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      Epigenetics Regulates Reproductive Development in Plants

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          Abstract

          Seed, resulting from reproductive development, is the main nutrient source for human beings, and reproduction has been intensively studied through genetic, molecular, and epigenetic approaches. However, how different epigenetic pathways crosstalk and integrate to regulate seed development remains unknown. Here, we review the recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction. In gametogenesis of flowering plants, epigenetics is dynamic between the companion cell and gametes. Cytosine DNA methylation occurs in CG, CHG, CHH contexts (H = A, C, or T) of genes and transposable elements, and undergoes dynamic changes during reproduction. Cytosine methylation in the CHH context increases significantly during embryogenesis, reaches the highest levels in mature embryos, and decreases as the seed germinates. Polycomb group proteins are important transcriptional regulators during seed development. Histone modifications and small RNA pathways add another layer of complexity in regulating seed development. In summary, multiple epigenetic pathways are pivotal in regulating seed development. It remains to be elucidated how these epigenetic pathways interplay to affect dynamic chromatin structure and control reproduction.

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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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            A gene complex controlling segmentation in Drosophila.

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            The bithorax gene complex in Drosophila contains a minimum of eight genes that seem to code for substances controlling levels of thoracic and abdominal development. The state of repression of at least four of these genes is controlled by cis-regulatory elements and a separate locus (Polycomb) seems to code for a repressor of the complex. The wild-type and mutant segmentation patterns are consistent with an antero-posterior gradient in repressor concentration along the embryo and a proximo-distal gradient along the chromosome in the affinities for repressor of each gene's cis-regulatory element.
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              Targeted mutation of the DNA methyltransferase gene results in embryonic lethality

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                Author and article information

                Journal
                Plants (Basel)
                Plants (Basel)
                plants
                Plants
                MDPI
                2223-7747
                02 December 2019
                December 2019
                : 8
                : 12
                : 564
                Affiliations
                [1 ]Department of Biology, Saint Louis University, St. Louis, MO 63103, USA arthur.bartels@ 123456slu.edu (A.B.); xi.cheng@ 123456slu.edu (X.C.);
                [2 ]Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
                [3 ]US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, MO 63132, USA; yong-qiang.an@ 123456ars.usda.gov
                [4 ]Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA; thsieh3@ 123456ncsu.edu
                [5 ]Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081, USA
                Author notes
                [* ]Correspondence: wenyan.xiao@ 123456slu.edu ; Tel.: +1-314-977-2547
                [†]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-6686-9863
                https://orcid.org/0000-0001-7584-3721
                Article
                plants-08-00564
                10.3390/plants8120564
                6963493
                31810261
                870ca154-6790-48ca-a244-40702ec3933b
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 26 October 2019
                : 27 November 2019
                Categories
                Review

                dna methylation,dynamics,polycomb group proteins,histone modifications,epigenetics,chromatin,sirna,rddm,gametogenesis,seed development

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