Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells.
Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells.
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DOI：
10.1371/journal.pgen.1002882
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Brem RB
中科院分区：
文献类型：
--
作者：
Yoon OK;Hsu TY;Im JH;Brem RB
群体个体之间的基因表达差异很大，而调控变化可能是进化和生物医学相关表型的基础。该领域的一个关键问题是 DNA 序列变异如何影响基因表达，迄今为止大多数机制研究都集中在遗传变化对蛋白质编码序列上游调控区域的影响。相比之下，RNA 3'端加工在调控变异中的作用仍然很大程度上未知，部分原因是识别 3' 非翻译区功能元件的挑战。在这项工作中，我们对来自遗传不同的人类个体的类淋巴母细胞的转录末端进行了基因组调查。我们的分析绘制了 3' 基因末端的顺式调控架构，发现转录物末端位置并非随机落在非翻译区域，而是优先位于 3' 调控元件（包括 miRNA 位点）位置的侧翼。这些转录物长度形式和基序的使用因人而异，多聚腺苷酸化信号和其他 3' 基序的多态性是它们所在基因表达水平的重要预测因子。独立的单基因实验证实了多聚腺苷酸化变体对其各自基因稳态表达的影响，并验证了介导这些不同RNA长度形式表达的3'顺式调节序列元件的调节功能。以免疫调节因子 IRF5 为重点，我们确定了 RNA 3' 末端加工的自然变异对抗原刺激的调节反应的影响。我们的结果强调了在 3' 末端变异遗传学中发挥作用的两种机制的重要性：不同 3' 末端处理信号的使用和决定转录本命运的 3' 序列元件的影响。我们的研究结果表明，将观察到的 3' 末端位置与推断的 3' 调控基序整合的策略将被证明是解释人类基因组变异的持续努力的关键工具。信使 RNA 携带合成对细胞有用的蛋白质所需的指令。超出给定 mRNA 的蛋白质编码序列的是一段额外的序列，其中包含控制蛋白质生成量以及 mRNA 在分解前在细胞中保留多长时间的信号。该末端区域并入成熟 mRNA 本身可能会发生变化；对于绝大多数人类基因来说，细胞如何以及为何使用不同的 mRNA 末端仍然很大程度上未知。在这项工作中，我们调查了来自基因不同的人类个体的免疫细胞中约 10,000 个基因的 mRNA 末端。我们发现 mRNA 末端位置不是随机分布的，而是优先位于控制 mRNA 命运的调节信号位置的侧翼。这些 mRNA 长度形式和调控元件的使用因个体而异，并且可以从分子角度进行剖析。我们的结果揭示了转录末端加工的关键机制和调节作用，特别是当这些机制和调节作用受到人类之间遗传差异的干扰时。
Gene expression varies widely between individuals of a population, and regulatory change can underlie phenotypes of evolutionary and biomedical relevance. A key question in the field is how DNA sequence variants impact gene expression, with most mechanistic studies to date focused on the effects of genetic change on regulatory regions upstream of protein-coding sequence. By contrast, the role of RNA 3′-end processing in regulatory variation remains largely unknown, owing in part to the challenge of identifying functional elements in 3′ untranslated regions. In this work, we conducted a genomic survey of transcript ends in lymphoblastoid cells from genetically distinct human individuals. Our analysis mapped the cis-regulatory architecture of 3′ gene ends, finding that transcript end positions did not fall randomly in untranslated regions, but rather preferentially flanked the locations of 3′ regulatory elements, including miRNA sites. The usage of these transcript length forms and motifs varied across human individuals, and polymorphisms in polyadenylation signals and other 3′ motifs were significant predictors of expression levels of the genes in which they lay. Independent single-gene experiments confirmed the effects of polyadenylation variants on steady-state expression of their respective genes, and validated the regulatory function of 3′ cis-regulatory sequence elements that mediated expression of these distinct RNA length forms. Focusing on the immune regulator IRF5, we established the effect of natural variation in RNA 3′-end processing on regulatory response to antigen stimulation. Our results underscore the importance of two mechanisms at play in the genetics of 3′-end variation: the usage of distinct 3′-end processing signals and the effects of 3′ sequence elements that determine transcript fate. Our findings suggest that the strategy of integrating observed 3′-end positions with inferred 3′ regulatory motifs will prove to be a critical tool in continued efforts to interpret human genome variation. Messenger RNAs carry the instructions necessary to synthesize proteins that do work for the cell. Extending beyond the protein-coding sequence of a given mRNA is an additional stretch of sequence, harboring signals that govern how much protein is made and how long the mRNA remains in the cell before it is broken down. The incorporation of this end region into mature mRNA is itself subject to change; for the vast majority of human genes, how and why cells use different mRNA ends remains largely unknown. In this work, we surveyed mRNA ends from ∼10,000 genes in immune cells from genetically distinct human individuals. We found that mRNA end positions were not randomly distributed, but rather preferentially flanked the locations of regulatory signals that govern mRNA fate. The usage of these mRNA length forms and regulatory elements varied across individuals and could be dissected molecularly. Our results uncover key mechanisms and regulatory effects of transcript end processing, particularly as these are perturbed by genetic differences between humans.
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影响因子：
16.2
作者：
Flavell, Steven W.;Kim, Tae-Kyung;Gray, Jesse M.;Harmin, David A.;Hemberg, Martin;Hong, Elizabeth J.;Markenscoff-Papadimitriou, Eirene;Bear, Daniel M.;Greenberg, Michael E.
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Greenberg, Michael E.
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3
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Xie, Xiaohui
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DEJONG, PJ
影响因子：
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作者：
Flomen, Rachel;Makoff, Andrew
通讯作者：
Makoff, Andrew