Integrated pseudogene annotation for human chromosome 22: Evidence for transcription
Integrated pseudogene annotation for human chromosome 22: Evidence for transcription
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DOI：
10.1016/j.jmb.2005.02.072
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发表时间：
2005-05-27
影响因子：
5.6
通讯作者：
Gerstein, M
中科院分区：
文献类型：
--
作者：
Zheng, DY;Zhang, ZL;Gerstein, M
假基因是可遗传的遗传元素，由两个属性正式定义：它们与功能基因相似，以及它们被推定为缺乏活性。然而，事实证明，它们的准确特征，特别是关于后一种质量，是难以捉摸的。最近出现的平铺微阵列数据显示基因间隔区(包含假基因)在很大程度上被转录，这为探索这一问题提供了机会。在这里，我们重点研究人类22号染色体上的假基因的转录活性。首先，我们整合了几组注释，定义了染色体上525个假基因的统一列表。为了进一步描述这些特征，我们根据相关生物的保守性、表达证据和上游调控位点的存在，开发了一份全面的基因组特征清单。在525个统一假基因中，我们可以很有把握地将154个归类为处理过的，49个归类为重复的。使用来自平铺微阵列的数据，特别是来自最近的高分辨率寡核苷酸阵列的数据，我们发现了一些证据，表明在525个假基因中，多达五分之一可能是转录的。表达序列标签(EST)的比对进一步验证了其中的一些，我们总共发现了17个假基因，它们强烈支持转录。特别是，其中一个具有EST和微阵列转录证据的假基因被证明是猫眼综合征临界区的重复假基因。虽然我们不能确定假基因附近有大量有意义的转录因子结合位点(基于染色质免疫沉淀芯片数据)，但我们确实发现大约12%的假基因具有上游CpG岛。最后，对小鼠、大鼠和黑猩猩基因组中相应的共线区域的分析表明，正如先前所建议的那样，假基因比基因保守，但比基因间背景更保守(所有符号均可从http://www.pseudogene.org).获得(C)2005爱思唯尔有限公司。保留所有权利。
Pseudogenes are inheritable genetic elements formally defined by two properties: their similarity to functioning genes and their presumed lack of activity. However, their precise characterization, particularly with respect to the latter quality, has proven elusive. An opportunity to explore this issue arises from the recent emergence of tiling-microarray data showing that intergenic regions (containing pseudogenes) are transcribed to a great degree. Here we focus on the transcriptional activity of pseudogenes on human chromosome 22. First, we integrated several sets of annotation to define a unified list of 525 pseudogenes on the chromosome. To characterize these further, we developed a comprehensive list of genomic features based on conservation in related organisms, expression evidence, and the presence of upstream regulatory sites. Of the 525 unified pseudogenes we could confidently classify 154 as processed and 49 as duplicated. Using data from tiling microarrays, especially from recent high-resolution oligonucleotide arrays, we found some evidence that up to a fifth of the 525 pseudogenes are potentially transcribed. Expressed sequence tags (EST) comparison further validated a number of these, and overall we found 17 pseudogenes with strong support for transcription. In particular, one of the pseudogenes with both EST and microarray evidence for transcription turned Out to be a duplicated pseudogene in the cat eye syndrome critical region. Although we could not identify a meaningful number of transcription factor-binding sites (based on chromatin immuno-precipitation-chip data) near pseudogenes, we did find that similar to 12% of the pseudogenes had upstream CpG islands. Finally, analysis of corresponding syntenic regions in the mouse, rat and chimp genomes indicates, as previously suggested, that pseudogenes are less conserved than genes, but more preserved than the intergenic background (all notation is available from http://www.pseudogene.org). (c) 2005 Elsevier Ltd. All rights reserved.