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...

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Bibliographic Details
Published in:Genome Biology Vol. 22; no. 1; p. 164
Main Authors: Lee, Da-Inn, Roy, Sushmita
Format: Journal Article
Language:English
Published: London BioMed Central 25.05.2021
Springer Nature B.V
BMC
Subjects:
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
Online Access:Get full text
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Summary: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.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-021-02378-z