Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.
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DOI：
10.1101/gr.134445.111
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发表时间：
2012-09
期刊：
影响因子：
7
通讯作者：
Guigó R
中科院分区：
文献类型：
--
作者：
Tilgner H;Knowles DG;Johnson R;Davis CA;Chakrabortty S;Djebali S;Curado J;Snyder M;Gingeras TR;Guigó R
剪接仍然是一个不完全理解的过程。最近的研究结果表明染色质结构参与其调节。在这里，我们分析了通过 RNA-seq 在细胞系 K562 中获得的亚细胞组分中的 RNA。我们表明，在人类基因组中，剪接主要发生在转录过程中。我们引入了 coSI 测量，基于映射到外显子连接和边界的 RNA-seq 读取，以评估内部外显子周围的剪接完成程度。我们发现，正如预期的那样，胞质 PolyA+ RNA 中的剪接几乎完全完成。在染色质相关 RNA（包括正在转录的 RNA）中，5.6% 的外显子完全完成了周围内含子的去除，相比之下，0.3% 的外显子未发生内含子去除。其余外显子以剪接分子和较少未剪接分子的混合物形式存在，中位 coSI 为 0.75。因此，大多数 RNA 在转录时会发生剪接：“共转录剪接”。与共转录剪接体组装和剪接一致，我们发现与其他细胞 RNA 片段和其他非剪接体 snRNA 相比，染色质相关 RNA 中的剪接体 snRNA 显着富集。 CoSI 分数沿着基因下降，表明“先转录，先剪接”的规则，但更多的下游外显子带有其他特征，有利于快速、共转录的内含子去除。 coSI 值低的外显子，即在剪接过程中，富含染色质标记，这与转录过程中染色质在剪接中的作用一致。对于替代外显子和长非编码 RNA，剪接往往发生较晚，并且后者在某些情况下可能保持未剪接状态。
Splicing remains an incompletely understood process. Recent findings suggest that chromatin structure participates in its regulation. Here, we analyze the RNA from subcellular fractions obtained through RNA-seq in the cell line K562. We show that in the human genome, splicing occurs predominantly during transcription. We introduce the coSI measure, based on RNA-seq reads mapping to exon junctions and borders, to assess the degree of splicing completion around internal exons. We show that, as expected, splicing is almost fully completed in cytosolic polyA+ RNA. In chromatin-associated RNA (which includes the RNA that is being transcribed), for 5.6% of exons, the removal of the surrounding introns is fully completed, compared with 0.3% of exons for which no intron-removal has occurred. The remaining exons exist as a mixture of spliced and fewer unspliced molecules, with a median coSI of 0.75. Thus, most RNAs undergo splicing while being transcribed: “co-transcriptional splicing.” Consistent with co-transcriptional spliceosome assembly and splicing, we have found significant enrichment of spliceosomal snRNAs in chromatin-associated RNA compared with other cellular RNA fractions and other nonspliceosomal snRNAs. CoSI scores decrease along the gene, pointing to a “first transcribed, first spliced” rule, yet more downstream exons carry other characteristics, favoring rapid, co-transcriptional intron removal. Exons with low coSI values, that is, in the process of being spliced, are enriched with chromatin marks, consistent with a role for chromatin in splicing during transcription. For alternative exons and long noncoding RNAs, splicing tends to occur later, and the latter might remain unspliced in some cases.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
影响因子：
10.5
作者：
Mancini-DiNardo, Debora;Steele, Scott J. S.;Tilghman, Shirley M.
通讯作者：
Tilghman, Shirley M.
影响因子：
14.9
作者：
Roberts, GC;Gooding, C;Smith, CWJ
通讯作者：
Smith, CWJ
影响因子：
16.8
作者：
Schwartz, Schraga;Meshorer, Eran;Ast, Gil
通讯作者：
Ast, Gil
影响因子：
16.8
作者：
Ameur, Adam;Zaghlool, Ammar;Feuk, Lars
通讯作者：
Feuk, Lars