Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.
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人类基因组中转录的已加工假伪基：一种表达重新素材的中间形式缺乏蛋白质编码能力。
DOI：
10.1093/nar/gki531
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发表时间：
2005
影响因子：
14.9
通讯作者：
Gerstein, M
中科院分区：
文献类型：
--
作者：
Harrison, PM;Zheng, DY;Zhang, ZL;Carriero, N;Gerstein, M
假基因，在蛋白质编码基因的情况下，是已经失去编码蛋白质的能力的基因拷贝;它们通常通过对失能、衰变或不完整的蛋白质编码序列的注释来识别。加工假基因（Ppeggs）是通过mRNA反转录转座产生的。有压倒性的基因组证据表明，人类有数千个P β-gene，也有数十个人类加工基因，它们包含其他基因的完整逆转录转座拷贝。在这里，我们调查一个中间实体，转录加工假基因（TP peptig），这是残疾，但仍然转录。如在小鼠makorin 1-p1 TP β g的情况下所观察到的，TP β g可能影响旁系同源基因的表达。为了阐明它们的作用，我们通过将表达的序列定位到TP β g上并从已知的mRNA中提取TP β g来鉴定人TP β g。我们只考虑那些与非哺乳动物真核蛋白或已知结构的蛋白质结构域同源的P β G，并且需要在表达序列和基因组序列中检测相同的编码序列失活。寡核苷酸微阵列数据提供了进一步的表达验证。总的来说，我们发现166-233个TP标记（占P标记的104 -6%）。具有最高数量的同源TP蛋白的蛋白质/转录物通常具有许多同源TP蛋白并且大量表达。在基因的5′端和3′端附近，TP β g的表达量明显过高;这表明TP β g可以通过基因-启动子共选择或侵入非翻译区形成。然而，大约有一半的TP启动子位于基因间DNA中远离基因的位置，因此可能是选择了未指定来源的隐蔽启动子。此外，TP β g在以下方面与其他TP β g和加工基因不同：（i）它们没有显示出存款或起源于X染色体的显著趋势;（ii）只有5%的人TP β g在小鼠中具有潜在的直系同源物。这后一发现表明，绝大多数的TP蛋白是谱系特异性的。这可能与有充分记录的广泛的谱系特异性SINE/LINE活动有关。TP标记列表可在以下网址获得：（或）。
Pseudogenes, in the case of protein-coding genes, are gene copies that have lost the ability to code for a protein; they are typically identified through annotation of disabled, decayed or incomplete protein-coding sequences. Processed pseudogenes (PΨgs) are made through mRNA retrotransposition. There is overwhelming genomic evidence for thousands of human PΨgs and also dozens of human processed genes that comprise complete retrotransposed copies of other genes. Here, we survey for an intermediate entity, the transcribed processed pseudogene (TPΨg), which is disabled but nonetheless transcribed. TPΨgs may affect expression of paralogous genes, as observed in the case of the mouse makorin1-p1 TPΨg. To elucidate their role, we identified human TPΨgs by mapping expressed sequences onto PΨgs and, reciprocally, extracting TPΨgs from known mRNAs. We consider only those PΨgs that are homologous to either non-mammalian eukaryotic proteins or protein domains of known structure, and require detection of identical coding-sequence disablements in both the expressed and genomic sequences. Oligonucleotide microarray data provide further expression verification. Overall, we find 166–233 TPΨgs (∼4–6% of PΨgs). Proteins/transcripts with the highest numbers of homologous TPΨgs generally have many homologous PΨgs and are abundantly expressed. TPΨgs are significantly over-represented near both the 5′ and 3′ ends of genes; this suggests that TPΨgs can be formed through gene–promoter co-option, or intrusion into untranslated regions. However, roughly half of the TPΨgs are located away from genes in the intergenic DNA and thus may be co-opting cryptic promoters of undesignated origin. Furthermore, TPΨgs are unlike other PΨgs and processed genes in the following ways: (i) they do not show a significant tendency to either deposit on or originate from the X chromosome; (ii) only 5% of human TPΨgs have potential orthologs in mouse. This latter finding indicates that the vast majority of TPΨgs is lineage specific. This is likely linked to well-documented extensive lineage-specific SINE/LINE activity. The list of TPΨgs is available at: (or) .
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DOI：
10.1111/j.1432-1033.1990.tb15598.x
发表时间：
1990-07-05
期刊：
EUROPEAN JOURNAL OF BIOCHEMISTRY
影响因子：
--
作者：
HAENDLER, B;HOFER, E
通讯作者：
HOFER, E
影响因子：
5.6
作者：
Harrison, PM;Carriero, N;Gerstein, M
通讯作者：
Gerstein, M
DOI：
10.1073/pnas.052692099
发表时间：
2002-03-05
影响因子：
11.1
作者：
Chen, CF;Gentles, AJ;Karlin, S
通讯作者：
Karlin, S
影响因子：
56.9
作者：
Bertone, P;Stolc, V;Snyder, M
通讯作者：
Snyder, M
影响因子：
5.6
作者：
Harrison, P;Kumar, A;Gerstein, M
通讯作者：
Gerstein, M