The Substrates of Nonsense-Mediated mRNA Decay in Caenorhabditis elegans.
The Substrates of Nonsense-Mediated mRNA Decay in Caenorhabditis elegans.
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DOI：
10.1534/g3.117.300254
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发表时间：
2018-01-04
期刊：
影响因子：
--
通讯作者：
Anderson P
中科院分区：
文献类型：
--
作者：
Muir VS;Gasch AP;Anderson P
无义介导的mRNA衰变（NMD）是一种强烈影响真核生物基因表达的保守途径。在许多物种中，NMD的失活或抑制会影响相当一部分转录组的丰度。在NMD缺陷细胞中丰度发生改变的转录本可能是NMD的直接底物，也可能是抑制NMD的间接作用。我们对秀丽隐杆线虫NMD的直接底物进行了全基因组研究。我们的目标是(i)鉴定NMD的mRNA底物，（ii）将这些mRNA与其他丰度受NMD缺失间接影响的mRNA区分开来。我们之前已经证明，在所有研究的真核生物中，NMD的中心效应物Upf1p/SMG-2优先与含有过早翻译终止密码子的mrna结合。通过将Upf1/SMG-2的免疫纯化与nmd缺陷突变体和nmd熟练对照的高通量mRNA测序相结合，我们利用这种优先关联来区分直接效应和间接效应。我们鉴定了680个NMD底物，其中171个含有新的剪接形式，(i)包括带注释的内含子序列，（ii）以前在秀丽隐杆线虫转录组中没有记录。在NMD熟练菌株中，NMD以足够的效率降解非生产性剪接mrna，这是以前不知道的。在鉴定的NMD底物中富集了两类基因：(i)表达假基因的mrna和（ii）最近在秀丽隐杆线虫基因组中基因数量增加的基因家族的mrna。我们的研究结果确定了新的NMD底物，并为理解NMD在正常基因表达和基因组进化中的作用提供了背景。
Nonsense-mediated mRNA decay (NMD) is a conserved pathway that strongly influences eukaryotic gene expression. Inactivating or inhibiting NMD affects the abundance of a substantial fraction of the transcriptome in numerous species. Transcripts whose abundance is altered in NMD-deficient cells may represent either direct substrates of NMD or indirect effects of inhibiting NMD. We present a genome-wide investigation of the direct substrates of NMD in Caenorhabditis elegans. Our goals were (i) to identify mRNA substrates of NMD and (ii) to distinguish those mRNAs from others whose abundance is indirectly influenced by the absence of NMD. We previously demonstrated that Upf1p/SMG-2, the central effector of NMD in all studied eukaryotes, preferentially associates with mRNAs that contain premature translation termination codons. We used this preferential association to distinguish direct from indirect effects by coupling immunopurification of Upf1/SMG-2 with high-throughput mRNA sequencing of NMD-deficient mutants and NMD-proficient controls. We identify 680 substrates of NMD, 171 of which contain novel spliced forms that (i) include sequences of annotated introns and (ii) have not been previously documented in the C. elegans transcriptome. NMD degrades unproductively spliced mRNAs with sufficient efficiency in NMD-proficient strains that such mRNAs were not previously known. Two classes of genes are enriched among the identified NMD substrates: (i) mRNAs of expressed pseudogenes and (ii) mRNAs of gene families whose gene number has recently expanded in the C. elegans genome. Our results identify novel NMD substrates and provide a context for understanding NMD’s role in normal gene expression and genome evolution.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
4.5
作者：
Chiu, SY;Serin, G;Maquat, LE
通讯作者：
Maquat, LE
影响因子：
11.4
作者：
Gudikote, JP;Wilkinson, MF
通讯作者：
Wilkinson, MF
DOI：
10.1016/j.bbagrm.2013.10.004
发表时间：
2013-12-01
影响因子：
4.7
作者：
Cho, Hana;Han, Sisu;Kim, Yoon Ki
通讯作者：
Kim, Yoon Ki
影响因子：
30.3
作者：
Garcia D;Garcia S;Voinnet O
通讯作者：
Voinnet O