Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.
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DOI：
10.1186/gb-2009-10-1-r2
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发表时间：
2009
期刊：
影响因子：
12.3
通讯作者：
Gerstein M
中科院分区：
文献类型：
--
作者：
Balasubramanian S;Zheng D;Liu YJ;Fang G;Frankish A;Carriero N;Robilotto R;Cayting P;Gerstein M
对四种哺乳动物基因组中核糖体蛋白假基因的分析表明，假基因数量与mRNA丰度之间没有相关性。
众多生物的基因组序列的可获得性使得对同线性区域的假基因进行比较研究成为可能。假基因的保守性表明它们在某些情况下可能具有功能作用。
我们报道了对四种哺乳动物基因组（人类、黑猩猩、小鼠和大鼠）中核糖体蛋白假基因的首次大规模比较分析。为此，我们使用自动化流程确定了这四种生物中的这些假基因，并将结果在网上公布。每种生物都有大量的核糖体蛋白假基因（大约1400到2800个）。它们中的大多数是加工过的（由反转录转座产生）。然而，我们没有发现与核糖体蛋白基因相关的假基因数量与其mRNA丰度之间存在相关性。对物种间同线性区域假基因的分析表明，大多数在人类和黑猩猩之间是保守的，但在灵长类和啮齿类之间只有极少数是保守的。有趣的是，同线性假基因的核苷酸替换率比其周围的基因间DNA要低。此外，来自表达序列标签的证据表明，在人类和小鼠之间保守的两个假基因被转录。详细分析表明，其中一个，即RPS27的假基因，很可能是一个蛋白质编码基因。这很重要，因为先前的报道表明人类基因组恰好编码80个核糖体蛋白基因。
我们的分析表明，加工过的核糖体蛋白假基因在哺乳动物基因组中大量存在，但在灵长类和啮齿类之间只有极少数是保守的。这凸显了哺乳动物中近期大量的反转录转座活动，以及在啮齿类谱系中相对更多的此类活动。
An analysis of ribosomal protein pseudogenes in the four mammalian genomes reveals no correlation between number of pseudogenes and mRNA abundance. The availability of genome sequences of numerous organisms allows comparative study of pseudogenes in syntenic regions. Conservation of pseudogenes suggests that they might have a functional role in some instances. We report the first large-scale comparative analysis of ribosomal protein pseudogenes in four mammalian genomes (human, chimpanzee, mouse and rat). To this end, we have assigned these pseudogenes in the four organisms using an automated pipeline and make the results available online. Each organism has a large number of ribosomal protein pseudogenes (approximately 1,400 to 2,800). The majority of them are processed (generated by retrotransposition). However, we do not see a correlation between the number of pseudogenes associated with a ribosomal protein gene and its mRNA abundance. Analysis of pseudogenes in syntenic regions between species shows that most are conserved between human and chimpanzee, but very few are conserved between primates and rodents. Interestingly, syntenic pseudogenes have a lower rate of nucleotide substitution than their surrounding intergenic DNA. Moreover, evidence from expressed sequence tags indicates that two pseudogenes conserved between human and mouse are transcribed. Detailed analysis shows that one of them, the pseudogene of RPS27, is likely to be a protein-coding gene. This is significant as previous reports indicated there are exactly 80 ribosomal protein genes encoded by the human genome. Our analysis indicates that processed ribosomal protein pseudogenes abound in mammalian genomes, but few of these are conserved between primates and rodents. This highlights the large amount of recent retrotranspositional activity in mammals and a relatively larger amount of it in the rodent lineage.
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影响因子：
11.4
作者：
Pavlicek, A;Gentles, AJ;Jurka, J
通讯作者：
Jurka, J
影响因子：
4.4
作者：
Uechi, T;Tanaka, T;Kenmochi, N
通讯作者：
Kenmochi, N
影响因子：
9.8
作者：
Marques, Ana Claudia;Dupanloup, Isabelle;Vinckenbosch, Nicolas;Reymond, Alexandre;Kaessmann, Henrik
通讯作者：
Kaessmann, Henrik
影响因子：
64.8
作者：
Tam, Oliver H.;Aravin, Alexei A.;Hannon, Gregory J.
通讯作者：
Hannon, Gregory J.
DOI：
10.1073/pnas.1932072100
发表时间：
2003-09-30
影响因子：
11.1
作者：
Kent, WJ;Baertsch, R;Haussler, D
通讯作者：
Haussler, D