Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
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DOI：
10.1101/gr.2094104
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发表时间：
2004-03-01
期刊：
影响因子：
7
通讯作者：
Gingeras, TR
中科院分区：
文献类型：
--
作者：
Kampa, D;Cheng, J;Gingeras, TR
在这份报告中，我们通过使用高密度寡核苷酸阵列油胞质聚(A)(+)RNA获得了更丰富的21号和22号染色体转录组的视图。保守地说，只有31.4%的转录核苷酸对应于注释良好的基因，而所有其他4.8%和14.7%的转录核苷酸分别对应于mRNAs和EST。大约85%的已知外显子被检测到，而在已知基因中，Lip到21%只有一个基于单一异构体的石油外显子跳过的替代表达。总体而言，特征明确的外显子的表达主要分为两类，唯一表达或普遍表达，所有可识别的比例反义转录本。其余观察到的转录本(49.0%)在已知注释之外。这些新的转录本似乎更具细胞系特异性，并且与特征良好的基因相比，具有更低和更少的变异不良表达。基于其与注释的距离、转录本大小、编码能力和对内含子序列的反义鉴定，进一步鉴定了新的转录本。通过RT-PCR，126个新的转录本被独立验证，验证率为65%。这些观察结果有力地支持了重新评估人类基因总数的论点，以及“基因”的所有替代术语，以涵盖人类基因组中这些不断增长的、新型的RNA转录本。
In this report, we have achieved a richer view of the transcriptome for Chromosomes 21 and 22 by using high-density Oligonucleotide arrays oil cytosolic poly(A)(+) RNA. Conservatively, only 31.4% of the observed transcribed nucleotides correspond to well-annotated genes, whereas all additional 4.8% and 14.7% correspond to mRNAs and ESTs, respectively. Approximately 85% of the known exons were detected, and LIP to 21% of known genes have only a single isoform based oil exon-skipping alternative expression. Overall, the expression of the well-characterized exons falls predominately into two categories, uniquely or ubiquitously expressed with all identifiable proportion of antisense transcripts. The remaining observed transcription (49.0%) was outside of ally known annotation. These novel transcripts appear to be more cell-line-specific and have lower and less variation ill expression than the well-characterized genes. Novel transcripts were further characterized based oil their distance to annotations, transcript size, coding capacity, and identification as antisense to intronic sequences. By RT-PCR, 126 novel transcripts were independently verified, resulting ill a 65% verification rate. These observations strongly support the argument for a re-evaluation of the total number of human genes and all alternative term for "gene" to encompass these growing, novel classes of RNA transcripts in the human genome.