# Editorial: Chromatin structure and function

Laxmi Narayan Mishra, Christophe Thiriet, Dileep Vasudevan

► To cite this version:

Laxmi Narayan Mishra, Christophe Thiriet, Dileep Vasudevan. Editorial: Chromatin structure and function. Frontiers in Genetics, 2023, 14, 10.3389/fgene.2023.1140534. [https://doi.org/10.3389/fgene.2023.1140519]

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OPEN ACCESS

EDITED AND REVIEWED BY

Michael E. Symonds,
University of Nottingham, United Kingdom

*CORRESPONDENCE

Laxmi Narayan Mishra,
✉ mishrabiotech@gmail.com
Christophe Thiriet,
✉ Christophe.Thiriet@univ-rennes1.fr,
Dileep Vasudevan,
✉ dileep@ils.res.in

¹Present address:

Laxmi Narayan Mishra, Regeneron
Pharmaceuticals Inc, Tarrytown, NY,
United States

SPECIALTY SECTION

This article was submitted to Epigenomics
and Epigenetics,
a section of the journal
Frontiers in Genetics

RECEIVED 09 January 2023

ACCEPTED 25 January 2023

PUBLISHED 07 February 2023

CITATION

Mishra LN, Thiriet C and Vasudevan D (2023), Editorial: Chromatin structure and function.
*Front. Genet.* 14:1140534.
doi: 10.3389/fgene.2023.1140534

COPYRIGHT

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Editorial: Chromatin structure and
function

Laxmi Narayan Mishra¹*†, Christophe Thiriet²* and
Dileep Vasudevan³*

¹Albert Einstein College of Medicine, Bronx, NY, United States, ²Université de Rennes 1, CNRS-UMR6290 Institut génétique et développement de Rennes (IGDR), Rennes, France, ³DBT-Institute of Life Sciences, Bhubaneswar, India

KEYWORDS

chromatin, histone, histone posttranslational modifications, chromatin remodeling, DNA
damage repair

Editorial on the Research Topic

Chromatin structure and function

Chromatin dynamics influence DNA-dependent processes such as transcription, repair, replication, and recombination (Hübner and Spector, 2010; Galvani and Thiriet, 2015). Because disorganized chromatin affects gene expression and eventually leads to disease onset, scientists are eager to learn more about the roles of histone PTMs, DNA methylation, and chromatin remodeling factors in chromatin dynamics. In eukaryotes, how genes are packaged in chromatin determines whether or not the genes can be expressed to produce the encoded product. Typically, DNA-binding factors cannot access DNA within the nucleosome, and nucleosomes must be disassembled for them to gain access to the underlying DNA (Mishra and Hayes, 2018; Sundaram and Vasudevan, 2020). Various high-throughput technologies have emerged to aid researchers in understanding chromatin structure and function (Marr et al., 2022). This Research Topic contains numerous articles on chromatin dynamics, transcription, DNA damage repair, and drug resistance.

In their study, Vinaychandran and Bhargava describe how the structural characteristics of nucleosomal DNA affect transcription factor binding and effective translation. Shi et al. reviewed recent advances in determining chromatin dynamics and their modulation by factors such as PTMs, histone variant incorporation, and effector protein binding. Seharawat et al. discuss how histone PTMs affect nucleosome structure and regulate chromatin accessibility in a review. Pavlenko et al.'s review article summarizes current knowledge on the functions of lysine-specific demethylase-5 and focuses on molecular interactions and their potential implications. They also bring unanswered questions about histone demethylation that require the scientific community's attention to understand it fully.

Genome attacks are common throughout cell life, and various factors can cause DNA
damage. When a DNA lesion occurs, the cell repairs it to preserve the genetic material's
integrity. Because the genome has been condensed into chromatin, the repair must occur within
the context of chromatin structure to access and repair damaged DNA (Hauer and Gasser,
2017). Bisht et al. in their research article, show that the interaction of SMARCAL1 and BRG1,
two chromatin remodeling factors that collaborate in the promoter region during double-
stranded DNA repair, is dependent on their ATPase activity. Based on BRCA1 and
53BP1 abundance and organization, Abate and Hendzel's study demonstrates the presence
of multiple classes of DNA double-strand break (DSB) repair compartments. Roemer et al.
discuss constitutive heterochromatin accessibility. They studied the chromocenter
concentrations and diffusion of several DSB sensors, mediators, and effector proteins in
mice without DNA damage using fluorescently labeled proteins involved in DNA damage detection and repair. In their review, Arichthota et al. discuss the role of histone acetylation in altering chromatin organization and promoting the recruitment of DSB repair proteins to DNA damage sites.

On the other hand, nucleosome assembly is required to restore the native nucleosomal template and the correct epigenetic landscape, which is most visible during DNA replication. The newly synthesized DNA must be packaged in a consistent, complementary, and epigenetically tagged fashion. At the replication fork, a highly orchestrated mechanism not only creates templates and produces an identical copy of DNA but also removes nucleosomes in front and reassembles histones into nucleosomes behind (Verreault, 2000). Zhao et al. reconstituted nucleosomes in vitro using the nucleosome positioning sequence Widom 601 and proposed a chemical-kinetic model of nucleosome assembly and disassembly using precise biophysical methods such as FRET and FTS assays. Gene regulation, recombination, and other fundamental processes rely on large-scale chromatin interactions, including chromosome interactions. Krajewski discusses how bulky post-translational histone modifications like ubiquitination, internucleosomal dynamics, and DNA stress work together to functionalize nucleosomes in a large nucleosome array in his hypothesis and theory paper.

Methylation of DNA regulates gene expression by generally turning the gene off (Moore and Fan, 2013). Li et al. discuss the limitations of identifying N6-methyladenine, a poorly studied DNA methylation in eukaryotes. They also discuss the potential applications of this recently discovered DNA modification. In a systematic review, Rawat et al. discuss the coexisting mutations and gene expression trends associated with K13-mediated artemisinin resistance in *Plasmodium falciparum*. They analyzed a large dataset of single nucleotide polymorphisms (SNPs) to determine the prevalence, geographic distribution,

and coexistence patterns of genetic markers associated with artemisinin resistance.

Overall, the breadth of the articles in this Research Topic demonstrates the remarkable progress being made in understanding the critical roles of chromatin structure in transcription, replication, and DNA damage repair. These articles also raise numerous unanswered questions that must be addressed in the near future to fully understand the disease biology associated with altered chromatin structure.

## Author contributions

As guest editors, LM, CT, and DV organized the Research Topic, invited authors, and oversaw manuscript review. LM wrote the editorial. LM, CT, and DV edited and approved the publication. All listed authors contributed significantly, directly, and intellectually to the work and approved its publication.

## Conflict of interest

LM is employed by Regeneron Pharmaceuticals Inc.

The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

## Publisher's note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

## References

Galvani, A., and Thiriet, C. (2015). Nucleosome dancing at the tempo of histone tail acetylation. *Genes. (Basel)* 6 (3), 607–621. doi:10.3390/genes6030607

Hauer, M. H., and Gasser, S. M. (2017). Chromatin and nucleosome dynamics in DNA damage and repair. *Genes. Dev.* 31 (22), 2204–2221. doi:10.1101/gad.307702.117

Hübner, M. R., and Spector, D. L. (2010). Chromatin dynamics. *Annu. Rev. Biophys.* 39, 471–489. doi:10.1146/annurev.biophys.093008.131348

Marr, L. T., Jaya, P., Mishra, L. N., and Hayes, J. J. (2022). Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin. *Biochem. Soc. Trans.* 50, 199–212. doi:10.1042/BST20210959

Mishra, L. N., and Hayes, J. J. (2018). A nucleosome-free region locally abrogates histone H1-dependent restriction of linker DNA accessibility in chromatin. *J. Biol. Chem.* 293 (50), 19191–19200. doi:10.1074/jbc.RA118.005721

Moore, L., and Fan, G. (2013). DNA methylation and its basic function. *Neuropsychopharmacol* 38, 23–38. doi:10.1038/npp.2012.112

Sundaram, R., and Vasudevan, D. (2020). Structural basis of nucleosome recognition and modulation. *Bioessays* 42 (9), e1900234. doi:10.1002/bies.201900234

Verreault, A. (2000). De novo nucleosome assembly: New pieces in an old puzzle. *Genes. Dev.* 14 (12), 1430–1438. doi:10.1101/gad.14.12.1430