Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage

Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation. However, we currently lack a detailed understanding of how chromatin and gene expression patterns are coordinated during developmental trans...

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Vydané v:	Cell Ročník 151; číslo 1; s. 206
Hlavní autori:	Wamstad, Joseph A, Alexander, Jeffrey M, Truty, Rebecca M, Shrikumar, Avanti, Li, Fugen, Eilertson, Kirsten E, Ding, Huiming, Wylie, John N, Pico, Alexander R, Capra, John A, Erwin, Genevieve, Kattman, Steven J, Keller, Gordon M, Srivastava, Deepak, Levine, Stuart S, Pollard, Katherine S, Holloway, Alisha K, Boyer, Laurie A, Bruneau, Benoit G
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	United States 28.09.2012
Predmet:	Animals Cell Differentiation Chromatin - metabolism Embryonic Stem Cells - metabolism Enhancer Elements, Genetic Epigenesis, Genetic Gene Regulatory Networks Heart - embryology Humans Mice Myocardium - cytology Transcription Factors - metabolism Transcriptome
ISSN:	1097-4172, 1097-4172
On-line prístup:	Zistit podrobnosti o prístupe
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Abstract	Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation. However, we currently lack a detailed understanding of how chromatin and gene expression patterns are coordinated during developmental transitions in the cardiac lineage. Here, we interrogated the transcriptome and several histone modifications across the genome during defined stages of cardiac differentiation. We find distinct chromatin patterns that are coordinated with stage-specific expression of functionally related genes, including many human disease-associated genes. Moreover, we discover a novel preactivation chromatin pattern at the promoters of genes associated with heart development and cardiac function. We further identify stage-specific distal enhancer elements and find enriched DNA binding motifs within these regions that predict sets of transcription factors that orchestrate cardiac differentiation. Together, these findings form a basis for understanding developmentally regulated chromatin transitions during lineage commitment and the molecular etiology of congenital heart disease.
AbstractList	Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation. However, we currently lack a detailed understanding of how chromatin and gene expression patterns are coordinated during developmental transitions in the cardiac lineage. Here, we interrogated the transcriptome and several histone modifications across the genome during defined stages of cardiac differentiation. We find distinct chromatin patterns that are coordinated with stage-specific expression of functionally related genes, including many human disease-associated genes. Moreover, we discover a novel preactivation chromatin pattern at the promoters of genes associated with heart development and cardiac function. We further identify stage-specific distal enhancer elements and find enriched DNA binding motifs within these regions that predict sets of transcription factors that orchestrate cardiac differentiation. Together, these findings form a basis for understanding developmentally regulated chromatin transitions during lineage commitment and the molecular etiology of congenital heart disease.Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation. However, we currently lack a detailed understanding of how chromatin and gene expression patterns are coordinated during developmental transitions in the cardiac lineage. Here, we interrogated the transcriptome and several histone modifications across the genome during defined stages of cardiac differentiation. We find distinct chromatin patterns that are coordinated with stage-specific expression of functionally related genes, including many human disease-associated genes. Moreover, we discover a novel preactivation chromatin pattern at the promoters of genes associated with heart development and cardiac function. We further identify stage-specific distal enhancer elements and find enriched DNA binding motifs within these regions that predict sets of transcription factors that orchestrate cardiac differentiation. Together, these findings form a basis for understanding developmentally regulated chromatin transitions during lineage commitment and the molecular etiology of congenital heart disease. Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation. However, we currently lack a detailed understanding of how chromatin and gene expression patterns are coordinated during developmental transitions in the cardiac lineage. Here, we interrogated the transcriptome and several histone modifications across the genome during defined stages of cardiac differentiation. We find distinct chromatin patterns that are coordinated with stage-specific expression of functionally related genes, including many human disease-associated genes. Moreover, we discover a novel preactivation chromatin pattern at the promoters of genes associated with heart development and cardiac function. We further identify stage-specific distal enhancer elements and find enriched DNA binding motifs within these regions that predict sets of transcription factors that orchestrate cardiac differentiation. Together, these findings form a basis for understanding developmentally regulated chromatin transitions during lineage commitment and the molecular etiology of congenital heart disease.
Author	Wamstad, Joseph A Alexander, Jeffrey M Kattman, Steven J Holloway, Alisha K Shrikumar, Avanti Keller, Gordon M Levine, Stuart S Boyer, Laurie A Truty, Rebecca M Eilertson, Kirsten E Wylie, John N Bruneau, Benoit G Ding, Huiming Capra, John A Li, Fugen Pico, Alexander R Pollard, Katherine S Erwin, Genevieve Srivastava, Deepak
Author_xml	– sequence: 1 givenname: Joseph A surname: Wamstad fullname: Wamstad, Joseph A organization: Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA – sequence: 2 givenname: Jeffrey M surname: Alexander fullname: Alexander, Jeffrey M – sequence: 3 givenname: Rebecca M surname: Truty fullname: Truty, Rebecca M – sequence: 4 givenname: Avanti surname: Shrikumar fullname: Shrikumar, Avanti – sequence: 5 givenname: Fugen surname: Li fullname: Li, Fugen – sequence: 6 givenname: Kirsten E surname: Eilertson fullname: Eilertson, Kirsten E – sequence: 7 givenname: Huiming surname: Ding fullname: Ding, Huiming – sequence: 8 givenname: John N surname: Wylie fullname: Wylie, John N – sequence: 9 givenname: Alexander R surname: Pico fullname: Pico, Alexander R – sequence: 10 givenname: John A surname: Capra fullname: Capra, John A – sequence: 11 givenname: Genevieve surname: Erwin fullname: Erwin, Genevieve – sequence: 12 givenname: Steven J surname: Kattman fullname: Kattman, Steven J – sequence: 13 givenname: Gordon M surname: Keller fullname: Keller, Gordon M – sequence: 14 givenname: Deepak surname: Srivastava fullname: Srivastava, Deepak – sequence: 15 givenname: Stuart S surname: Levine fullname: Levine, Stuart S – sequence: 16 givenname: Katherine S surname: Pollard fullname: Pollard, Katherine S – sequence: 17 givenname: Alisha K surname: Holloway fullname: Holloway, Alisha K – sequence: 18 givenname: Laurie A surname: Boyer fullname: Boyer, Laurie A – sequence: 19 givenname: Benoit G surname: Bruneau fullname: Bruneau, Benoit G
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/22981692$$D View this record in MEDLINE/PubMed
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References	23493303 - Circ Res. 2013 Mar 15;112(6):881-3 23122282 - Cell Stem Cell. 2012 Nov 2;11(5):581-2
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SubjectTerms	Animals Cell Differentiation Chromatin - metabolism Embryonic Stem Cells - metabolism Enhancer Elements, Genetic Epigenesis, Genetic Gene Regulatory Networks Heart - embryology Humans Mice Myocardium - cytology Transcription Factors - metabolism Transcriptome
Title	Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage
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