Computational identification of putative lincRNAs in mouse embryonic stem cell.
Computational identification of putative lincRNAs in mouse embryonic stem cell.
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小鼠胚胎干细胞中假定的 lincRNA 的计算鉴定
DOI：
10.1038/srep34892
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发表时间：
2016-10-07
影响因子：
4.6
通讯作者：
Wu Q
中科院分区：
文献类型：
--
作者：
Liu H;Lyu J;Liu H;Gao Y;Guo J;He H;Han Z;Zhang Y;Wu Q
作为调控因子，lncRNAs在胚胎干细胞中发挥着至关重要的作用。而lincRNAs是研究最广泛的lncRNAs，但可能仍存在大量未被发现的lncRNAs。在这项研究中，我们构建了转录组的从头组装，以检测在小鼠胚胎干细胞(ESCs)中表达的6701个可能的长基因间非编码转录本(LincRNAs)，这些转录本可能是不完整的，通过笼峰估计缺乏5‘端的覆盖。比较已知的lincRNAs及其邻近蛋白编码转录本的TSS近端区域，我们的结果显示lincRNATSS近端区域与特有的基因组和表观遗传学特征相关。随后，使用基于基因组和表观遗传学特征的TSS近端预测模型预测的可能的lincRNA TSS区域，在其5‘端对1,293个lincRNA进行了校正。最后，利用基因本体论术语对43个可能的lincRNAs进行了标注。综上所述，本工作提供了一个具有相对完整转录长度的小鼠ESCs表达的lincRNAs的新目录，这可能有助于研究小鼠ESCs甚至哺乳动物发育中lincRNA的转录和转录后调控。
As the regulatory factors, lncRNAs play critical roles in embryonic stem cells. And lincRNAs are most widely studied lncRNAs, however, there might still might exist a large member of uncovered lncRNAs. In this study, we constructed the de novo assembly of transcriptome to detect 6,701 putative long intergenic non-coding transcripts (lincRNAs) expressed in mouse embryonic stem cells (ESCs), which might be incomplete with the lack coverage of 5′ ends assessed by CAGE peaks. Comparing the TSS proximal regions between the known lincRNAs and their closet protein coding transcripts, our results revealed that the lincRNA TSS proximal regions are associated with the characteristic genomic and epigenetic features. Subsequently, 1,293 lincRNAs were corrected at their 5′ ends using the putative lincRNA TSS regions predicted by the TSS proximal region prediction model based on genomic and epigenetic features. Finally, 43 putative lincRNAs were annotated by Gene Ontology terms. In conclusion, this work provides a novel catalog of mouse ESCs-expressed lincRNAs with the relatively complete transcript length, which might be useful for the investigation of transcriptional and post-transcriptional regulation of lincRNA in mouse ESCs and even mammalian development.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
3
作者：
Khrameeva EE;Gelfand MS
通讯作者：
Gelfand MS
影响因子：
10.6
作者：
Hame Y;Angelini ED;Hoffman EA;Barr RG;Laine AF
通讯作者：
Laine AF
DOI：
10.1242/dev.116996
发表时间：
2015-03-01
期刊：
Development (Cambridge, England)
影响因子：
--
作者：
Hamazaki N;Uesaka M;Nakashima K;Agata K;Imamura T
通讯作者：
Imamura T
DOI：
10.1109/tnnls.2014.2342533
发表时间：
2015-07-01
影响因子：
10.4
作者：
Gu, Bin;Sheng, Victor S.;Li, Shuo
通讯作者：
Li, Shuo