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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes
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Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes

机译：来自人类基因组非编码部分的短片段在几乎所有已知基因中都有实例，并且与生物学过程有关

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Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities above what is expected by chance. Among the millions of discovered patterns, we found a subset of 127,998 patterns, termed pyknons, which have additional nonoverlapping instances in the untranslated and protein-coding regions of 30,675 transcripts from 20,059 human genes. The pyknons arrange combinatorially in the untranslated and coding regions of numerous human genes where they form mosaics. Consecutive instances of pyknons in these regions show a strong bias in their relative placement, favoring distances of approximate to 22 nucleotides. We also found pyknons to be enriched in a statistically significant manner in genes involved in specific processes, e.g., cell communication, transcription, regulation of transcription, signaling, transport, etc. For approximate to 1/3 of the pyknons, the intergenic/intronic instances of their reverse complement lie within 380,084 nonoverlapping regions, typically 60-80 nucleotides long, which are predicted to form double-stranded, energetically stable, hairpin-shaped RNA secondary structures; additionally, the pyknons subsume approximate to 40% of the known microRNA sequences, thus suggesting a possible link with post-transcriptional gene silencing and RNA interference. Cross-genome comparisons reveal that many of the pyknons have instances in the 3' UTRs of genes from other vertebrates and invertebrates where they are overrepresented in similar biological processes, as in the human genome. These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome.
机译：使用无监督的模式发现方法，我们处理了人类的基因间和内含子区域，并对所有可变长度模式进行了分类，并保留了相同的保守拷贝和多重性，超出了偶然的预期。在数百万个发现的模式中，我们发现了127,998个模式的子集，称为pyknons，在来自20,059个人类基因的30,675个转录本的非翻译和蛋白质编码区域中具有其他不重叠的实例。矮人组合在一起地排列在许多人类基因的非翻译和编码区域，在那里它们形成镶嵌。在这些区域中连续的pyknon实例在其相对位置上表现出强烈的偏见，偏向于大约22个核苷酸的距离。我们还发现pyknon在涉及特定过程（例如细胞通讯，转录，转录调节，信号传导，转运等）的基因中以统计学上显着的方式富集。对于大约1/3的pyknon，基因间/内含子其反向补体的实例位于380,084个非重叠区域内，通常长60-80个核苷酸，预计将形成双链，能量稳定的发夹状RNA二级结构；此外，pyknons约占已知microRNA序列的40％，因此暗示可能与转录后基因沉默和RNA干扰有关。跨基因组比较显示，许多矮人在其他脊椎动物和无脊椎动物的基因的3'UTR中都有实例，在人类生物基因组中，它们在类似的生物过程中过分表达。这些出乎意料的发现表明，人类基因组的编码和非编码部分之间可能存在独特的功能联系。

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