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June 10, 2024
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Nucleosomal DNA has topological memory

Publicated to: Nature Communications. 15 (1): 4526- - 2024-05-28 15(1), DOI: 10.1038/s41467-024-49023-4

Authors:

Segura, J; Díaz-Ingelmo, O; Martínez-García, B; Ayats-Fraile, A; Nikolaou, C; Roca, J
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Affiliations

BSRC Alexander Fleming, Computat Genom Grp, Athens, Greece - Author
CSIC, Mol Biol Inst Barcelona IBMB, DNA Topol Lab, Barcelona, Spain - Author
UAM, Ctr Biol Mol Severo Ochoa, CSIC, Madrid, Spain - Author
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Abstract

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 (triangle Lk) of about -1.26. However, whether this capacity is uniform across the genome is unknown. Here, we calculate the triangle 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 triangle Lk values depending on their genomic origin. Nucleosome DNA topologies differ at gene bodies (triangle Lk = -1.29), intergenic regions (triangle Lk = -1.23), rDNA genes (triangle Lk = -1.24) and telomeric regions (triangle 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. Here, the authors develop Topo-seq to measure the DNA topology (triangle Lk) restrained by individual nucleosomes in vivo. They show that nucleosome DNA topology is imprinted by its native chromatin context and persists when the nucleosome is relocated.
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Keywords

ChromatinDnaDna, fungalGene-expressionNucleic acid conformationNucleosomesOrganizationPositionsSaccharomyces cerevisiaeSaccharomyces-cerevisiaeSequenceTelomereYeast

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nature Communications due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2024 there are still no calculated indicators, but in 2023, it was in position 10/136, thus managing to position itself as a Q1 (Primer Cuartil), in the category Multidisciplinary Sciences. Notably, the journal is positioned above the 90th percentile.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-05:

  • WoS: 1
  • Scopus: 1
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-05:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 18.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 18 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 7.
  • The number of mentions on the social network X (formerly Twitter): 13 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Greece.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Segura, Joana) .

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Awards linked to the item

The authors thank the CNAG Sequencing Service and the CRG Bioinformatics Core Facility for assistance; F. Azorin, G. Vicent and V. Zhurkin for discussing results. This work is supported by the Plan Estatal de Investigacion Cientifica y Tecnica of Spain, with grant PID2019-109482GB-I00 to J.R.; research fellowships BES-2012-061167 to J.S. and PRE2020-093378 to A.A-F.
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