Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.
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DOI：
10.1186/gb-2010-11-3-r26
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发表时间：
2010
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：
Zhang ZD;Frankish A;Hunt T;Harrow J;Gerstein M
新的人类假基因被确定为具有先前的功能，并估计它们的年龄。功能丧失的发生率一致。单一假基因是一类在基因组中没有功能对应物的未加工的假基因。它们仅构成人类基因组中注释的假基因的一小部分。然而，随着时间的推移，它们代表了不同的功能丧失，它们揭示了人类在灵长类进化中的独特特征。我们已经开发了一个管道，通过分析人类基因组及其哺乳动物亲属之间的直系同源物的全球库存来检测人类单一假基因。我们关注的是大约7500万年前从啮齿动物分化出来后，人类谱系中沿着的基因丢失。总之，我们确定了76个单一的假基因，包括以前注释的，和许多新的。通过将这些基因与其他哺乳动物中的功能同源基因进行比较，我们可以大致确定每个单一假基因的创建日期（即基因的“死亡日期”），并表明对于我们的76个小组来说，功能基因似乎在灵长类动物进化过程中以相当均匀的速度被禁用-而不是一次全部，例如，与“Alu爆发”相关。此外，我们确定了11个单一的假基因是多态性的-也就是说，他们有非功能性和功能性等位基因目前在人群中分离。将它们与其他灵长类动物的直系同源基因进行比较，我们发现其中两个基因实际上是非人类灵长类动物中的假基因，这表明它们代表了人类谱系中基因复活的情况。这种单一的假基因的分析提供了不同的生物体所面临的进化限制和人类功能基因丢失的时间尺度的见解。
Novel human pseudogenes are identified that had previous functionality and their age is estimated. The rate of loss-of-function occurred uniformly. Unitary pseudogenes are a class of unprocessed pseudogenes without functioning counterparts in the genome. They constitute only a small fraction of annotated pseudogenes in the human genome. However, as they represent distinct functional losses over time, they shed light on the unique features of humans in primate evolution. We have developed a pipeline to detect human unitary pseudogenes through analyzing the global inventory of orthologs between the human genome and its mammalian relatives. We focus on gene losses along the human lineage after the divergence from rodents about 75 million years ago. In total, we identify 76 unitary pseudogenes, including previously annotated ones, and many novel ones. By comparing each of these to its functioning ortholog in other mammals, we can approximately date the creation of each unitary pseudogene (that is, the gene 'death date') and show that for our group of 76, the functional genes appear to be disabled at a fairly uniform rate throughout primate evolution - not all at once, correlated, for instance, with the 'Alu burst'. Furthermore, we identify 11 unitary pseudogenes that are polymorphic - that is, they have both nonfunctional and functional alleles currently segregating in the human population. Comparing them with their orthologs in other primates, we find that two of them are in fact pseudogenes in non-human primates, suggesting that they represent cases of a gene being resurrected in the human lineage. This analysis of unitary pseudogenes provides insights into the evolutionary constraints faced by different organisms and the timescales of functional gene loss in humans.
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非par体6：具有内核的真核直系同源群。
影响因子：
14.9
作者：
Berglund AC;Sjölund E;Ostlund G;Sonnhammer EL
通讯作者：
Sonnhammer EL
影响因子：
64.8
作者：
Chamero, Pablo;Marton, Tobias F.;Stowers, Lisa
通讯作者：
Stowers, Lisa
影响因子：
4.4
作者：
Birtle Z;Goodstadt L;Ponting C
通讯作者：
Ponting C
影响因子：
10.6
作者：
Edwards DR;Handsley MM;Pennington CJ
通讯作者：
Pennington CJ
DOI：
10.1073/pnas.0306880101
发表时间：
2004-08-10
影响因子：
11.1
作者：
Caenepeel, S;Charydczak, G;Manning, G
通讯作者：
Manning, G