文章一(植物表观遗传学特刊)

Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants

H3K36甲基化对温度调节RNA拼接的影响以及对植物开花的作用

A. Pajoro, E.Severing, G. C. Angenent and R. G. H. Immink

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1235-x

【导读】随着6月的开始，大家将看到更多植物表观遗传特刊的发表工作。前几周我们已经介绍了表观遗传调控接收到环境信号后对植物的发育起着非常重要的作用。植物，作为一个不间断发育的物种群体，它们的开花可想而知也会受到表观遗传调控，同时这种调控也是对环境作出的反应。在特朗普美国退出巴黎协定的当下，我们来看看全球变暖是如何通过植物的组蛋白修饰影响到RNA的拼接，然后进一步调控植物开花时间的。

Abstract

Background: Global warming severely affects flowering time and reproductive success of plants.Alternative splicing of pre-messenger RNA (mRNA) is an important mechanism underlying ambient temperature-controlled responses in plants, yet its regulation is poorly understood. An increase in temperature promotes changes inplant morphology as well as the transition from the vegetative to the reproductive phase in Arabidopsis thaliana via changes in splicing of key regulatory genes. Here we investigate whether a particular histone modification affects ambient temperature-induced alternative splicing and flowering time.

Results: We use a genome-wide approach and perform RNA-sequencing (RNA-seq) analyses and histone H3 lysine 36 tri-methylation (H3K36me3) chromatin immunoprecipitation sequencing (ChIP-seq) in plants exposed to different ambient temperatures.Analysis and comparison of these datasets reveal that temperature-induced differentially spliced genes are enriched in H3K36me3. Moreover, we find thatreduction of H3K36me3 deposition causes alteration in temperature-induced alternative splicing. We also show that plants with mutations in H3K36me3 writers, eraser,or readers have altered high ambient temperature-induced flowering.

Conclusions:Our results show a key role for the histone mark H3K36me3 in splicing regulation and plant plasticity to fluctuating ambient temperature. Our findings open new perspectives for the breeding of crops that can better cope with environmental changes due to climate change.

 

文章二 (植物表观遗传学特刊)

Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons

表观遗传与多倍体棉花的进化与驯化

Qingxin Song,Tianzhen Zhang, David M. Stelly and Z. Jeffrey Chen

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1229-8

【导读】棉花是非常重要的经济作物，它的驯化以及进化中性状的改变对纺织、材料等产业有很大的影响。6月3日BioMed Central开放获取出版官方微信的头条，我们邀请这一工作的第一作者宋庆鑫博士为我们深度解读，希望能为棉花生产大国的中国广大研究者提供帮助。

 

Abstract

Background: Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can producemeiotically stable epialleles, which are transmissible through selection and breeding. However, the relationship between DNA methylation and polyploid plant domestication remains elusive.

Results: We report comprehensive epigenomic and functional analyses,including ~12 million differentially methylated cytosines in domesticated allotetraploid cottons and their tetraploid and diploid relatives. Methylated genes evolve faster than unmethylated genes; DNA methylation changes between homoeologous loci are associated with homoeolog-expression bias in the allotetraploids. Significantly, methylation changes induced in the interspecific hybrids are largely maintained in the allotetraploids. Among 519 differentially methylated genes identified between wild and cultivated cottons,some contribute to domestication traits, including flowering time and seed dormancy. CONSTANS (CO) and CO-LIKE (COL)genes regulate photo periodicity in Arabidopsis. COL2 is anepiallele in allotetraploid cottons. COL2A is hypermethylated and silenced, while COL2D is repressed in wild cottons buthighly expressed due to methylation loss in all domesticated cottons tested.Inhibiting DNA methylation activates COL2 expression, and repressing COL2 in cultivated cotton delays flowering.

Conclusions: We uncover epigenomic signatures of domestication traits during cotton evolution. Demethylation of COL2 increases its expression, inducing photoperiodic flowering, which could have contributed to the suitability of cotton for cultivation worldwide. These resources should facilitate epigenetic engineering, breeding, and improvement of polyploidcrops.

  

文章三(植物表观遗传学特刊)

The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

染色质重塑因子PKL在RNA介导的DNA甲基化中的功能

Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, DaisukeMiki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu,Xin-Jian He and Heng Zhang

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1226-y

【导读】 RNA介导的DNA甲基化机制研究是近期的一个热点问题，是一种重要的建立全新DNA甲基化式样和沉默基因转录的一个机制。在6月1日BioMed Central开放获取出版的官方微信上，我们邀请了本文的作者为我们解读了这个工作，详细解释PKL如何通过重塑核小体改变染色质环境，从而影响非编码RNA的产生和转录沉默，希望大家觉得有所帮助。

Abstract

Background:The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in Arabidopsis thaliana.

Results:Through forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter.Mutation of PKL results in DNA methylation changes at morethan half of the loci that are targeted by RNA-directed DNA methylation (RdDM).A small number of transposable elements and genes had reduced DNA methylation correlated with derepression in the pkl mutant, though for the majority, decreases in DNA methylation are not sufficient to cause release of silencing. The changes in DNA methylation in the pkl mutantare positively correlated with changes in 24-nt siRNA levels. Inaddition, PKL is required for the accumulation of PolV-dependent transcripts and for the positioning of Pol V-stabilized nucleosomesat several tested loci, indicating that RNA polymerase V-related functions are impaired in the pkl mutant.

Conclusions:PKL is required for transcriptional silencing and has significant effects on RdDM in plants. The changes in DNA methylation in the pkl mutant are correlated with changes in the non-coding RNAs produced by Pol IV and Pol V. We propose that at RdDM target regions, PKL may be required to create achromatin environment that influences non-coding RNA production, DNAmethylation, and transcriptional silencing.

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