The cis-Regulatory Atlas of the Mouse Immune System.
Animals
Binding Sites
/ genetics
Chromatin
Chromatin Immunoprecipitation
/ methods
Enhancer Elements, Genetic
/ genetics
Epigenomics
/ methods
Gene Expression Regulation
/ genetics
Immune System
/ immunology
Mice
Mice, Inbred C57BL
Promoter Regions, Genetic
/ genetics
Protein Binding
/ genetics
Regulatory Elements, Transcriptional
/ genetics
Transcription Factors
/ metabolism
Transcriptome
/ genetics
ATAC-seq
Transcriptional regulation
chromatin
enhancer
epigenomics
immune cell differentiation
transcription factor
Journal
Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066
Informations de publication
Date de publication:
07 02 2019
07 02 2019
Historique:
received:
05
07
2018
revised:
26
10
2018
accepted:
20
12
2018
pubmed:
29
1
2019
medline:
4
12
2019
entrez:
29
1
2019
Statut:
ppublish
Résumé
A complete chart of cis-regulatory elements and their dynamic activity is necessary to understand the transcriptional basis of differentiation and function of an organ system. We generated matched epigenome and transcriptome measurements in 86 primary cell types that span the mouse immune system and its differentiation cascades. This breadth of data enable variance components analysis that suggests that genes fall into two distinct classes, controlled by either enhancer- or promoter-driven logic, and multiple regression that connects genes to the enhancers that regulate them. Relating transcription factor (TF) expression to the genome-wide accessibility of their binding motifs classifies them as predominantly openers or closers of local chromatin accessibility, pinpointing specific cis-regulatory elements where binding of given TFs is likely functionally relevant, validated by chromatin immunoprecipitation sequencing (ChIP-seq). Overall, this cis-regulatory atlas provides a trove of information on transcriptional regulation through immune differentiation and a foundational scaffold to define key regulatory events throughout the immunological genome.
Identifiants
pubmed: 30686579
pii: S0092-8674(18)31650-7
doi: 10.1016/j.cell.2018.12.036
pmc: PMC6785993
mid: NIHMS1538358
pii:
doi:
Substances chimiques
Chromatin
0
Transcription Factors
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
897-912.e20Subventions
Organisme : NIAID NIH HHS
ID : R24 AI072073
Pays : United States
Informations de copyright
Copyright © 2018 Elsevier Inc. All rights reserved.
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