Wang Eric T, Sandberg Rickard, Luo Shujun, Khrebtukova Irina, Zhang Lu, Mayr Christine, Kingsmore Stephen F, Schroth Gary P, Burge Christopher B
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Nature. 2008 Nov 27;456(7221):470-6. doi: 10.1038/nature07509.
Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing, 86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that most alternative splicing and alternative cleavage and polyadenylation events vary between tissues, whereas variation between individuals was approximately twofold to threefold less common. Extreme or 'switch-like' regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of alternative splicing and alternative cleavage and polyadenylation were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3' untranslated regions suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.
通过前体信使核糖核酸（pre-messenger RNA）的可变加工，单个哺乳动物基因通常会产生多种信使核糖核酸（mRNA）和蛋白质异构体，它们可能具有相关、不同甚至相反的功能。在此，我们基于互补DNA片段的深度测序，对15种不同的人类组织和细胞系转录组进行了深入分析，得出了基因和mRNA异构体表达的数字清单。将序列读数定位到外显子-外显子连接点的分析表明，92% - 94%的人类基因会发生可变剪接，其中86%的次要异构体频率达到15%或更高。异构体特异性读数密度的差异表明，大多数可变剪接以及可变切割和多聚腺苷酸化事件在不同组织之间存在差异，而个体之间的差异则要少大约两到三倍。组织间剪接的极端或“开关样”调控与调控区域序列保守性增加以及全长开放阅读框的产生有关。可变剪接以及可变切割和多聚腺苷酸化模式在不同组织之间高度相关，表明这些过程受到协同调控，并且在可变内含子和3'非翻译区中一部分已知调控基序的序列保守性表明，特定因子共同参与了剪接和多聚腺苷酸化的组织水平调控。
