Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories.
Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories.
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DOI：
10.1093/nar/gkv390
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发表时间：
2015-08-18
影响因子：
14.9
通讯作者：
Papantonis A
中科院分区：
文献类型：
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作者：
Caudron-Herger M;Cook PR;Rippe K;Papantonis A
虽然绘制总转录组和聚腺苷化的人类转录组已经成为常规，但描绘新生转录组的特征仍然具有挑战性，主要是因为新生rna的半衰期很短。在这里，我们描述了一种简单、快速和经济的方法来分离与转录工厂相关的RNA，转录工厂是负责大部分核转录的位点。在用促炎细胞因子TNFα刺激人内皮细胞后，我们通过测序分离并分析了工厂的RNA含量。与总RNA、多聚(A)+ RNA和染色质RNA的比较表明，纯化的工厂RNA测序可以绘制完整的新生转录组；它富含内含子未加工转录物，以及长基因间非编码rna （lincRNAs）和增强子相关rna （eRNAs）、微rna前体和重复源rna。因此，我们证实转录工厂产生大多数新生RNA，并通过与一组特异性保留的非编码转录物的关联赋予调控作用。
While mapping total and poly-adenylated human transcriptomes has now become routine, characterizing nascent transcripts remains challenging, largely because nascent RNAs have such short half-lives. Here, we describe a simple, fast and cost-effective method to isolate RNA associated with transcription factories, the sites responsible for the majority of nuclear transcription. Following stimulation of human endothelial cells with the pro-inflammatory cytokine TNFα, we isolate and analyse the RNA content of factories by sequencing. Comparison with total, poly(A)+ and chromatin RNA fractions reveals that sequencing of purified factory RNA maps the complete nascent transcriptome; it is rich in intronic unprocessed transcript, as well as long intergenic non-coding (lincRNAs) and enhancer-associated RNAs (eRNAs), micro-RNA precursors and repeat-derived RNAs. Hence, we verify that transcription factories produce most nascent RNA and confer a regulatory role via their association with a set of specifically-retained non-coding transcripts.