Evidence for transcript networks composed of chimeric RNAs in human cells.
Evidence for transcript networks composed of chimeric RNAs in human cells.
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DOI：
10.1371/journal.pone.0028213
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Gingeras TR
中科院分区：
文献类型：
--
作者：
Djebali S;Lagarde J;Kapranov P;Lacroix V;Borel C;Mudge JM;Howald C;Foissac S;Ucla C;Chrast J;Ribeca P;Martin D;Murray RR;Yang X;Ghamsari L;Lin C;Bell I;Dumais E;Drenkow J;Tress ML;Gelpí JL;Orozco M;Valencia A;van Berkum NL;Lajoie BR;Vidal M;Stamatoyannopoulos J;Batut P;Dobin A;Harrow J;Hubbard T;Dekker J;Frankish A;Salehi-Ashtiani K;Reymond A;Antonarakis SE;Guigó R;Gingeras TR
基因结构的经典组织遵循了50多年前提出的雅各布和莫诺德细菌基因模型。从那时起，在酵母中发现的转录本对人类的复杂性的经验确定模糊了基因的定义和物理边界。利用多种分析方法，我们已经确定了人类21号和22号染色体上的单个基因边界图谱。对492个蛋白质编码基因的5‘和3’转录末端位置的分析表明，其中85%的基因的边界延伸到当前注释的末端之外，最常与其他注释良好的基因的转录本的外显子相连。这些嵌合转录本的生物学和进化重要性体现在：(1)所涉及基因的非随机相互连接，(2)参与许多嵌合相互作用的基因的更大系统发育深度，(3)相关基因表达的协调，(4)正在转录的基因组区域在体内和三维上的接近，并对部分嵌合RNA做出贡献。相关基因连接的非随机性表明，不应单独研究嵌合转录本，而应将其作为一个RNA网络一起研究。
The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5′ and 3′ transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network.
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