Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
16 10 2023
16 10 2023
Historique:
received:
17
05
2023
accepted:
05
10
2023
medline:
23
10
2023
pubmed:
17
10
2023
entrez:
16
10
2023
Statut:
epublish
Résumé
The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.
Identifiants
pubmed: 37845234
doi: 10.1038/s41467-023-42274-7
pii: 10.1038/s41467-023-42274-7
pmc: PMC10579264
doi:
Substances chimiques
Chromatin
0
RNA
63231-63-0
DNA
9007-49-2
RNA, Small Nuclear
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
6519Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM136922
Pays : United States
Organisme : NHLBI NIH HHS
ID : U01 HL156059
Pays : United States
Informations de copyright
© 2023. Springer Nature Limited.
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