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Analysis of institutional authors

Stik, GAuthorVidal, ECorresponding AuthorGraf, TAuthorStadhouders RCorresponding Author
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Article

CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells

Publicated to:Nature Cell Biology. 23 (8): 881-+ - 2021-08-01 23(8), DOI: 10.1038/s41556-021-00722-w

Authors: Soochit, W; Sleutels, F; Stik, G; Bartkuhn, M; Basu, S; Hernandez, SC; Merzouk, S; Vidal, E; Boers, R; Boers, J; van der Reijden, M; Geverts, B; van Cappellen, WA; van den Hout, M; Ozgur, Z; van IJcken, WFJ; Gribnau, J; Renkawitz, R; Graf, T; Houtsmuller, A; Grosveld, F; Stadhouders, R; Galjart, N

Affiliations

Barcelona Inst Sci & Technol BIST, Ctr Genom Regulat CRG, Barcelona, Spain - Author
Barcelona Institute of Science and Technology (BIST) - Author
Erasmus MC - Author
Erasmus MC, Ctr Biom, Rotterdam, Netherlands - Author
Erasmus MC, Dept Cell Biol, Rotterdam, Netherlands - Author
Erasmus MC, Dept Dev Biol, Rotterdam, Netherlands - Author
Erasmus MC, Dept Pulm Med, Rotterdam, Netherlands - Author
Erasmus MC, Josephine Nefkens Inst, Dept Pathol, Rotterdam, Netherlands - Author
Josephine Nefkens Institute - JNI - Author
Justus Liebig Univ Giessen, Inst Genet, Giessen, Germany - Author
Justus-Liebig-Universität Gießen - Author
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Abstract

The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8–ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.

Keywords
3d genomearchitectureassociating domainsbindingcohesinmammalian genomesprinciplesrevealstranscription factorsInactive x-chromosome

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nature Cell Biology 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, 2021, it was in position 9/195, thus managing to position itself as a Q1 (Primer Cuartil), in the category Cell Biology. Notably, the journal is positioned above the 90th percentile.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 1.3. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 1.63 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 9.77 (source consulted: Dimensions May 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-05-13, the following number of citations:

  • WoS: 31
  • Scopus: 33
  • Europe PMC: 20
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 2025-05-13:

  • 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: 112.
  • 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: 112 (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: 26.8.
  • The number of mentions on the social network X (formerly Twitter): 54 (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.
Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Germany; Netherlands.

the authors responsible for correspondence tasks have been VIDAL OCABO, ENRIQUE and Stadhouders, Ralph.