Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions

Epigenetics & Chromatin
Idan NurickRan Elkon

Abstract

Our appreciation of the critical role of the genome's 3D organization in gene regulation is steadily increasing. Recent 3C-based deep sequencing techniques elucidated a hierarchy of structures that underlie the spatial organization of the genome in the nucleus. At the top of this hierarchical organization are chromosomal territories and the megabase-scale A/B compartments that correlate with transcriptional activity within cells. Below them are the relatively cell-type-invariant topologically associated domains (TADs), characterized by high frequency of physical contacts between loci within the same TAD, and are assumed to function as regulatory units. Within TADs, chromatin loops bring enhancers and target promoters to close spatial proximity. Yet, we still have only rudimentary understanding how differences in chromatin organization between different cell types affect cell-type-specific gene expression programs that are executed under basal and challenged conditions. Here, we carried out a large-scale meta-analysis that integrated Hi-C data from thirteen different cell lines and dozens of ChIP-seq and RNA-seq datasets measured on these cells, either under basal conditions or after treatment. Pairwise comparisons between cell ...Continue Reading

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Citations

Sep 6, 2019·Scientific Reports·Shay Ben-ElazarZohar Yakhini
Jul 3, 2021·Cells·Jekaterina ErenpreisaAlessandro Giuliani

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Datasets Mentioned

BETA
GM12878
The

Methods Mentioned

BETA
ChIP-seq
RNA-seq
Hi–C

Software Mentioned

PSYCHIC
ENCODE
MACS2
Bowtie2
TopHat2
DESeq

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