近日,，在中國科學(xué)院北京基因組研究所副所長,、基因組科學(xué)與信息重點(diǎn)實(shí)驗(yàn)室主任于軍研究員和“百人計(jì)劃”雷紅星研究員的指導(dǎo)下,，基因組所王大鵬博士,、博士研究生蘇堯等科研人員在哺乳動(dòng)物基因組內(nèi)含子擴(kuò)張與基因功能關(guān)系研究,，以及突變和自然選擇在基因組進(jìn)化中的作用研究中取得新進(jìn)展,。相關(guān)學(xué)術(shù)論文在Evolutionary Bioinformatics雜志發(fā)表,。
基因組重復(fù)序列（Repetitive Sequence，RS）是復(fù)雜且進(jìn)化活躍的,，其對(duì)基因和基因組結(jié)構(gòu)的穩(wěn)定和動(dòng)態(tài)性有著很大影響,，并且與生物學(xué)功能密切相關(guān),。處于不同基因結(jié)構(gòu)區(qū)域如外顯子、內(nèi)含子和基因間區(qū)的重復(fù)序列受到不同程度選擇壓力的影響,。一般來說,，這些序列重復(fù)的DNA片段通常被分為兩類：即衛(wèi)星序列（Satellite Sequences，SSs）和轉(zhuǎn)座元件（transposable elements,，TEs）,。目前，許多脊椎動(dòng)物的基因組測序工作已經(jīng)完成,，這為研究不同脊椎動(dòng)物物種中TE和SS引導(dǎo)的內(nèi)含子擴(kuò)張?zhí)峁┝藯l件,。
為了研究內(nèi)含子序列中TE和SS的進(jìn)化特征，科研人員選取了12種哺乳動(dòng)物的基因組,，按進(jìn)化分支分成4組：靈長類,、大型哺乳類、嚙齒類和原始哺乳類,，并用4種非哺乳類脊椎動(dòng)物作為外群,。研究表明：受TE或SS支配的內(nèi)含子擴(kuò)張機(jī)制在內(nèi)含子長度、位置和基因功能等方面具有特定的分支特異性,。研究發(fā)現(xiàn),，TE增加內(nèi)含子長度的趨勢比SS要強(qiáng)，TE和SS對(duì)哺乳動(dòng)物的綜合影響要大于任何兩者之一的單獨(dú)影響之簡單加和,，而在非哺乳脊椎動(dòng)物中的情況則相反,。
在自然選擇的作用下，TE和SS衍生的重復(fù)序列表現(xiàn)出的作用在不同程度和作用機(jī)制上影響了脊椎動(dòng)物基因和基因組的大小及組分,，也是造成物種分化（脊椎動(dòng)物各種層次的類別）和物種多樣性的重要因素,。該研究成果將幫助科研人員加深對(duì)于基因組非編碼區(qū)域的功能調(diào)控和進(jìn)化規(guī)律的理解和認(rèn)識(shí)。（生物谷Bioon.com）
doi:10.4137/EBO.S9758
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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.
