A comprehensive survey of non-canonical splice sites in the human transcriptome.
A comprehensive survey of non-canonical splice sites in the human transcriptome.
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DOI：
10.1093/nar/gku744
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发表时间：
2014
影响因子：
14.9
通讯作者：
Gysling K
中科院分区：
文献类型：
--
作者：
Parada GE;Munita R;Cerda CA;Gysling K
我们使用深度转录组分析揭示了人类转录组中非典型剪接位点的多样性。我们绘制了总共37亿个人类RNA-seq读数，并开发了一套严格的过滤器，以避免错误的非典型剪接位点检测。我们确定了184个剪接位点与非典型的二核苷酸和U2/U12样的共识序列。我们选择了10个本文鉴定的U2/U12样非典型剪接位点事件，并通过逆转录酶-聚合酶链反应和桑格测序成功验证了其中9个。对184个U2/U12样非典型剪接位点的分析表明，其中51%未在GENCODE中注释。此外，其中28%在小鼠中是保守的，76%参与选择性剪接事件，其中一些具有组织特异性选择性剪接模式。有趣的是，我们的分析确定了一些U2/U12样的非典型剪接位点，这些位点通过RNA A-to-I编辑转化为典型剪接位点。此外，U2/U12样非典型剪接位点具有剪接调控序列的差异分布，这可能有助于它们的识别和调控。我们的分析提供了一个高置信度组的U2/U12样非典型剪接位点，其中表现出独特的功能之间的总人类剪接位点。
We uncovered the diversity of non-canonical splice sites at the human transcriptome using deep transcriptome profiling. We mapped a total of 3.7 billion human RNA-seq reads and developed a set of stringent filters to avoid false non-canonical splice site detections. We identified 184 splice sites with non-canonical dinucleotides and U2/U12-like consensus sequences. We selected 10 of the herein identified U2/U12-like non-canonical splice site events and successfully validated 9 of them via reverse transcriptase-polymerase chain reaction and Sanger sequencing. Analyses of the 184 U2/U12-like non-canonical splice sites indicate that 51% of them are not annotated in GENCODE. In addition, 28% of them are conserved in mouse and 76% are involved in alternative splicing events, some of them with tissue-specific alternative splicing patterns. Interestingly, our analysis identified some U2/U12-like non-canonical splice sites that are converted into canonical splice sites by RNA A-to-I editing. Moreover, the U2/U12-like non-canonical splice sites have a differential distribution of splicing regulatory sequences, which may contribute to their recognition and regulation. Our analysis provides a high-confidence group of U2/U12-like non-canonical splice sites, which exhibit distinctive features among the total human splice sites.
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影响因子：
5.8
作者：
Byun, Yanga;Han, Kyungsook
通讯作者：
Han, Kyungsook
影响因子：
48
作者：
Engstrom, Par G.;Steijger, Tamara;Sipos, Botond;Grant, Gregory R.;Kahles, Andre;Raetsch, Gunnar;Goldman, Nick;Hubbard, Tim J.;Harrow, Jennifer;Guigo, Roderic;Bertone, Paul
通讯作者：
Bertone, Paul
影响因子：
64.5
作者：
AEBI, M;HORNIG, H;WEISSMANN, C
通讯作者：
WEISSMANN, C
影响因子：
12.3
作者：
Denoeud F;Aury JM;Da Silva C;Noel B;Rogier O;Delledonne M;Morgante M;Valle G;Wincker P;Scarpelli C;Jaillon O;Artiguenave F
通讯作者：
Artiguenave F
DOI：
10.1073/pnas.0506139102
发表时间：
2005-09-06
影响因子：
11.1
作者：
Baek, D;Green, P
通讯作者：
Green, P