Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, New York, NY 10003, USA.
Science. 2010 Jul 23;329(5990):432-5. doi: 10.1126/science.1191244. Epub 2010 Jun 3.
Three-prime untranslated regions (3'UTRs) of metazoan messenger RNAs (mRNAs) contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3' rapid amplification of complementary DNA (cDNA) ends, full-length cDNAs, and RNA-seq, we defined approximately 26,000 distinct 3'UTRs in Caenorhabditis elegans for approximately 85% of the 18,328 experimentally supported protein-coding genes and revised approximately 40% of gene models. Alternative 3'UTR isoforms are frequent, often differentially expressed during development. Average 3'UTR length decreases with animal age. Surprisingly, no polyadenylation signal (PAS) was detected for 13% of polyadenylation sites, predominantly among shorter alternative isoforms. Trans-spliced (versus non-trans-spliced) mRNAs possess longer 3'UTRs and frequently contain no PAS or variant PAS. We identified conserved 3'UTR motifs, isoform-specific predicted microRNA target sites, and polyadenylation of most histone genes. Our data reveal a rich complexity of 3'UTRs, both genome-wide and throughout development.
真核生物信使 RNA（mRNA）的 3' 非翻译区（3'UTR）含有许多调节元件，但仍在很大程度上未被描述。通过 polyA 捕获、3' 快速 cDNA 末端扩增、全长 cDNA 和 RNA-seq，我们在秀丽隐杆线虫中定义了大约 26000 个独特的 3'UTR，这些 3'UTR 约占 18328 个经实验支持的蛋白质编码基因的 85%，并对大约 40%的基因模型进行了修订。替代的 3'UTR 异构体很常见，在发育过程中通常会有差异表达。平均 3'UTR 长度随着动物年龄的增长而减少。令人惊讶的是，在 13%的多聚腺苷酸化位点中没有检测到多聚腺苷酸化信号 (PAS)，主要是在较短的替代异构体中。反式拼接（与非反式拼接相比）的 mRNA 具有更长的 3'UTR，并且通常不含 PAS 或变体 PAS。我们鉴定了保守的 3'UTR 基序、异构体特异性预测的 microRNA 靶位点以及大多数组蛋白基因的多聚腺苷酸化。我们的数据揭示了 3'UTR 在全基因组和整个发育过程中的丰富复杂性。
