TAD cliques predict key features of chromatin organization.
BMC Genomics
; 22(1): 499, 2021 Jul 03.
Article
in En
| MEDLINE
| ID: mdl-34217222
ABSTRACT
BACKGROUND:
Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and interactions with the nuclear lamina dynamically act on chromatin at multiple levels. Here, we explore long-range interaction patterns between topologically associated domains (TADs) in several cell types.RESULTS:
We find that TAD long-range interactions are connected to many key features of chromatin organization, including open and closed compartments, compaction and loop extrusion processes. Domains that form large TAD cliques tend to be repressive across cell types, when comparing gene expression, LINE/SINE repeat content and chromatin subcompartments. Further, TADs in large cliques are larger in genomic size, less dense and depleted of convergent CTCF motifs, in contrast to smaller and denser TADs formed by a loop extrusion process.CONCLUSIONS:
Our results shed light on the organizational principles that govern repressive and active domains in the human genome.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Chromatin
/
Chromatin Assembly and Disassembly
Type of study:
Prognostic_studies
/
Risk_factors_studies
Limits:
Animals
/
Humans
Language:
En
Journal:
BMC Genomics
Journal subject:
GENETICA
Year:
2021
Document type:
Article
Affiliation country: