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Latest Epigenetic Research in Plants

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 December 2024) | Viewed by 2333

Special Issue Editor


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Guest Editor
Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
Interests: epigenetics; histones; histone chaperones; post-translational modifications of histones
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Special Issue Information

Dear Colleagues,

Eukaryotic DNA is compacted within chromatin. This sophisticated nucleoproteic structure bears the epigenetic information and is made of DNA wrapped around histone octamers. The histone core is composed by a H3/H4 tetramer flanked by two H2A/H2B dimers. Besides, the H1 linker is associated to the “linker” DNA. Histones can be classified in two categories: (i) canonical histones expressed during the S-phase and (ii) histone variants that can replace canonical isoforms and are expressed throughout the cell cycle. Histones harbor post-translational modifications (PTMs) such as acetylation or methylation. DNA also display chemical modifications such as cytosine methylation that participates to the epigenetic information, besides PTMs and histone isoforms and small RNAs. Histone PTMs and DNA modifications are deposited or removed by various enzymes and histone isoforms are incorporated in chromatin by histone chaperones. Photosynthetic organisms, i.e., land plants and algae (Rhodophytes, Chlorophyta and Chromalveolata for brown algae) are highly diverse organisms that belong to independent lineages sharing the ability to do photosynthesis in various and fluctuating environments.

The Special Edition “Latest Epigenetic Research in Plants” will focus on the molecular players that participates to the epigenetic mechanisms. Plants are plastic organisms that present unique epigenetic mechanisms and constitute interesting models to untangle epigenetic mechanisms operating in various environmental cues.

We invite submission of works that investigate these mechanisms by various and combined approaches, such as biochemistry, molecular biology, genetics and omics approaches, as well as review articles that offer a comprehensive view of the current knowledge and its limits or method papers with new techniques to analyze these mechanisms.

Dr. Céline Duc
Guest Editor

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Keywords

  • chromatin
  • histones
  • post-translational modification
  • histone chaperones
  • DNA modification
  • small RNAs
  • epigenomics
  • epigenetics

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Published Papers (1 paper)

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Research

17 pages, 7548 KiB  
Article
Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing RNA-Binding Protein Family in Cinnamomum camphora
by Jingjing Zhang, Sheng Yao, Xiang Cheng, Yulu Zhao, Wenya Yu, Xingyue Ren, Kongshu Ji and Qiong Yu
Int. J. Mol. Sci. 2024, 25(11), 5960; https://doi.org/10.3390/ijms25115960 - 29 May 2024
Cited by 4 | Viewed by 1886
Abstract
N6-methyladenosine (m6A) is one of the most abundant chemical modifications on mRNA in eukaryotes. RNA-binding proteins containing the YT521-B (YTH) domain play crucial roles in post-transcriptional regulation of plant growth, development, and stress response by reading the m6 [...] Read more.
N6-methyladenosine (m6A) is one of the most abundant chemical modifications on mRNA in eukaryotes. RNA-binding proteins containing the YT521-B (YTH) domain play crucial roles in post-transcriptional regulation of plant growth, development, and stress response by reading the m6A mark. However, the YTH domain-containing RNA-binding protein family has not been studied in a valuable and medicinal tree such as Cinnamomum camphora (C. camphora) yet. In this study, we identified 10 YTH genes in C. camphora, located on eight out of 12 chromosomes. Phylogenetic analysis revealed that these genes can be classified into two major classes, YTHDF (CcDF) and YTHDC (CcDC). Closely related CcYTHs within the same class exhibited a similar distribution of conserved motifs and domain organization, suggesting functional similarities among these closely related CcYTHs. All CcYTH proteins possessed a highly conserved YTH domain, with CcDC1A containing an additional CCCH domain. The liquid–liquid phase separation (LLPS) predictions indicate that CcDC1A, CcDF1A, CcDF1C, CcDF3C, CcDF4C, and CcDF5C may undergo phase transitions. Quantitative expression analysis revealed that tissue-specific expression was observed fo CcYTHs. Notably, there were two genes, CcDF1A and CcDF5C; both exhibited significantly higher expression levels in various tissues than other genes, indicating that the m6A-YTH regulatory network in C. camphora might be quite distinct from that in most plants such as Arabidopsis thaliana (A. thaliana) with only one abundant YTH protein. According to the analysis of the up-stream cis-regulatory elements of these YTH genes, these genes could be closely related to stress, hormones, and development. The following stress response experiments further verified that their expression levels indeed changed under both PEG and NaCl treatments. These findings not only provide a foundation for future functional analysis of CcYTHs in C. camphora, but also provide insights into the functions of epigenetic mark m6A in forest trees. Full article
(This article belongs to the Special Issue Latest Epigenetic Research in Plants)
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