Genome Research：番木瓜基因组研究揭秘性别起源

在长达30多亿年的生命进化史上，生命何时出现雌雄之分？这个问题一直困扰着科学家，在2008年最后一期的世界著名杂志《基因组研究》上，中外科学家发表了《番木瓜原始Y染色体的雄性特异区中DNA甲基化和异染色质化》的研究论文，初步揭示了性染色体的起源变化机制。番木瓜的雄性区域很有可能和人类2亿至3亿年前的Y染色体相似。这种水果Y染色体基因为人类性染色体起源和进化的初始阶段所发生的事件提供了间接证据。
论文作者之一，南京农业大学作物遗传与种质创新国家重点实验室王秀娥教授说，番木瓜这种植物不同寻常，因为它有三性——雄株、雌株和雌雄同株。代表它还正处于性别分化的起始阶段。通过它或许能够找到“性别起源”的秘密。
专家在一株雌雄同株的番木瓜身上发现了一条刚刚处于起源阶段的原始性染色体，雄性区域很小，约占该条染色体的10%，说明它是一条初始的性染色体，同时这个雄性区域似乎已经丢失了一些编码蛋白的DNA。这种丢失通常被认为是Y染色体从X染色体中分化的一个步骤。专家说，这样的雄性区域与两亿年到三亿年前人类的Y染色体的进化状况有相似之处。
专家们通过DNA分子原位杂交和免疫荧光分析直观地研究了这条初始性染色体的重组抑制过程后发现，在番木瓜的雄性区域，大约占到Y染色体的13%，而与X染色体相对应的区域相比，番木瓜的这段雄性区域积累了更多的DNA，导致了该区域的X和Y染色体配对异常。而通过NDA的分子原位杂交，专家在番木瓜的雄性区域发现了该区域有4个特异的异染色质疖，免疫荧光分析则揭示出这个区域与X染色体的相应区域发生了较大的分化，具有高度的甲基化。
这些研究结果为人类性染色体起源和进化的初始阶段所发生的事件，提供了一个直接的证据。（生物谷Bioon.com）
生物谷推荐原始出处：
Genome Research Published in Advance July 1, 2008, doi:10.1101/gr.078808.108 Genome Res. 2008. 18: 1938-1943
DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya
Wenli Zhang1,5, Xiue Wang1,2,5, Qingyi Yu3, Ray Ming4, and Jiming Jiang1,6
1 Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA;2 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People’s Republic of China;3 Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA;4 Department of Plant Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, USA5 These authors contributed equally to this work.
Abstract
Sex chromosomes evolved from autosomes. Recombination suppression in the sex-determining region and accumulation of deleterious mutations lead to degeneration of the Y chromosomes in many species with heteromorphic X/Y chromosomes. However, how the recombination suppressed domain expands from the sex-determining locus to the entire Y chromosome remains elusive. The Y chromosome of papaya (Carica papaya) diverged from the X chromosome approximately 2–3 million years ago and represents one of the most recently emerged Y chromosomes. Here, we report that the male-specific region of the Y chromosome (MSY) spans ～13% of the papaya Y chromosome. Interestingly, the centromere of the Y chromosome is embedded in the MSY. The centromeric domain within the MSY has accumulated significantly more DNA than the corresponding X chromosomal domain, which leads to abnormal chromosome pairing. We observed four knob-like heterochromatin structures specific to the MSY. Fluorescence in situ hybridization and immunofluorescence assay revealed that the DNA sequences associated with the heterochromatic knobs are highly divergent and heavily methylated compared with the sequences in the corresponding X chromosomal domains. These results suggest that DNA methylation and heterochromatinization play an important role in the early stage of sex chromosome evolution.

Genome Biology：mRNA间调控网络的研究

细胞的不同蛋白分子之间会通过不同的相互作用形成复杂的调控网络。近年来，细胞内不同RNA分子之间的关系受到了越来越多的重视。过去的研究表明长的反义转录本会影响基因的转录与翻译，但是长反义转录本在细胞的转录本中很少，相反，编码蛋白的RNA间短片段互补非常丰富。microRNA及siRNA仅约22 nt长，却能通过与目标片段的互补起到重要调控基因转录和翻译的作用，那么编码蛋白的RNA间是否存在通过短片段互补而相互作用的可能性呢？
健康所分子遗传学实验室博士生王萍等，在孔祥银研究员的指导下，并与巴斯大学Hurst教授合作，通过在人的24，968个编码蛋白的mRNA中寻找15-25 bp的互补区，发现与一系列随机序列的比较mRNA中明显富集短的配对；对区非随机分布，集于mRNA 5＇非翻译区；且，配对区的单核苷酸多态性密度低于旁侧区。这些结果表明mNA间互补短片段经历了进化选择。更重要的是配对数多的mRNA的表达值较低；组织特异表达的基因中的配对显著多于管家基因中的配对。通过与已有的小RNA的数据的比较，并没有发现mRNA间的短配对与已发现的小RNA有关， 提示其影响基因表达的作用并非通过产生小RNA实现。
本工作提示mRNA间很有可能通过短片段的配对相互作用，形成基因间相互影响的网络，是RNA间的一种新的相互作用机制。这一研究结果发表在2008年的《基因组生物学》（Genome Biology）杂志上。
该项工作得到了国家科技部、国家自然科学基金委和中科院项目的大力支持。（生物谷Bioon.com）
生物谷推荐原始出处：
Genome Biology 2008, 9:R169doi:10.1186/gb-2008-9-12-r169
Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes
Ping Wang1,2 , Shanye Yin1,2 , Zhenguo Zhang1,2 , Dedong Xin1 , Landian Hu1 , Xiangyin Kong1,3 and Laurence D Hurst4
1 Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) and Shanghai Jiao Tong University School of Medicine (SJTUSM), 225 South Chong Qing Road, Shanghai 200025, PR China2 Graduate School of the Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, PR China3 State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiaotong University, 197 Rui Jin Road II, Shanghai 200025, PR China4 Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
Abstract
Background
There is increasing realization that regulation of genes is done partly at the RNA level by sense-antisense binding. Studies typically concentrate on the role of non-coding RNAs in regulating coding RNA. But the majority of transcripts in a cell are likely to be coding. Is it possible that coding RNA might regulate other coding RNA by short perfect sense-antisense binding? Here we compare all well-described human protein coding mRNAs against all others to identify sites 15-25 bp long that could potentially perfectly match sense-antisense.
Results
From 24,968 protein coding mRNA RefSeq sequences, none failed to find at least one match in the transcriptome. By randomizations generating artificial transcripts matched for G+C content and length, we found that there are more such trans short sense-antisense pairs than expected. Several further features are consistent with functionality of some of the putative matches. First, transcripts with more potential partners have lower expression levels, and the pair density of tissue specific genes is significantly higher than that of housekeeping genes. Further, the single nucleotide polymorphism density is lower in short pairing regions than it is in flanking regions. We found no evidence that the sense-antisense pairing regions are associated with small RNAs derived from the protein coding genes.
Conclusions
Our results are consistent with the possibility of common short perfect sense-antisense pairing between transcripts of protein coding genes.

Nature：酵母菌株基因图谱助酿美酒

专题：Nature报道
英国研究人员成功绘制出几十种用于酿酒、制作面食和生物燃料的酵母菌株基因图谱。这一研究成果有望应用于酿酒等工业，也可为人类基因图谱绘制提供借鉴。
路透社11日报道，英国诺丁汉大学教授埃德·路易斯和他的同事以世界各地酵母菌株为研究对象，绘制出其中70多种的基因图谱。
路易斯说，酿酒商可以据此选取优质酵母菌株，酿造更多口味的啤酒和葡萄酒，延长酒开盖后的保质期。
酵母基因与人体基因存在诸多类似之处，也有许多变种，一直用于癌症、衰老和疾病研究。因此这一成果对人体基因研究具有参考价值。路易斯说，研究人员可以根据酵母基因编制计算机软件，用于扫描更为复杂的人体基因。
这项研究成果发表在最新一期的英国《自然》杂志上。（生物谷Bioon.com）
生物谷推荐原始出处：
Nature advance online publication 11 February 2009 doi:10.1038/nature07743
Population genomics of domestic and wild yeasts
Gianni Liti1,9, David M. Carter2,9, Alan M. Moses2,3, Jonas Warringer4, Leopold Parts2, Stephen A. James5, Robert P. Davey5, Ian N. Roberts5, Austin Burt6, Vassiliki Koufopanou6, Isheng J. Tsai6, Casey M. Bergman7, Douda Bensasson7, Michael J. T. O'Kelly8, Alexander van Oudenaarden8, David B. H. Barton1, Elizabeth Bailes1, Alex N. Nguyen3, Matthew Jones2, Michael A. Quail2, Ian Goodhead2,10, Sarah Sims2, Frances Smith2, Anders Blomberg4, Richard Durbin2,9 & Edward J. Louis1,9
1 Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK2 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK3 Department of Cell & Systems Biology, University of Toronto, Ontario M5S 2J4, Canada4 Department of Cell and Molecular Biology, Lundberg Laboratory, University of Gothenburg, Medicinaregatan 9c, 41390 Gothenburg, Sweden5 National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK6 Division of Biology, Imperial College London, Silwood Park, Ascot SL5 7PY, UK7 Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK8 Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA9 These authors contributed equally to this work.10 Present address: School of Biological Sciences, University of Liverpool, Liverpool LG9 3BX, UK.
Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions3, 4, population structure5, 6, 7, 8 and sexual versus asexual reproduction9, 10. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.