MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.
Chromatin
/ metabolism
Chromatin Assembly and Disassembly
/ physiology
Chromatin Immunoprecipitation
/ methods
Chromosome Mapping
/ methods
Computational Biology
/ methods
Computer Simulation
Genome
Genomics
/ methods
High-Throughput Nucleotide Sequencing
/ methods
Histone Code
Humans
Sequence Analysis, DNA
/ methods
Software
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
04 2019
04 2019
Historique:
received:
25
09
2018
accepted:
28
03
2019
revised:
25
04
2019
pubmed:
16
4
2019
medline:
22
5
2019
entrez:
16
4
2019
Statut:
epublish
Résumé
Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in the analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.
Identifiants
pubmed: 30986246
doi: 10.1371/journal.pcbi.1006982
pii: PCOMPBIOL-D-18-01649
pmc: PMC6483256
doi:
Substances chimiques
Chromatin
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1006982Subventions
Organisme : NIDDK NIH HHS
ID : U54 DK107977
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL129132
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Science. 2002 Feb 15;295(5558):1306-11
pubmed: 11847345
Genes Dev. 2003 Mar 15;17(6):759-73
pubmed: 12651894
Genes Dev. 2008 Mar 1;22(5):575-80
pubmed: 18283123
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Nature. 2010 Sep 23;467(7314):430-5
pubmed: 20720539
Bioinformatics. 2011 Apr 1;27(7):1017-8
pubmed: 21330290
Nat Genet. 2011 Oct 16;43(11):1059-65
pubmed: 22001755
Nat Methods. 2012 Oct;9(10):999-1003
pubmed: 22941365
Nature. 2012 Sep 6;489(7414):109-13
pubmed: 22955621
Nat Methods. 2012 Oct;9(10):969-72
pubmed: 22961246
Bioinformatics. 2012 Dec 1;28(23):3131-3
pubmed: 23023982
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Cell. 2013 Dec 19;155(7):1507-20
pubmed: 24360274
Genome Res. 2014 Jun;24(6):999-1011
pubmed: 24501021
PLoS One. 2014 Dec 08;9(12):e114485
pubmed: 25486255
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Genome Res. 2015 Apr;25(4):582-97
pubmed: 25752748
Bioinformatics. 2015 Oct 1;31(19):3092-8
pubmed: 26034063
Cell. 2015 Dec 17;163(7):1611-27
pubmed: 26686651
Nat Rev Mol Cell Biol. 2016 Dec;17(12):743-755
pubmed: 27580841
Nat Methods. 2016 Nov;13(11):919-922
pubmed: 27643841
Cell Rep. 2016 Nov 15;17(8):2042-2059
pubmed: 27851967
Cell Res. 2016 Dec;26(12):1345-1348
pubmed: 27886167
Genome Res. 2017 Feb;27(2):246-258
pubmed: 27895109
Annu Rev Cell Dev Biol. 2017 Oct 6;33:265-289
pubmed: 28783961
Nat Genet. 2017 Nov;49(11):1602-1612
pubmed: 28945252
Cell. 2017 Oct 19;171(3):557-572.e24
pubmed: 29053968
Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266
pubmed: 29140473
Nat Methods. 2018 Feb 28;15(3):155-156
pubmed: 29489746
Cell. 2018 Jul 26;174(3):744-757.e24
pubmed: 29887377
Nature. 2019 Jan;565(7740):448-453
pubmed: 30626972