Submit to Plants Review for Plants Propose a Special Issue

Journal Browser

► Journal Browser

Chromatin Dynamics for Developmental Transitions in Plants

Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of Plants (ISSN 2223-7747).

Deadline for manuscript submissions: closed (30 September 2020) | Viewed by 16613

Share This Special Issue

Special Issue Editors

Dr. Christel Carles

E-Mail Website
Guest Editor

University Grenoble Alpes, Plant and Cell Physiology Lab (LPCV), IRIG, CEA, 17 rue des Martyrs, bât. C2 - Bureau 433, 38054 GRENOBLE Cedex 9 - FRANCE
Interests: chromatin dynamics; plant development and stem cell fate

Dr. Alexandre Berr

E-Mail Website
Guest Editor

Institut de Biologie Moléculaire des Plantes (IBMP), 12, rue du General Zimmer, CEDEX 02, 67084 Strasbourg, France
Interests: chromatin organisation and regulation

Dr. Leor Eshed Williams

E-Mail Website
Guest Editor

The Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.Box 12, Rehovot 76100, Israel
Interests: chromatin dynamics during plant regeneration; meristem development

Special Issue Information

Dear Colleagues,

How do higher plants transform their chromatin landscape to deploy flexible and adjustable developmental programs?

We invite submission of works dedicated to tackle this question, on developmental programs that are core to plant morphogenesis or induced by changes in growth conditions.

Plasticity is central to the continuous postembryonic morphogenesis of plants and to their sessile lifestyle. It provides them with the ability to go through developmental transitions and to cope with varied and variable environments. Chromatin regulatory mechanisms, by allowing differential usage of the genome for modulation of gene expression, are highly instrumental in developmental plasticity. While numerous maintainers of chromatin states have been characterized, emphasis should now be put on the precise sequences of events enabling chromatin state switches from transcriptionally repressive to permissive and vice versa. Among the chromatin mechanisms responsible for these changes, it is essential to elucidate those influencing the three-dimensional organization of the nucleus, nucleosome positioning and occupancy, post-translational modifications of histone, loading of histone variants, and incorporation of linker histones or non-histone chromatin-associated proteins.

The Special Issue “Chromatin Dynamics for Developmental Transitions in Plants” will focus on functions operating at the transcriptional, chromatin, and nuclear organization levels, which induce cellular reprograming events involved in developmental transitions. The transitions of interest, characterized by massive and/or fine-tuned gene expression changes, shall be part of intrinsic developmental programs, promoted during tissue regeneration, or initiated in response to altered environmental conditions.

We encourage the submission of integrative and multidisciplinary studies connecting developmental genetics, transcriptomics, epigenomics, biochemistry, and structural biology, as well as review/opinion articles and method papers covering the latest advances in the field.

Dr. Christel Carles
Dr. Alexandre Berr
Dr. Leor Eshed Williams
Guest Editors

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

nuclear structure
chromatin domains
histone variants
histone marks
chromatin readers
chromatin remodelers
gene accessibility
gene expression
transcription
cell fate
differentiation
regeneration
developmental switch
environmental responses.

Published Papers (4 papers)

Download All Papers

Research

Jump to: Review

16 pages, 1285 KiB

Open AccessArticle

A Systems Biology Approach to Identify Essential Epigenetic Regulators for Specific Biological Processes in Plants

by Rachel M. McCoy, Russell Julian, Shoban R. V. Kumar, Rajeev Ranjan, Kranthi Varala and Ying Li

Plants 2021, 10(2), 364; https://doi.org/10.3390/plants10020364 - 13 Feb 2021

Cited by 5 | Viewed by 3812

Abstract

Upon sensing developmental or environmental cues, epigenetic regulators transform the chromatin landscape of a network of genes to modulate their expression and dictate adequate cellular and organismal responses. Knowledge of the specific biological processes and genomic loci controlled by each epigenetic regulator will greatly advance our understanding of epigenetic regulation in plants. To facilitate hypothesis generation and testing in this domain, we present EpiNet, an extensive gene regulatory network (GRN) featuring epigenetic regulators. EpiNet was enabled by (i) curated knowledge of epigenetic regulators involved in DNA methylation, histone modification, chromatin remodeling, and siRNA pathways; and (ii) a machine-learning network inference approach powered by a wealth of public transcriptome datasets. We applied GENIE3, a machine-learning network inference approach, to mine public Arabidopsis transcriptomes and construct tissue-specific GRNs with both epigenetic regulators and transcription factors as predictors. The resultant GRNs, named EpiNet, can now be intersected with individual transcriptomic studies on biological processes of interest to identify the most influential epigenetic regulators, as well as predicted gene targets of the epigenetic regulators. We demonstrate the validity of this approach using case studies of shoot and root apical meristem development. Full article

(This article belongs to the Special Issue Chromatin Dynamics for Developmental Transitions in Plants)

► Show Figures

Figure 1

15 pages, 2311 KiB

Open AccessArticle

Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes

by Ezgi Süheyla Karaaslan, Natalie Faiß, Chang Liu and Kenneth Wayne Berendzen

Plants 2020, 9(11), 1478; https://doi.org/10.3390/plants9111478 - 3 Nov 2020

Cited by 4 | Viewed by 2663

Abstract

The capacity for achieving immense specificity and resolution in science increases day to day. Fluorescence-activated nuclear sorting (FANS) offers this great precision, enabling one to count and separate distinct types of nuclei from specific cells of heterogeneous mixtures. We developed a workflow to collect nuclei from Arabidopsis thaliana by FANS according to cell lineage and endopolyploidy level with high efficiency. We sorted GFP-labeled nuclei with different ploidy levels from the epidermal tissue layer of three-day, dark-grown hypocotyls followed by a shift to light for one day and compared them to plants left in the dark. We then accessed early chromatin accessibility patterns associated with skotomorphogenesis and photomorphogenesis by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) within primarily stomatal 2C and fully endoreduplicated 16C nuclei. Our quantitative analysis shows that dark- and light-treated samples in 2C nuclei do not exhibit any different chromatin accessibility landscapes, whereas changes in 16C can be linked to transcriptional changes involved in light response. Full article

(This article belongs to the Special Issue Chromatin Dynamics for Developmental Transitions in Plants)

► Show Figures

Graphical abstract

Review

Jump to: Research

19 pages, 1724 KiB

Open AccessReview

Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination

by Eduardo Luján-Soto and Tzvetanka D. Dinkova

Plants 2021, 10(2), 236; https://doi.org/10.3390/plants10020236 - 26 Jan 2021

Cited by 16 | Viewed by 4577

Abstract

Plants make decisions throughout their lifetime based on complex networks. Phase transitions during seed growth are not an exception. From embryo development through seedling growth, several molecular pathways control genome stability, environmental signal transduction and the transcriptional landscape. Particularly, epigenetic modifications and small non-coding RNAs (sRNAs) have been extensively studied as significant handlers of these processes in plants. Here, we review key epigenetic (histone modifications and methylation patterns) and sRNA-mediated regulatory networks involved in the progression from seed maturation to germination, their relationship with seed traits and crosstalk with environmental inputs. Full article

(This article belongs to the Special Issue Chromatin Dynamics for Developmental Transitions in Plants)

► Show Figures

Figure 1

14 pages, 1474 KiB

Open AccessReview

Plant Histone HTB (H2B) Variants in Regulating Chromatin Structure and Function

by Janardan Khadka, Anat Pesok and Gideon Grafi

Plants 2020, 9(11), 1435; https://doi.org/10.3390/plants9111435 - 25 Oct 2020

Cited by 13 | Viewed by 4650

Abstract

Besides chemical modification of histone proteins, chromatin dynamics can be modulated by histone variants. Most organisms possess multiple genes encoding for core histone proteins, which are highly similar in amino acid sequence. The Arabidopsis thaliana genome contains 11 genes encoding for histone H2B (HTBs), 13 for H2A (HTAs), 15 for H3 (HTRs), and 8 genes encoding for histone H4 (HFOs). The finding that histone variants may be expressed in specific tissues and/or during specific developmental stages, often displaying specific nuclear localization and involvement in specific nuclear processes suggests that histone variants have evolved to carry out specific functions in regulating chromatin structure and function and might be important for better understanding of growth and development and particularly the response to stress. In this review, we will elaborate on a group of core histone proteins in Arabidopsis, namely histone H2B, summarize existing data, and illuminate the potential function of H2B variants in regulating chromatin structure and function in Arabidopsis thaliana. Full article

(This article belongs to the Special Issue Chromatin Dynamics for Developmental Transitions in Plants)

► Show Figures