Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape

Kong, Siyuan; Lu, Yuhui; Tan, Shuhao; Li, Rongrong; Gao, Yan; Li, Kui; Zhang, Yubo

doi:10.3390/genes13071114

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Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape

by

Siyuan Kong

^†

,

Yuhui Lu

^†,

Shuhao Tan

,

Rongrong Li

,

Yan Gao

,

Kui Li

and

Yubo Zhang

^*

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China

^*

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Genes 2022, 13(7), 1114; https://doi.org/10.3390/genes13071114

Submission received: 20 May 2022 / Revised: 14 June 2022 / Accepted: 17 June 2022 / Published: 22 June 2022

(This article belongs to the Special Issue DNA and RNA Epigenetics and Transcriptomics Research)

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Abstract

Genetic information is loaded on chromatin, which involves DNA sequence arrangement and the epigenetic landscape. The epigenetic information including DNA methylation, nucleosome positioning, histone modification, 3D chromatin conformation, and so on, has a crucial impact on gene transcriptional regulation. Out of them, nucleosomes, as basal chromatin structural units, play an important central role in epigenetic code. With the discovery of nucleosomes, various nucleosome-level technologies have been developed and applied, pushing epigenetics to a new climax. As the underlying methodology, next-generation sequencing technology has emerged and allowed scientists to understand the epigenetic landscape at a genome-wide level. Combining with NGS, nucleosome-omics (or nucleosomics) provides a fresh perspective on the epigenetic code and 3D genome landscape. Here, we summarized and discussed research progress in technology development and application of nucleosome-omics. We foresee the future directions of epigenetic development at the nucleosome level.

Keywords: epigenetics; nucleosomes; MNase-seq; Micro-C; 3D genome

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MDPI and ACS Style

Kong, S.; Lu, Y.; Tan, S.; Li, R.; Gao, Y.; Li, K.; Zhang, Y. Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape. Genes 2022, 13, 1114. https://doi.org/10.3390/genes13071114

AMA Style

Kong S, Lu Y, Tan S, Li R, Gao Y, Li K, Zhang Y. Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape. Genes. 2022; 13(7):1114. https://doi.org/10.3390/genes13071114

Chicago/Turabian Style

Kong, Siyuan, Yuhui Lu, Shuhao Tan, Rongrong Li, Yan Gao, Kui Li, and Yubo Zhang. 2022. "Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape" Genes 13, no. 7: 1114. https://doi.org/10.3390/genes13071114

APA Style

Kong, S., Lu, Y., Tan, S., Li, R., Gao, Y., Li, K., & Zhang, Y. (2022). Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape. Genes, 13(7), 1114. https://doi.org/10.3390/genes13071114

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Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape

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