植物学人|20171018-技术上的变革，清华北大联合中心孙前文开发检测R-Loop新方法（推荐）

致谢：感谢中科院上海生科院的马同学提供了信息。

iNature：在植物学主流专刊中，主要有Plant Cell，Molecular Plant，Plant Journal，PLANT PHYSIOLOGY，NEW PHYTOLOGIST，Plant Biotech J，Plant Cell &Environ，Nature Plants等8种期刊。现在经过前期的测试，iNature决定每天遴选8大植物学主刊各1篇（福利版），共8篇文章，推送给大家，使大家能及时的了解植物学领域的动态：

Plant Cell:中科院遗传所程祝宽等人确定了水稻新型F盒蛋白ZYGO1，并证实其在早期减数分裂期间花束形成中的重要作用；

Nature Plants:清华北大联合中心孙前文等人发现R环是拟南芥基因组中的常见特征，及其在基因组组织和基因调控中的作用；

Molecular Plant: 福建农林科技大学秦源等发现H2A.Z通过调节启动子核小体结构和增强子组蛋白来抑制基因的表达；

Plant Journal:中科院遗传所黄海等建立叶片近轴- 背面极性模式下生长素极性运输模型；

PLANT PHYSIOLOGY:武汉大学Lijia Li等揭示植物激素赤霉酸引发谷物糊粉末细胞的程序性死亡；

NEW PHYTOLOGIST:西澳大利亚大学Edwards等人发表在植物中的CRISPR应用综述；

Plant Biotech J:中国农业大学Shaojiang Chen等综述双倍体系发展的新技术；

Plant Cell &Environ:植生所朱新广等分析了叶肉抗性成分及其环境互作的理论模型。

1Plant Cell：中科院遗传所程祝宽等人确定了水稻新型F盒蛋白ZYGO1，并证实其在早期减数分裂期间花束形成中的重要作用

Abstract

Telomere bouquet formation, a highlyconserved meiotic event, plays an important role in homologous pairing andtherefore progression of meiosis; however, the underlying molecular mechanismremains largely unknown. Here, we identified ZYGOTENE 1 (ZYGO1), a novel F-boxprotein in rice (Oryza sativa), and verified its essential role in bouquetformation during early meiosis. In zygo1 mutants, zygotene chromosomeaggregation and telomere clustering failed to occur. The suppressed telomere clusteringin homologous pairing aberration in rice meiosis 1 (pair1) zygo1 and ricecompletion of meiotic recombination(Oscom1) zygo1 double mutants, together withthe altered localization of OsSAD1 (a SUN protein associated with the nuclearenvelope) in zygo1 showed that ZYGO1 has a significant function in bouquet formation. Inaddition, the interaction between ZYGO1 and rice SKP1-like protein 1 (OSK1)suggested that ZYGO1 might modulate bouquet formation as a component of theSKP1-Cullin1-F-box (SCF) complex. Although double-strand break formation andearly recombination element installation occurred normally, zygo1 mutants showeddefects in full-length pairing and synaptonemal complex assembly. Furthermore, crossover(CO) formation was disturbed, and foci of Human enhancer of invasion 10 (HEI10)were restricted to the partially-synapsed chromosome regions, indicating thatCO reduction might be caused by the failure of full-length chromosome alignmentin zygo1. Therefore, we propose that ZYGO1 mediates bouquet formation to efficientlypromote homolog pairing, synapsis, and CO formation in rice meiosis.

原文链接：

http://www.plantcell.org/content/early/2017/09/21/tpc.17.00287

2Nature Plants：清华北大联合中心孙前文等人发现R环是拟南芥基因组中的常见特征，及其在基因组组织和基因调控中的作用

Abstract

R-loops are functional structures inchromatin comprising one single-stranded DNA and a DNA: RNA hybrid. Here, wereport ssDRIP-seq, a single-strand DNA ligation-based library preparationtechnique for genome-wide identification of R-loops. When applied inArabidopsis, ssDRIP-seq exhibits high efficiency, low bias and strandspecificity. We found that Arabidopsis R-loops are enriched by both AT and GCskews, and are formed in the sense and antisense orientations. R-loops arestrongly enriched in gene promoters and gene bodies, and are highly associatedwith noncoding RNA and repetitive genomic regions. Furthermore, R-loops arenegatively correlated with CG DNA hypermethylation, and are prevalent inregions with multiple chromatin modifications, showing strong correlations withthe activated and repressed gene loci. Our analyses indicate that R-loops arecommon features in the Arabidopsis genome and suggest that the R-loops playdiverse roles in genome organization and gene regulation, thereby providinginsights into plant nuclear genome formation and function.

原文链接：

https://www.nature.com/articles/s41477-017-0004-x

3Molecular Plant：福建农林科技大学秦源等发现H2A.Z通过调节启动子核小体结构和增强子组蛋白来抑制基因的表达

Abstract

Deposition of the histone variant H2A.Z atgene bodies regulates transcription by modifying chromatin accessibility in plants.However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear,and how H2A.Z interacts with other mechanisms of chromatin modification toregulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z,H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsisinflorescence. We showed that H2A.Z preferentially associated with H3K4me3 atpromoters, while it was found with H3K27me3 at enhancers, and that H2A.Z depositionnegatively correlated with gene expression. In addition, we demonstrated thatH2A.Z represses gene expression by establishing low gene accessibility at +1nucleosome and maintaining high gene accessibility at 1 nucleosome. We furthershowed that the high measures of gene responsiveness correlate with theH2A.Z-associated closed +1 nucleosome structure. Moreover, we found that H2A.Zrepresses enhancer activity by promoting H3K27me3 and preventing H3K4me3histone modifications. This study provides a framework for future studies of H2A.Zfunctions and opens up new aspects for decoding the interplay between chromatinmodification and histone variants in transcriptional control.

原文链接：

http://www.cell.com/molecular-plant/fulltext/S1674-2052(17)30270-8

4Plant Journal：中科院遗传所黄海等建立叶片近轴- 背面极性模式下生长素极性运输模型

Abstract

Leaf adaxial–abaxial polarity refers tothe two leaf faces, which have different types of cells performing distinctbiological functions. In 1951, Ian Sussex reported that when an incipient leafprimordium was surgically isolated by an incision across the vegetative shoot apicalmeristem (SAM), a radialized structure without an adaxial domain would form.This led to the proposal that a signal, now called the Sussex signal, istransported from the SAM to emerging primordia to direct leaf adaxial–abaxialpatterning. It was recently proposed that instead of the Sussex signal, polartransport of the plant hormone auxin is critical in leaf polarity formation.However, how auxin polar transport functions in the process is unknown. Throughlive imaging, we established a profile of auxin polar transport in and aroundyoung leaf primordia. Here we show that auxin polar transport in lateralregions of an incipient primordium forms auxin convergence points. Wedemonstrated that blocking auxin polar transport in the lateral regions of theincipient primordium by incisions abolished the auxin convergence points andcaused abaxialized leaves to form. The lateral incisions also blocked theformation of leaf middle domain and margins and disrupted expression of themiddle domain/margin-associated marker gene WUSCHEL-RELATED HOMEOBOX 1(SlWOX1). Based on these results we propose that the auxin convergence pointsare required for the formation of leaf middle domain and margins, and thefunctional middle domain and margins ensure leaf adaxial–abaxial polarity. Howmiddle domain and margins function in the process is discussed.

原文链接：

http://onlinelibrary.wiley.com/doi/10.1111/tpj.13670/full

5PLANT PHYSIOLOGY：武汉大学Lijia Li等揭示植物激素赤霉酸引发谷物糊粉末细胞的程序性死亡

Abstract

Recent discoveries have shown that epigenetic regulationis an integral part of phytohormone-mediatedprocesses. The phytohormone gibberellic acid (GA) triggers a series of events in cereal aleurone cells thatlead to programmed cell death (PCD), but the signaling cascade mediatingGA-induced PCD in cereal aleurone layers remainslargely unknown. Here, we showed that histone deacetylase (HDAC) activity gradually increased relative to histoneacetyltransferase (HAT) activity, leading to a globaldecrease in histone H3 and H4 acetylation levels during PCD of maize embryoless aleurone layers after 3 d of treatmentwith GA. HDAC inhibition prevented GA-inducedPCD in embryoless aleurone cells, whereas HAT inhibition resulted in PCD even in the absence of GA. H2O2 concentrationsincreased in GA- or HAT-inhibitor-treatedaleurone cells due to reduced levels of reactive oxygen species (ROS) scavengers. H2O2-treated aleurone cellsshowed no changes in the activity or expressionof HATs and HDACs. We show that it is possible to predict whether epigenetic modification enzymes serve as aregulator of the GA-triggered PCD signalingpathway in maize aleurone layers. Taken together, these findings reveal thatHDAC activity is required for GA-induced PCD in maize aleurone layers andregulates PCD via the ROS-mediated signal transduction pathway.

原文链接：

http://www.plantphysiol.org/content/early/2017/09/29/pp.17.00953

6NEW PHYTOLOGIST：西澳大利亚大学Edwards等人发表在植物中的CRISPR应用综述

Abstract

With the rapid increase in the global population and the impact of climate change on agriculture, there is a need for crops with higher yields and greater tolerance to abiotic stress. However, traditional crop improvement via genetic recombination or random mutagenesis is a laborious process and cannot keep pace with increasing crop demand. Genome editing technologies such as clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) allow targeted modification of almost any crop genome sequence to generate novel variation and accelerate breeding efforts. We expect a gradual shift in crop improvement away from traditional breeding towards cycles of targeted genome editing. Crop improvement using genome editing is not constrained by limited existing variation or the requirement to select alleles over multiple breeding generations. However, current applications of crop genome editing are limited by the lack of complete reference genomes, the sparse knowledge of potential modification targets, and the unclear legal status of edited crops. We argue that overcoming technical and social barriers to the application of genome editing will allow this technology to produce a new generation of high-yielding, climate ready crops.

原文链接：

http://onlinelibrary.wiley.com/doi/10.1111/nph.14702/full

7Plant Biotech J：中国农业大学Shaojiang Chen等综述双倍体系发展的新技术

Abstract

Haploid inducer line can betransferred (DH) technology can not only shorten the breeding process but alsoincrease genetic gain. Haploid induction and subsequent genome doubling are thetwo main steps required for DH technology. Haploids have been generated throughthe culture of immature male and female gametophytes, and through inter- andintraspecific via chromosome elimination. Here, we focus on haploidization viachromosome elimination, especially the recent advances in centromere-mediatedhaploidization. Once haploids have been induced, genome doubling is needed toproduce DH lines. This study has proposed a new strategy to improve haploidgenome doubling by combing haploids and minichromosome technology. With theprogress in haploid induction and genome doubling methods, DH technology canfacilitate reverse breeding, cytoplasmic male sterile (CMS) line production,gene stacking and a variety of other genetic analysis.

原文链接：

http://onlinelibrary.wiley.com/doi/10.1111/pbi.12805/full

8Plant Cell &Environ：植生所朱新广等分析了叶肉抗性成分及其环境互作的理论模型

Abstract

Mesophyll resistance (rm), stomatal resistance, andbiochemical limitations are recognized as three critical factors limiting leafphotosynthesis. Contrary to the expectation of being a constant, rm not onlyvaries with light and CO2 conditions but also shows different responses amongspecies. To elucidate the mechanistic basis of these responses, we derived ananalytical model of rm, which incorporates various anatomical and biochemicalfactors including permeabilities of cell wall and chloroplast envelope to CO2and HCO3−, carbonic anhydrase activities in cytosol and stroma, Rubiscoactivities, and relative location of mitochondria and chloroplast. Therobustness of this model was confirmed by comparing the predicted rm and itscomponents to numerical models developed at cell and leaf levels, which incorporatedetailed 3-dimensional cell and leaf anatomies, CO2 hydration anddiffusion processes from intercellular air space to stroma, and CO2fixation by Rubisco. A combination of these model analyses shows that thevarying rm is influenced by four biochemical factors: (a) nonuniform photosynthesisstatus across the leaf, (b) photorespiration and respiration, (c) bicarbonateleakage on the chloroplast envelope, and (d) hydration activity in cytosol andstroma. This study provides a theoretical framework to study components of rm and their responses to environmentalperturbations.

原文链接：

http://onlinelibrary.wiley.com/doi/10.1111/pce.13040/full

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