Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation.
Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation.
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DOI：
10.1101/gr.193995.115
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发表时间：
2016-01
期刊：
影响因子：
7
通讯作者：
Furger A
中科院分区：
文献类型：
--
作者：
Neve J;Burger K;Li W;Hoque M;Patel R;Tian B;Gullerova M;Furger A
选择性切割和多聚腺苷酸化 (APA) 在真核生物基因表达调控中发挥着至关重要的作用。尽管 APA 已被广泛研究，但其在细胞区室中的调节及其生理影响在很大程度上仍然是个谜。在这里，我们使用严格的亚细胞分级分离方法来比较人类细胞系细胞质和核 RNA 级分的 APA 谱。这种方法使我们能够提取受到差异调节的 APA 亚型，并为我们提供了一个平台来探究在不同亚细胞位置形成 APA 谱的分子调节途径。在这里，我们发现具有较短 3' UTR 的 APA 同种型往往在细胞质中过多出现，并且似乎是细胞类型特异性事件。较长 APA 同种型的核保留发生，部分是由于不完全剪接导致观察到的具有较短 3' UTR 的转录物的细胞质偏差。我们证明核糖核酸内切酶 III (DICER1) 不仅通过预期的细胞质 miRNA 介导的 APA mRNA 亚型不稳定，而且还通过影响多腺苷酸化位点选择，有助于亚细胞 APA 谱的建立。
Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we used a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape APA profiles in different subcellular locations. Here, we show that APA isoforms with shorter 3′ UTRs tend to be overrepresented in the cytoplasm and appear to be cell-type–specific events. Nuclear retention of longer APA isoforms occurs and is partly a result of incomplete splicing contributing to the observed cytoplasmic bias of transcripts with shorter 3′ UTRs. We demonstrate that the endoribonuclease III, DICER1, contributes to the establishment of subcellular APA profiles not only by expected cytoplasmic miRNA-mediated destabilization of APA mRNA isoforms, but also by affecting polyadenylation site choice.