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Plants
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Epigenetic Control Mechanisms and Transcriptional Reprogramming in Plants
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Epigenetic Control Mechanisms and Transcriptional Reprogramming in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 8885

Special Issue Editor

Prof. Dr. Klaus Humbeck

E-Mail Website
Guest Editor
Director of the Institute of Biology/Plant Physiology, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany
Interests: Plant physiology; plant epigenetics; leaf senescence; plant responses to abiotic stresses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Reprogramming gene expression enables plants to undertake major developmental steps and to respond to environmental threats. The central motor of this process is a coordinated, fine-tuned reorientation of expression of genes, preparing the cells for new tasks. We know that the network-like structured action of transcription factors downstream of different signal pathways plays a central role in this process. Rather recently, it became obvious that upstream of transcription factors there is an epigenetic control level, regulating reprogramming of gene expression via histone modifications and DNA methylation.

This Special Issue of Plants will bring together work on epigenetic mechanisms, controlling major developmental steps or stress responses in plants, with interconnected regulatory levels of gene expression via trans-acting factors.

Prof. Dr. Klaus Humbeck
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Epigenetic control
  • plant development
  • stress responses
  • histone modifications
  • DNA methylation
  • transcription factors

Published Papers (3 papers)

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Research

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16 pages, 2691 KiB  
Article
Heterosis and Differential DNA Methylation in Soybean Hybrids and Their Parental Lines
by Liangyu Chen, Yanyu Zhu, Xiaobo Ren, Dan Yao, Yang Song, Sujie Fan, Xueying Li, Zhuo Zhang, Songnan Yang, Jian Zhang and Jun Zhang
Plants 2022, 11(9), 1136; https://doi.org/10.3390/plants11091136 - 22 Apr 2022
Cited by 6 | Viewed by 1913
Abstract
Heterosis is an important biological phenomenon and is widely applied to increase agricultural productivity. However, the underlying molecular mechanisms of heterosis are still unclear. Here we constructed three combinations of reciprocal hybrids of soybean, and subsequently used MethylRAD-seq to detect CCGG and CCWGG [...] Read more.
Heterosis is an important biological phenomenon and is widely applied to increase agricultural productivity. However, the underlying molecular mechanisms of heterosis are still unclear. Here we constructed three combinations of reciprocal hybrids of soybean, and subsequently used MethylRAD-seq to detect CCGG and CCWGG (W = A or T) methylation in the whole genome of these hybrids and their parents at the middle development period of contemporary seed. We were able to prove that changes in DNA methylation patterns occurred in immature hybrid seeds and the parental variation was to some degree responsible for differential expression between the reciprocal hybrids. Non-additive differential methylation sites (DMSs) were also identified in large numbers in hybrids. Interestingly, most of these DMSs were hyper-methylated and were more concentrated in gene regions than the natural distribution of the methylated sites. Further analysis of the non-additive DMSs located in gene regions exhibited their participation in various biological processes, especially those related to transcriptional regulation and hormonal function. These results revealed DNA methylation reprogramming pattern in the hybrid soybean, which is associated with phenotypic variation and heterosis initiation. Full article
(This article belongs to the Special Issue Epigenetic Control Mechanisms and Transcriptional Reprogramming in Plants)
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Review

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25 pages, 3063 KiB  
Review
Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation
by Mateusz Bajczyk, Artur Jarmolowski, Monika Jozwiak, Andrzej Pacak, Halina Pietrykowska, Izabela Sierocka, Aleksandra Swida-Barteczka, Lukasz Szewc and Zofia Szweykowska-Kulinska
Plants 2023, 12(2), 342; https://doi.org/10.3390/plants12020342 - 11 Jan 2023
Cited by 15 | Viewed by 3758
Abstract
MicroRNAs are small RNAs, 20–22 nt long, the main role of which is to downregulate gene expression at the level of mRNAs. MiRNAs are fundamental regulators of plant growth and development in response to internal signals as well as in response to abiotic [...] Read more.
MicroRNAs are small RNAs, 20–22 nt long, the main role of which is to downregulate gene expression at the level of mRNAs. MiRNAs are fundamental regulators of plant growth and development in response to internal signals as well as in response to abiotic and biotic factors. Therefore, the deficiency or excess of individual miRNAs is detrimental to particular aspects of a plant’s life. In consequence, the miRNA levels must be appropriately adjusted. To obtain proper expression of each miRNA, their biogenesis is controlled at multiple regulatory layers. Here, we addressed processes discovered to influence miRNA steady-state levels, such as MIR transcription, co-transcriptional pri-miRNA processing (including splicing, polyadenylation, microprocessor assembly and activity) and miRNA-encoded peptides synthesis. MiRNA stability, RISC formation and miRNA export out of the nucleus and out of the plant cell also define the levels of miRNAs in various plant tissues. Moreover, we show the evolutionary conservation of miRNA biogenesis core proteins across the plant kingdom. Full article
(This article belongs to the Special Issue Epigenetic Control Mechanisms and Transcriptional Reprogramming in Plants)
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13 pages, 2000 KiB  
Review
Concerto on Chromatin: Interplays of Different Epigenetic Mechanisms in Plant Development and Environmental Adaptation
by Jiao Liu and Cheng Chang
Plants 2021, 10(12), 2766; https://doi.org/10.3390/plants10122766 - 14 Dec 2021
Cited by 6 | Viewed by 2569
Abstract
Epigenetic mechanisms such as DNA methylation, histone post-translational modifications, chromatin remodeling, and noncoding RNAs, play important roles in regulating plant gene expression, which is involved in various biological processes including plant development and stress responses. Increasing evidence reveals that these different epigenetic mechanisms [...] Read more.
Epigenetic mechanisms such as DNA methylation, histone post-translational modifications, chromatin remodeling, and noncoding RNAs, play important roles in regulating plant gene expression, which is involved in various biological processes including plant development and stress responses. Increasing evidence reveals that these different epigenetic mechanisms are highly interconnected, thereby contributing to the complexity of transcriptional reprogramming in plant development processes and responses to environmental stresses. Here, we provide an overview of recent advances in understanding the epigenetic regulation of plant gene expression and highlight the crosstalk among different epigenetic mechanisms in making plant developmental and stress-responsive decisions. Structural, physical, transcriptional and metabolic bases for these epigenetic interplays are discussed. Full article
(This article belongs to the Special Issue Epigenetic Control Mechanisms and Transcriptional Reprogramming in Plants)
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