Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
Instituto Sírio-Libanês de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo, Brazil.
Adv Genet. 2019;103:39-90. doi: 10.1016/bs.adgen.2018.09.002. Epub 2019 Jan 17.
Pre-mRNA splicing, an essential step in eukaryotic gene expression, relies on recognition of short sequences on the primary transcript intron ends and takes place along transcription by RNA polymerase II. Exonic and intronic auxiliary elements may modify the strength of exon definition and intron recognition. Splicing DNA variants (SV) have been associated with human genetic diseases at canonical intron sites, as well as exonic substitutions putatively classified as nonsense, missense or synonymous variants. Their effects on mRNA may be modulated by cryptic splice sites associated to the SV allele, comprehending exon skipping or shortening, and partial or complete intron retention. As splicing mRNA outputs result from combinatorial effects of both intrinsic and extrinsic factors, in vitro functional assays supported by computational analyses are recommended to assist SV pathogenicity assessment for human Mendelian inheritance diseases. The increasing use of next-generating sequencing (NGS) targeting full genomic gene sequence has raised awareness of the relevance of deep intronic SV in genetic diseases and inclusion of pseudo-exons into mRNA. Finally, we take advantage of recent advances in sequencing and computational technologies to analyze alternative splicing in cancer. We explore the Catalog of Somatic Mutations in Cancer (COSMIC) to describe the proportion of splice-site mutations in cis and trans regulatory elements. Genomic data from large cohorts of different cancer types are increasingly available, in addition to repositories of normal and somatic genetic variations. These are likely to bring new insights to understanding the genetic control of alternative splicing by mapping splicing quantitative trait loci in tumors.
前体 mRNA 剪接是真核生物基因表达的一个基本步骤，依赖于对初级转录本内含子末端短序列的识别，并且在 RNA 聚合酶 II 转录过程中进行。外显子和内含子辅助元件可以改变外显子定义和内含子识别的强度。剪接 DNA 变体 (SV) 已在经典内含子位点与人类遗传疾病相关，以及假定为无义、错义或同义变体的外显子替换。它们对 mRNA 的影响可能会被与 SV 等位基因相关的隐藏剪接位点所调节，包括外显子跳跃或缩短，以及部分或完全内含子保留。由于剪接 mRNA 的输出是由内在和外在因素的组合效应产生的，因此推荐使用基于计算分析的体外功能测定来辅助人类孟德尔遗传疾病中 SV 致病性的评估。靶向全基因组基因序列的新一代测序 (NGS) 的广泛应用提高了人们对遗传疾病中深内含子 SV 和假外显子纳入 mRNA 的重要性的认识。最后，我们利用测序和计算技术的最新进展来分析癌症中的可变剪接。我们探索了癌症体细胞突变目录 (COSMIC)，以描述顺式和反式调控元件中剪接位点突变的比例。越来越多的不同癌症类型的大型队列的基因组数据，以及正常和体细胞遗传变异的存储库，都可以获得。这些可能通过在肿瘤中映射剪接数量性状基因座，为理解基因对可变剪接的控制带来新的见解。
