GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection...

Celý popis

Uloženo v:

Podrobná bibliografie
Vydáno v:	Genome Biology Ročník 22; číslo 1; s. 164
Hlavní autoři:	Lee, Da-Inn, Roy, Sushmita
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London BioMed Central 25.05.2021 Springer Nature B.V BMC
Témata:	Algorithms Animal Genetics and Genomics Bioinformatics Biomedical and Life Sciences Cell Line Chromatin Chromatin - genetics Chromosomes Chromosomes - genetics Conformation Databases, Genetic Datasets Evolutionary Biology Gene expression genes Genome Genomes High-throughput chromosomal conformation capture (Hi-C) Histones - metabolism Human Genetics Humans Life Sciences Matrix factorization Method Methods Microbial Genetics and Genomics Neighborhoods Plant Genetics and Genomics Protein Processing, Post-Translational Proteins Regulatory Sequences, Nucleic Acid - genetics Sparsity Three-dimensional (3D) genome organization Time Factors Topologically associating domains (TADs) topology Matrix factorization Three-dimensional (3D) genome organization High-throughput chromosomal conformation capture (Hi-C) Topologically associating domains (TADs)
ISSN:	1474-760X, 1474-7596, 1474-760X
On-line přístup:	Získat plný text
Tagy:	Přidat tag Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!

Popis
Shrnutí:	High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior performance against seven TAD-calling methods and three smoothing methods. GRiNCH is applicable to multiple platforms including SPRITE and HiChIP and can predict novel boundary factors with potential roles in genome organization.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	1474-760X 1474-7596 1474-760X
DOI:	10.1186/s13059-021-02378-z