文章一

Strong epistatic and additive effects of linked candidate SNPs for Drosophila pigmentation have implications for analysis of genome-wideassociation studies results

从果蝇色素沉着研究中得到的GWAS启示

Jean-MichelGibert, Jorge Blanco, Marlies Dolezal, Viola Nolte, Frédérique Peronnet andChristian Schlötterer

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1262-7

【导读】全基因组相关性研究常被用于分析人群中基因型与某种表型的关系，可以是疾病、肿瘤也可能是某一种外型特质。但是在进化历史上产生的重组以及重组产生的效果往往归因于区块性的单体型，而无法归因于单碱基的变化。果蝇的腹部色素沉着是一个非常便捷的遗传研究工具，通过对三个已知紧密链接并影响色素沉着的果蝇单碱基突变的研究，作者们发现三个碱基变异型皆通过对t-MSE增强子活性起作用，并呈叠加作用模式。这与全基因组相关性的结论有不一致的地方，因为其中一个变异型常常通过连锁不平衡与集中功能性碱基变异连锁。这一别出心裁的设计让我们看到了全基因组相关性研究中的结论不仅受到基因与表型调控的作用，还受到基因组结构性的调控，故而更凸显了功能性验证实验的重要性。

Abstract

Background:The mapping resolution ofgenome-wide association studies (GWAS) is limited by historic recombinationevents and effects are often assigned to haplotype blocks rather thanindividual SNPs. It is not clear how many of the SNPs in the block, and whichones, are causative. Drosophila pigmentation is a powerfulmodel to dissect the genetic basis of intra-specific and inter-specificphenotypic variation. Three tightly linked SNPs in the t-MSE enhancer have beenidentified in three D. melanogaster populations as majorcontributors to female abdominal pigmentation. This enhancer controls theexpression of the pigmentation gene tan (t) in the abdominalepidermis. Two of the three SNPs were confirmed in an independent study usingthe D. melanogaster Genetic Reference Panel established from aNorth American population.

Results:We determined the functional impactof SNP1, SNP2, and SNP3 using transgenic lines to test all possible haplotypesin vivo. We show that all three candidate SNPs contribute to female Drosophila abdominalpigmentation. Interestingly, only two SNPs agree with the effect predicted byGWAS; the third one goes in the opposite direction because of linkagedisequilibrium between multiple functional SNPs. Our experimental designuncovered strong additive effects for the three SNPs, but we also foundsignificant epistatic effects explaining up to 11% of the total variation.

Conclusions:Our results suggest that linkedcausal variants are important for the interpretation of GWAS and functionalvalidation is needed to understand the genetic architecture of traits.

 

文章二 (植物表观遗传学特刊)

MAPK-triggered chromatin reprogramming by histonedeacetylase in plant innate immunity

由MAPK激活的染色质重组在植物先天免疫中的作用

David Latrasse,Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras,Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, JuanSebastian Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, BaptisteGenot, Ton Bisseling, Moussa Benhamed and Heribert Hirt

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1261-8

【导读】有丝分裂原活化蛋白激酶(MAPK)是我们非常熟悉的级联反应的重要分子。在植物中（在本期的这一工作是在拟南芥上完成的）微生物特异性分子能触发有丝分裂原活化蛋白激酶，进而使宿主特异性组蛋白脱乙酰酶HD2B磷酸化，并调控其功能。这个信号传导过程是拟南芥先天免疫的一个重要组成部分，通过病原体响应蛋白激酶信号，传导至染色质，从而产生表观遗传基因组变化，将微生物信号传导与染色质响应建立起联系。

Abstract

Background:Microbial-associated molecular patterns activate severalMAP kinases, which are major regulators of the innate immune response in Arabidopsisthaliana that induce large-scale changes in gene expression. Here, wedetermine whether microbial-associated molecular pattern-triggered geneexpression involves modifications at the chromatin level.

Results:Histone acetylation and deacetylation are major regulatorsof microbial-associated molecular pattern-triggered gene expression andimplicate the histone deacetylase HD2B in the reprogramming of defence geneexpression and innate immunity. The MAP kinase MPK3 directly interacts with andphosphorylates HD2B, thereby regulating the intra-nuclear compartmentalizationand function of the histone deacetylase.

Conclusions:By studying a number of gene loci that undergomicrobial-associated molecular pattern-dependent activation or repression, ourdata reveal a mechanistic model for how protein kinase signaling directlyimpacts chromatin reprogramming in plant defense.

 

文章三

Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding

RNAPol II 抑制对植物转座子的影响

Michael Thieme,Sophie Lanciano, Sandrine Balzergue, Nicolas Daccord, Marie Mirouze and EtienneBucher

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1265-4

【导读】基因组中的重复序列常常被大量甲基化修饰沉默，这种沉默对于转座子来说起到抑制它们在基因组跳跃复制。本周这一植物表观遗传研究，在拟南芥和水稻两种模式生物上显示Pol II的缺失会增加染色质外的转座元件DNA，这与热反应密切相关，并能在传代中对子代热反应能力增加异质性。利用Pol II的功能抑制，产生的结果是转座元件活化，最终导致的现象是加速植物进化的步伐，提示这种方法可能成为一种育种选种的备选方法。

Abstract

Background: Retrotransposonsplay a central role in plant evolution and could be a powerful endogenoussource of genetic and epigenetic variability for crop breeding. To ensuregenome integrity several silencing mechanisms have evolved to repressretrotransposon mobility. Even though retrotransposons fully depend ontranscriptional activity of the host RNA polymerase II (Pol II) for theirmobility, it was so far unclear whether Pol II is directly involved inrepressing their activity.

Results: Here weshow that plants defective in Pol II activity lose DNA methylation at repeatsequences and produce more extrachromosomal retrotransposon DNA upon stressin Arabidopsis and rice. We demonstrate that combinedinhibition of both DNA methylation and Pol II activity leads to a strongstress-dependent mobilization of the heat responsive ONSEN retrotransposonin Arabidopsis seedlings. The progenies of these treatedplants contain up to 75 new ONSEN insertions in their genomewhich are stably inherited over three generations of selfing. Repeatedapplication of heat stress in progeny plants containing increased numbers ofONSEN copiesdoes not result in increased activation of this transposon compared to controllines. Progenies with additional ONSEN copies show a broadpanel of environment-dependent phenotypic diversity.

Conclusions: Wedemonstrate that Pol II acts at the root of transposon silencing. This isimportant because it suggests that Pol II can regulate the speed of plantevolution by fine-tuning the amplitude of transposon mobility. Our findingsshow that it is now possible to study induced transposon bursts in plants andunlock their use to induce epigenetic and genetic diversity for crop breeding.

 

文章四 (植物表观遗传学社论)

Plant epigenomics—deciphering the mechanisms of epigenetic inheritance and plasticity in plants

植物表观遗传学——解码植物表观遗传与可塑性机制

Claudia Köhlerand Nathan Springer

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1260-9

【导读】我们2017上半年的植物表观遗传学特刊内容终于在七月上旬画上句号。特刊的两位特邀编辑通过这篇社论为我们总结了本期特刊的精彩内容。在今日BioMedCentral开放获取出版的公众微信号上，我们给大家带来这篇社论的全中文翻译，希望大家喜欢。

Abstract

It is an excitingtime to study plant epigenetics. Technological advances are providingunprecedented opportunities to monitor chromatin modifications, geneexpression, and genome structure. Many classical epigenetic phenomena(transposable element inactivation, imprinting, paramutation, transgenesilencing, and co-suppression) were first documented in plants. Combined withclassical genetic studies, newly available sequencing technologies are facilitatingthe study of these and other epigenetic phenomena at a level of detail that wasunthinkable only a few years ago. Studies of epigenetics in plants are of greatimportance. Plants are heavily dependent upon changes in gene expression inorder to respond to environmental stimuli, and chromatin-based regulation ofgene expression is likely crucial for these responses. Furthermore, the levelof chromatin ‘resetting’ during sexual reproduction appears to be lower inplants in comparison with animal species, potentially allowing inheritance ofepimutations acquired during plant life. In addition, many plant species canpropagate asexually and produce vegetative clones, providing opportunities formitotic inheritance of epigenetic states leading to important traits. Thisissue of Genome Biology highlights exciting progress in manyareas of plant epigenetics and epigenomics..

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