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首页 » 华人研究 » Evol Bioinfor:于军等重复序列与哺乳动物基因组内含子扩张关系研究获进展

Evol Bioinfor:于军等重复序列与哺乳动物基因组内含子扩张关系研究获进展

来源:北京基因组研究所 2012-07-02 17:31

近日,在中国科学院北京基因组研究所副所长、基因组科学与信息重点实验室主任于军研究员和“百人计划”雷红星研究员的指导下,基因组所王大鹏博士、博士研究生苏尧等科研人员在哺乳动物基因组内含子扩张与基因功能关系研究,以及突变和自然选择在基因组进化中的作用研究中取得新进展。相关学术论文在Evolutionary Bioinformatics杂志发表。

基因组重复序列(Repetitive Sequence,RS)是复杂且进化活跃的,其对基因和基因组结构的稳定和动态性有着很大影响,并且与生物学功能密切相关。处于不同基因结构区域如外显子、内含子和基因间区的重复序列受到不同程度选择压力的影响。一般来说,这些序列重复的DNA片段通常被分为两类:即卫星序列(Satellite Sequences,SSs)和转座元件(transposable elements,TEs)。目前,许多脊椎动物的基因组测序工作已经完成,这为研究不同脊椎动物物种中TE和SS引导的内含子扩张提供了条件。

为了研究内含子序列中TE和SS的进化特征,科研人员选取了12种哺乳动物的基因组,按进化分支分成4组:灵长类、大型哺乳类、啮齿类和原始哺乳类,并用4种非哺乳类脊椎动物作为外群。研究表明:受TE或SS支配的内含子扩张机制在内含子长度、位置和基因功能等方面具有特定的分支特异性。研究发现,TE增加内含子长度的趋势比SS要强,TE和SS对哺乳动物的综合影响要大于任何两者之一的单独影响之简单加和,而在非哺乳脊椎动物中的情况则相反。

在自然选择的作用下,TE和SS衍生的重复序列表现出的作用在不同程度和作用机制上影响了脊椎动物基因和基因组的大小及组分,也是造成物种分化(脊椎动物各种层次的类别)和物种多样性的重要因素。该研究成果将帮助科研人员加深对于基因组非编码区域的功能调控和进化规律的理解和认识。(生物谷Bioon.com)

Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion

Dapeng Wang, Yao Su, Xumin Wang, Hongxing Lei and Jun Yu

Background: Repetitive sequences (RSs) are redundant, complex at times, and often lineage-specific, representing significant “building” materials for genes and genomes. According to their origins, sequence characteristics, and ways of propagation, repetitive sequences are divided into transposable elements (TEs) and satellite sequences (SSs) as well as related subfamilies and subgroups hierarchically. The combined changes attributable to the repetitive sequences alter gene and genome architectures, such as the expansion of exonic, intronic, and intergenic sequences, and most of them propagate in a seemingly random fashion and contribute very significantly to the entire mutation spectrum of mammalian genomes. Principal findings: Our analysis is focused on evolutional features of TEs and SSs in the intronic sequence of twelve selected mammalian genomes. We divided them into four groups—primates, large mammals, rodents, and primary mammals—and used four non-mammalian vertebrate species as the out-group. After classifying intron size variation in an intron-centric way based on RS-dominance (TE-dominant or SS-dominant intron expansions), we observed several distinct profiles in intron length and positioning in different vertebrate lineages, such as retrotransposon-dominance in mammals and DNA transposon-dominance in the lower vertebrates, amphibians and fishes. The RS patterns of mouse and rat genes are most striking, which are not only distinct from those of other mammals but also different from that of the third rodent species analyzed in this study—guinea pig. Looking into the biological functions of relevant genes, we observed a two-dimensional divergence; in particular, genes that possess SS-dominant and/or RS-free introns are enriched in tissue-specific development and transcription regulation in all mammalian lineages. In addition, we found that the tendency of transposons in increasing intron size is much stronger than that of satellites, and the combined effect of both RSs is greater than either one of them alone in a simple arithmetic sum among the mammals and the opposite is found among the four non-mammalian vertebrates. Conclusions: TE- and SS-derived RSs represent major mutational forces shaping the size and composition of vertebrate genes and genomes, and through natural selection they either fine-tune or facilitate changes in size expansion, position variation, and duplication, and thus in functions and evolutionary paths for better survival and fitness. When analyzed globally, not only are such changes significantly diversified but also comprehensible in lineages and biological implications.

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