Nucleosomal DNA has topological memory.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
28 May 2024
28 May 2024
Historique:
received:
22
06
2023
accepted:
21
05
2024
medline:
29
5
2024
pubmed:
29
5
2024
entrez:
28
5
2024
Statut:
epublish
Résumé
One elusive aspect of the chromosome architecture is how it constrains the DNA topology. Nucleosomes stabilise negative DNA supercoils by restraining a DNA linking number difference (∆Lk) of about -1.26. However, whether this capacity is uniform across the genome is unknown. Here, we calculate the ∆Lk restrained by over 4000 nucleosomes in yeast cells. To achieve this, we insert each nucleosome in a circular minichromosome and perform Topo-seq, a high-throughput procedure to inspect the topology of circular DNA libraries in one gel electrophoresis. We show that nucleosomes inherently restrain distinct ∆Lk values depending on their genomic origin. Nucleosome DNA topologies differ at gene bodies (∆Lk = -1.29), intergenic regions (∆Lk = -1.23), rDNA genes (∆Lk = -1.24) and telomeric regions (∆Lk = -1.07). Nucleosomes near the transcription start and termination sites also exhibit singular DNA topologies. Our findings demonstrate that nucleosome DNA topology is imprinted by its native chromatin context and persists when the nucleosome is relocated.
Identifiants
pubmed: 38806488
doi: 10.1038/s41467-024-49023-4
pii: 10.1038/s41467-024-49023-4
doi:
Substances chimiques
Nucleosomes
0
DNA, Fungal
0
Chromatin
0
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
4526Subventions
Organisme : Ministerio de Educación, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain)
ID : PID2019-109482GB-I00
Organisme : Ministerio de Educación, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain)
ID : PRE2020-093378
Informations de copyright
© 2024. The Author(s).
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