: LINE-1 RNA splicing and influences on mammalian gene expression publication-title: Nucleic Acids Res doi: 10.1093/nar/gkl027 – volume: 42 start-page: 1 issue: 7 year: 2011 ident: 2020121613440458100_msaa194-B143 article-title: Multivariate and propensity score matching software with automated balance optimization: the matching package for R publication-title: J Stat Softw doi: 10.18637/jss.v042.i07 – volume: 27 start-page: 863 issue: 6 year: 2011 ident: 2020121613440458100_msaa194-B141 article-title: Quality control and preprocessing of metagenomic datasets publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr026 – volume: 390 start-page: 28 issue: 1–2 year: 2007 ident: 2020121613440458100_msaa194-B82 article-title: Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies publication-title: Gene doi: 10.1016/j.gene.2006.07.040 – volume: 40 start-page: 1124 issue: 9 year: 2008 ident: 2020121613440458100_msaa194-B113 article-title: A common sequence motif associated with recombination hot spots and genome instability in humans publication-title: Nat Genet doi: 10.1038/ng.213 – volume: 34 start-page: 852 issue: 8 year: 2016 ident: 2020121613440458100_msaa194-B108 article-title: Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction publication-title: Nat Biotechnol doi: 10.1038/nbt.3598 – volume: 201 start-page: 1213 issue: 3 year: 2015 ident: 2020121613440458100_msaa194-B36 article-title: The impact of recombination hotspots on genome evolution of a fungal plant pathogen publication-title: Genetics doi: 10.1534/genetics.115.180968 – volume: 39 start-page: 383 year: 2011 ident: 2020121613440458100_msaa194-B60903427 article-title: Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes publication-title: Nucleic Acids Res doi: 10.1093/nar/gkq1170 – volume: 6 start-page: 283 issue: 4 year: 2009 ident: 2020121613440458100_msaa194-B62 article-title: Global mapping of protein-DNA interactions in vivo by digital genomic footprinting publication-title: Nat Methods doi: 10.1038/nmeth.1313 – volume: 16 start-page: 78 issue: 1 year: 2005 ident: 2020121613440458100_msaa194-B77 article-title: Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates publication-title: Genome Res doi: 10.1101/gr.4001406 – year: 2015 ident: 2020121613440458100_msaa194-B148 – volume: 12 start-page: 996 issue: 6 year: 2002 ident: 2020121613440458100_msaa194-B76 article-title: The human genome browser at UCSC publication-title: Genome Res doi: 10.1101/gr.229102 – volume: 553 start-page: 228 issue: 7687 year: 2018 ident: 2020121613440458100_msaa194-B95 article-title: Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators publication-title: Nature doi: 10.1038/nature25179 – volume: 21 start-page: 985 issue: 6 year: 2011 ident: 2020121613440458100_msaa194-B43 article-title: Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans publication-title: Genome Res doi: 10.1101/gr.114777.110 – volume: 14 start-page: 603 issue: 6 year: 2004 ident: 2020121613440458100_msaa194-B69 article-title: Evolutionary impact of human Alu repetitive elements publication-title: Curr Opin Genet Dev doi: 10.1016/j.gde.2004.08.008 |
| SSID | ssj0014466 |
| Score | 2.376161 |
| Snippet | Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is... |
| SourceID | pubmedcentral proquest pubmed crossref oup |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 3576 |
| SubjectTerms | Biological Evolution Chromatin Data analysis Datasets Discoveries DNA methylation DNA Transposable Elements Functionals Functions (mathematics) Genome, Human Genomes Genomics Humans Insertion Long Interspersed Nucleotide Elements Mathematical functions Models, Genetic Mutagenesis Mutagenesis, Insertional Statistical methods Transposition |
| Title | Human L1 Transposition Dynamics Unraveled with Functional Data Analysis |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/32722770 https://www.proquest.com/docview/3171297103 https://www.proquest.com/docview/2428416183 https://pubmed.ncbi.nlm.nih.gov/PMC7743743 |
| Volume | 37 |
| WOSCitedRecordID | wos000606021400013&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1537-1719 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0014466 issn: 0737-4038 databaseCode: TOX dateStart: 20020101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1537-1719 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0014466 issn: 0737-4038 databaseCode: TOX dateStart: 19831201 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1Lb9QwEB7RFiQuvKGBsjIIiZO169iOkxMC2oVD2a7QIu0tsh1bVNpm22ZbiX_POE5CFwk4cLEUeaQ8xvOefAPwxmdeSq4EzbQwVKCJpNrLCXXam8wHjuuW08dqNsuXy2LeJdyarq2y14mtoq7WNuTIx2jn0DShPeTvzi9omBoVqqvdCI0d2AsoCWnbujcfqgh9rVJxhXESzwfQRj4-W6-Mux6fNVqzQmwZpa0f3W74m7-3Td6wQ9P7__sGD-Be54GS9_HIPIRbrn4Ed-JMyh-P4VOb1ifHjHS457GpixzG0fUN-VaHiUUrV5GQwyVTNIwxn0gO9UaTHuXkCSymR4uPn2k3bYFaIdMNZUJJq43Nikr5zEyst0WFrBJM5wadCp1jMJUp4z1nqRMsN3nFZCWLzGdKcf4Udut17faBqElug-OhcRUcQyptnETPR0uOatmKBGj_tUvbIZGHgRirMlbEeRm5U3bcSeDtQH8eMTj-SPkamfdPooOeP2UnsE35izkJvBq2UdRC_UTXbn3VlOjNhCItKsEEnsWjMNyKpypNlZokoLYOyUAQYLy3d-rT7y2cNzrgKCz8-d8f6wXcTUOoz1LKsgPY3VxeuZdw215vTpvLEeyopWrXfAR7H45m86949SU9GbUSgeviZPkThCUT6g |
| linkProvider | ProQuest |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lj9MwEB6tFhBceD8CCxgE4mS1fsXJASFEKbvaUjgUaW-R49iiUpsum-6i_ij-I-O82CIBpz1wycWW4sSf55uXZwBe-NgrJbSksZE5lUiR1Hg1pM74PPZhx0290xM9nSZHR-nnHfjR3YUJaZWdTKwFdbGywUc-QJ5DakI-FG-Ov9HQNSpEV7sWGg0sDt3mO5ps1euDEe7vS87H72fv9mnbVYBaqfiaMqmVNbmN00L7OB9ab9MClySZSXIkT5Og0RDr3HvBuJMsyZOCqUKlsY-1Dv5PlPiXZDCEQqYg_9QHLbrQqBYazTKR9DUixWC5WuTubLCsjGGp3OLArXt159Tb37M0z9He-MZ_9sNuwvVWvyZvmwNxC3ZceRuuNB03N3fgQx20IBNG2qruTcoaGW1Ks5zbinwpQz-mhStI8FCTMdJ-4y0lI7M2pKvhchdmF_ER92C3XJXuARA9TGxQqww-pUCD0eROoV5nlEDSsTIC2m1uZts666HdxyJr4v0ia8CQtWCI4FU__7ipMPLHmc8RK_-ctNfBIWvFUZX9wkIEz_phFCQhOmRKtzqtMtTVQggaRXwE9xvk9a8SXHOu9TACvYXJfkIoUr49Us6_1sXK0bxAUSAe_n1ZT-Hq_uzjJJscTA8fwTUenBqMUxbvwe765NQ9hsv2bD2vTp7UR45AdsGI_QkvnmoP |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Human+L1+Transposition+Dynamics+Unraveled+with+Functional+Data+Analysis&rft.jtitle=Molecular+biology+and+evolution&rft.au=Chen%2C+Di&rft.au=Cremona%2C+Marzia+A&rft.au=Qi%2C+Zongtai&rft.au=Mitra%2C+Robi+D&rft.date=2020-12-16&rft.eissn=1537-1719&rft.volume=37&rft.issue=12&rft.spage=3576&rft_id=info:doi/10.1093%2Fmolbev%2Fmsaa194&rft_id=info%3Apmid%2F32722770&rft.externalDocID=32722770 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0737-4038&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0737-4038&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0737-4038&client=summon |