Extensive alternative polyadenylation during zebrafish development.
Extensive alternative polyadenylation during zebrafish development.
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DOI：
10.1101/gr.139733.112
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发表时间：
2012-10
期刊：
影响因子：
7
通讯作者：
Bartel DP
中科院分区：
文献类型：
--
作者：
Ulitsky I;Shkumatava A;Jan CH;Subtelny AO;Koppstein D;Bell GW;Sive H;Bartel DP
信使RNA（mRNA）的转录后命运在很大程度上取决于其3′非翻译区（3′ UTR），其由前mRNA的切割和多聚腺苷酸化（CPA）限定。我们使用poly（A）-位置分析测序（3 P-seq）来绘制斑马鱼8个发育阶段和组织的poly（A）位点。对超过6000万个3 P-seq读段的分析大大增加和改进了现有的3′ UTR注释，从而为斑马鱼中超过79%的注释蛋白质编码基因确定了3′ UTR。来自大多数斑马鱼基因的mRNA经历交替CPA，来自一千多个基因的mRNA在不同阶段使用不同的显性3′ UTR。这些包括一个poly（A）聚合酶基因，对于该基因，替代CPA加强了其在卵巢中的抑制。3′ UTR在卵巢中最短，在大脑中最长。具有一些最短3′ UTR的异构体在卵巢中高度表达，但在胚胎的母体贡献的RNA中不存在，可能是因为它们的3′ UTR太短而不能容纳母体mRNA稳定所需的富含尿苷的基序。受精后2 h，在缺乏典型多聚腺苷酸化信号的位置出现数千个独特的poly（A）位点，这表明mRNA降解中间产物的广泛细胞质多聚腺苷酸化波。我们对斑马鱼3′ UTR的身份，形成和进化的见解为研究脊椎动物发育过程中的基因调控提供了资源。
The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3′ untranslated regions (3′ UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-seq reads substantially increased and improved existing 3′ UTR annotations, resulting in confidently identified 3′ UTRs for >79% of the annotated protein-coding genes in zebrafish. mRNAs from most zebrafish genes undergo alternative CPA, with those from more than a thousand genes using different dominant 3′ UTRs at different stages. These included one of the poly(A) polymerase genes, for which alternative CPA reinforces its repression in the ovary. 3′ UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3′ UTRs are highly expressed in the ovary, yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3′ UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At 2 h post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3′ UTRs provide a resource for studying gene regulation during vertebrate development.
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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.
通讯作者：
Greenberg, Michael E.
影响因子：
56.9
作者：
Giraldez, AJ;Mishima, Y;Schier, AF
通讯作者：
Schier, AF
影响因子：
2.5
作者：
KIMMEL, CB;BALLARD, WW;SCHILLING, TF
通讯作者：
SCHILLING, TF
DOI：
10.1073/pnas.0900028106
发表时间：
2009-04-28
影响因子：
11.1
作者：
Ji, Zhe;Lee, Ju Youn;Tian, Bin
通讯作者：
Tian, Bin
影响因子：
7
作者：
Linhart, Chaim;Halperin, Yonit;Shamir, Ron
通讯作者：
Shamir, Ron