Origin and evolution of new exons in the rodent zinc finger protein 39 gene

The origin of new structures and functions is an important process in evolution. In the past decades, we have obtained some preliminary knowledge of the origin and evolution of new genes. However, as the basic unit of genes, the origin and evolution of exons remain unclear. Because young exons retain the footprints of origination, they can be good materials for studying origin and evolution of new exons. In this paper, we report two young exons in a zinc finger protein gene of rodents. Since they are unique sequences in mouse and rat genome and no homologous sequences were found in the orthologous genes of human and pig, the young exons might originate after the divergence of primates and rodents through exonization of intronic sequences. Strong positive selection was detected in the new exons between mouse and rat, suggesting that these exons have undergone significant functional divergence after the separation of the two species. On the other hand, population genetics data of mouse demonstrate that the new exons have been subject to functional constraint, indicating an important function of the new exons in mouse. Functional analyses suggest that these new exons encode a nuclear localization signal peptide, which may mediate new ways of nuclear protein transport. To our knowledge, this is the first example of the origin and evolution of young exons.     

<Emphasis Type="Italic">Cis</Emphasis>-regulatory change and expression divergence between duplicate genes formed by genome duplication of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

As an index of functional divergence, expression divergence between duplicate gene copies has been observed and correlated with protein coding sequence divergence and bias in gene functional classes. However, the changes in the cis-regulatory region of the duplicate genes which is thought to have important role in expression divergence, has not been explored on the genome-wide scale. We analyzed functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in Arabidopsis thaliana. The divergence in cis-regulatory regions between two copies is positively correlated with the magnitude difference of expression. Moreover, we find that highly expressed duplicate gene pairs have a more diverged cis-regulatory region than weakly expressed gene pairs. We also show that the correlation between expression functional constraint and protein functional constraint is different in old and young duplicate pairs. Our results suggest that cis-regulatory sequence divergence contributes to the expression divergence of duplicate genes formed by genome-wide du-plication. Cis-regulatory region diverges faster in highly expressed duplicate pairs. The diversify selection strengths that act on cis-regulatory region and protein coding region are negatively correlated in young duplicate pairs under expression con-straint.     

Delayed biological recovery from extinctions throughout the fossil record

How quickly does biodiversity rebound after extinctions? Palaeobiologists have examined the temporal, taxonomic and geographic patterns of recovery following individual mass extinctions in detail, but have not analysed recoveries from extinctions throughout the fossil record as a whole. Here, we measure how fast biodiversity rebounds after extinctions in general, rather than after individual mass extinctions, by calculating the cross-correlation between extinction and origination rates across the entire Phanerozoic marine fossil record. Our results show that extinction rates are not significantly correlated with contemporaneous origination rates, but instead are correlated with origination rates roughly 10 million years later. This lagged correlation persists when we remove the 'Big Five' major mass extinctions, indicating that recovery times following mass extinctions and background extinctions are similar. Our results suggest that there are intrinsic limits to how quickly global biodiversity can recover after extinction events, regardless of their magnitude. They also imply that today's anthropogenic extinctions will diminish biodiversity for millions of years to come.     

上海市百岁老人的调查及其遗传分析

本文报导了上海市百岁老人的调查结果。全市人口11857478人,其中百岁老人72人,占0.615/10万。百岁老人中年龄最大的107岁,平均101.6岁。女性61人,男性11人,性比0.16。父母双方或一方寿命等于和超过70岁的41人,占70.7％,不足70岁的17人,占29.3％,其余的不详。说明人类的寿命受遗传因素控制。72名百岁老人共生育子女314人,现已自然死亡242人,其寿命分布接近正态分布。寿命也是一种性状,由于最高寿命和最低寿命之间存在一系列中间类型,彼此只有数量的区别,没有明显的质的界限,所以寿命是一种数量性状。据此,作者提出一个新观点,即人类的寿命受多基因(即多对等位基因)控制,同时又受家庭经济、家庭关系和性格类型等环境条件的明显影响。每对等位基因都由一个隐性基因和一个显性完全的显性基因组成,但只有显性基因对长寿有作用;各显性基因的单独作用是微小的,但彼此相等,而它们对寿命的共同作用是累加的。因此,一般来说,在性格温和、工作环境和生活环境良好的条件下,一个人带有决定长寿的显性基因数越多,其寿命就越长。     

上海市百岁老人的调查及其遗传分析

本文报导了上海市百岁老人的调查结果.全市人口11857478人,其中百岁老人72人,占0.615/10万.百岁老人中年龄最大的107岁,平均101.6岁.女性61人,男性11人,性比0.16.父母双方或一方寿命等于和超过70岁的41人,占70.7%,不足70岁的17人,占29.3%,其余的不详.说明人类的寿命受遗传因素控制.72名百岁老人共生育子女314人,现已自然死亡242人,其寿命分布接近正态分布.寿命也是一种性状,由于最高寿命和最低寿命之间存在一系列中间类型,彼此只有数量的区别,没有明显的质的界限,所以寿命是一种数量性状.据此,作者提出一个新观点,即人类的寿命受多基因(即多对等位基因)控制,同时又受家庭经济、家庭关系和性格类型等环境条件的明显影响.每对等位基因都由一个隐性基因和一个显性完全的显性基因组成,但只有显性基因对长寿有作用;各显性基因的单独作用是微小的,但彼此相等,而它们对寿命的共同作用是累加的.因此,一般来说,在性格温和、工作环境和生活环境良好的条件下,一个人带有决定长寿的显性基因数越多,其寿命就越长.     

Demasculinization of X chromosomes in the Drosophila genus

X chromosomes evolve differently from autosomes, but general governing principles have not emerged. For example, genes with male-biased expression are under-represented on the X chromosome of D. melanogaster, but are randomly distributed in the genome of Anopheles gambiae. In direct global profiling experiments using species-specific microarrays, we find a nearly identical paucity of genes with male-biased expression on D. melanogaster, D. simulans, D. yakuba, D. ananassae, D. virilis and D. mojavensis X chromosomes. We observe the same under-representation on the neo-X of D. pseudoobscura. It has been suggested that precocious meiotic silencing of the X chromosome accounts for reduced X chromosome male-biased expression in nematodes, mammals and Drosophila. We show that X chromosome genes with male-biased expression are under-represented in somatic cells and in mitotic male germ cells. These data are incompatible with simple X chromosome inactivation models. Using expression profiling and comparative sequence analysis, we show that selective gene extinction on the X chromosome, creation of new genes on autosomes and changed genomic location of existing genes contribute to the unusual X chromosome gene content.     

基于肿瘤基因表达数据的简单有效的基因选择算法

结合了基因表达数据类内和类间表达差异的信息,提出一种新的基因选择算法,利用它选择出来的特征基因表达作为支持向量机的输入特征向量,对四个常用数据集进行分类,结果表明,该方法可以显著提高分类精度,同时通过对选取出来的特征基因在相关信号通路上的分析,表明该方法能够得到更多的肿瘤相关基因,具有很强的鲁棒性和很高的精确度.     

基于模型的基因表达聚类分析技术研究进展

基因表达数据聚类分析能将功能相关的基因按表达谱的相似程度归纳成类,有助于对未知功能基因进行研究.基于判别的基因表达数据聚类方法具有无法准确确定类别的局限性,研究工作已转向具有更好聚类效果的基于模型的聚类方法.文中介绍了常见的基于模型的聚类方法及其特点,并就如何开发新的适合基因表达数据分析的基于模型的聚类算法进行了讨论.     

小麦新种质241主要特异性状的遗传性

为了探求小麦新种质241巨穗、粒大、结实率高等优良性状的遗传机理,应用单体分析和双端体分析方法对241材料进行遗传学研究。结果表明,小麦种质材料241的3A、5A、2B、1D和6D染色体上具有控制穗长的基因,其中2B染色体上的基因表现为强效,3A、5A、1D和6D染色体上的基因表现为弱效。控制穗长的基因定位在3AL、5AL、1DL和6DL染色体臂上,其中6DL染色体臂上可能具有控制241穗长的1个新基因。     

湘文一号抗虫棉幼叶总RNA提取技术研究

棉花抗虫Bt基因克隆技术第一步就是从抗虫Bt基因特异性表达的幼叶中提取总RNA,基因的表达可以在RNA产生的不同阶段进行调控,纯化完整的总RNA是进行基因表达研究和从cDNA克隆新基因的基础.对比分析了CTAB-licl法、改良异硫氰酸胍一步法、Trizol一步法和试剂盒提取方法4种RNA提取技术,经琼脂糖凝胶电泳谱带结果检验和紫外分光光度计检测,发现前2种方法很难提取到理想的RNA,而后2种提取的RNA完整性较好,但用RNA Out试剂盒提取的RNA更加适用于反转录cDNA.     

Transcription regulation and animal diversity

Whole-genome sequence assemblies are now available for seven different animals, including nematode worms, mice and humans. Comparative genome analyses reveal a surprising constancy in genetic content: vertebrate genomes have only about twice the number of genes that invertebrate genomes have, and the increase is primarily due to the duplication of existing genes rather than the invention of new ones. How, then, has evolutionary diversity arisen? Emerging evidence suggests that organismal complexity arises from progressively more elaborate regulation of gene expression.     

Functional genomics reveals genes involved in protein secretion and Golgi organization

Yeast genetics and in vitro biochemical analysis have identified numerous genes involved in protein secretion. As compared with yeast, however, the metazoan secretory pathway is more complex and many mechanisms that regulate organization of the Golgi apparatus remain poorly characterized. We performed a genome-wide RNA-mediated interference screen in a Drosophila cell line to identify genes required for constitutive protein secretion. We then classified the genes on the basis of the effect of their depletion on organization of the Golgi membranes. Here we show that depletion of class A genes redistributes Golgi membranes into the endoplasmic reticulum, depletion of class B genes leads to Golgi fragmentation, depletion of class C genes leads to aggregation of Golgi membranes, and depletion of class D genes causes no obvious change. Of the 20 new gene products characterized so far, several localize to the Golgi membranes and the endoplasmic reticulum.     

Sequencing and comparison of yeast species to identify genes and regulatory elements

Identifying the functional elements encoded in a genome is one of the principal challenges in modern biology. Comparative genomics should offer a powerful, general approach. Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species (S. paradoxus, S. mikatae and S. bayanus). We first aligned the genomes and characterized their evolution, defining the regions and mechanisms of change. We then developed methods for direct identification of genes and regulatory motifs. The gene analysis yielded a major revision to the yeast gene catalogue, affecting approximately 15% of all genes and reducing the total count by about 500 genes. The motif analysis automatically identified 72 genome-wide elements, including most known regulatory motifs and numerous new motifs. We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human.     

Human disease genes

The complete human genome sequence will facilitate the identification of all genes that contribute to disease. We propose that the functional classification of disease genes and their products will reveal general principles of human disease. We have determined functional categories for nearly 1,000 documented disease genes, and found striking correlations between the function of the gene product and features of disease, such as age of onset and mode of inheritance. As knowledge of disease genes grows, including those contributing to complex traits, more sophisticated analyses will be possible; their results will yield a deeper understanding of disease and an enhanced integration of medicine with biology.     

ACE2、AT2R、eNOS基因与原发性高血压相关性研究

原发性高血压（EH）是一种由遗传因素和环境因素共同作用导致的严重危害人类健康的心血管疾病。高血压疾病基因的研究有助于高血压发病机制的探讨,对其早期预防和及时治疗具有十分重要的理论意义和巨大的临床应用前景。至今研究者们已经发现有一百多种基因与原发性高血压的发病有关,特别是内皮型一氧化氮合酶（eNOS）更是研究的热点。已经确定肾素血管紧张素系统（RAS）在调控心血管功能时发挥重要作用,最近又在该系统中新发现了两个成员——血管紧张素转换酶2（ACE2）和血管紧张素Ⅱ2型受体（AT2R）,但是对其研究报道较少。文章分别从eNOS,ACE2和AT2R的生物学特性和作用机制的情况,探讨其与原发性高血压的相关性。     

The complete DNA sequence of yeast chromosome III.

The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.     

基因表达系列分析在肿瘤研究中的应用

基因表达系列分析(serial analysis of gene expression, SAGE)是一种快速分析基因表达信息的技术.它不但能快速、详细地分析成千上万个基因,还能发现新基因,因此是基因表达定性和定量研究的一种新的有效手段.近年来此技术广泛应用于肿瘤的研究,了解肿瘤发病机制,识别诊断和治疗肿瘤的新基因.可以预测SAGE在肿瘤研究和诊断过程中的应用将会对肿瘤的认识和治疗产生深远的影响.