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      Genetic and epigenetic control of plant heat responses

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          Abstract

          Plants have evolved sophisticated genetic and epigenetic regulatory systems to respond quickly to unfavorable environmental conditions such as heat, cold, drought, and pathogen infections. In particular, heat greatly affects plant growth and development, immunity and circadian rhythm, and poses a serious threat to the global food supply. According to temperatures exposing, heat can be usually classified as warm ambient temperature (about 22–27°C), high temperature (27–30°C) and extremely high temperature (37–42°C, also known as heat stress) for the model plant Arabidopsis thaliana. The genetic mechanisms of plant responses to heat have been well studied, mainly focusing on elevated ambient temperature-mediated morphological acclimation and acceleration of flowering, modulation of circadian clock and plant immunity by high temperatures, and thermotolerance to heat stress. Recently, great progress has been achieved on epigenetic regulation of heat responses, including DNA methylation, histone modifications, histone variants, ATP-dependent chromatin remodeling, histone chaperones, small RNAs, long non-coding RNAs and other undefined epigenetic mechanisms. These epigenetic modifications regulate the expression of heat-responsive genes and function to prevent heat-related damages. This review focuses on recent progresses regarding the genetic and epigenetic control of heat responses in plants, and pays more attention to the role of the major epigenetic mechanisms in plant heat responses. Further research perspectives are also discussed.

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          Most cited references116

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          Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

          Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences. Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels. However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.
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            Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response.

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              Small silencing RNAs: an expanding universe.

              Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. There is a growing realization that, despite their differences, these distinct small RNA pathways are interconnected, and that small RNA pathways compete and collaborate as they regulate genes and protect the genome from external and internal threats.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                24 April 2015
                2015
                : 6
                : 267
                Affiliations
                [1] 1National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences – Chinese Academy of Sciences Shanghai, China
                [2] 2School of Life Science and Technology, ShanghaiTech University Shanghai, China
                [3] 3Plant Signaling Laboratory, The Plant Stress Biology Center, Shanghai Institutes for Biological Sciences – Chinese Academy of Sciences Shanghai, China
                Author notes

                Edited by: Mahmoud W. Yaish, Sultan Qaboos University, Oman

                Reviewed by: Hongchang Cui,Florida State University, USA; Clelia De-la-Peña, Centro de Investigación Científica de Yucatán, Mexico

                *Correspondence: Zuhua He, National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences – Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China zhhe@ 123456sibs.ac.cn ; Jianming Li, Plant Signaling Laboratory, The Plant Stress Biology Center, Shanghai Institutes for Biological Sciences – Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang District, Shanghai 201602, China jmli@ 123456sibs.ac.cn

                This article was submitted to Plant Physiology, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2015.00267
                4408840
                25964789
                7f451774-2f3d-4072-a2fd-b1ca1719d286
                Copyright © 2015 Liu, Feng, Li and He.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 07 January 2015
                : 03 April 2015
                Page count
                Figures: 1, Tables: 2, Equations: 0, References: 147, Pages: 21, Words: 0
                Categories
                Plant Science
                Review

                Plant science & Botany
                heat,genetic mechanism,epigenetic regulation,small rnas,transgenerational memory

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