Methods for comparative ChIA-PET and Hi-C data analysis.
Journal
Methods (San Diego, Calif.)
ISSN: 1095-9130
Titre abrégé: Methods
Pays: United States
ID NLM: 9426302
Informations de publication
Date de publication:
01 01 2020
01 01 2020
Historique:
received:
19
03
2019
revised:
27
09
2019
accepted:
28
09
2019
pubmed:
20
10
2019
medline:
22
12
2020
entrez:
20
10
2019
Statut:
ppublish
Résumé
The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin interaction analysis with paired-end tag sequencing). There is widespread interest in utilizing and interpreting ChIA-PET and Hi-C. We review methods for comparative ChIA-PET and Hi-C data analysis and visualization. The topics reviewed include: downloading ChIA-PET and Hi-C data from the ENCODE and 4DN portals; processing ChIA-PET data using ChIA-PIPE; processing Hi-C data using Juicer or distiller and cooler; viewing 2D contact maps using Juicebox or Higlass; viewing peaks, loops, and domains using BASIC Browser; annotating convergent and tandem CTCF loops.
Identifiants
pubmed: 31629084
pii: S1046-2023(19)30100-8
doi: 10.1016/j.ymeth.2019.09.019
pii:
doi:
Substances chimiques
Chromatin
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
69-74Subventions
Organisme : NHGRI NIH HHS
ID : UM1 HG009409
Pays : United States
Organisme : NIDDK NIH HHS
ID : U54 DK107967
Pays : United States
Informations de copyright
Published by Elsevier Inc.