Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.
Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.
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DOI：
10.1371/journal.pone.0148940
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Salem M
中科院分区：
文献类型：
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作者：
Al-Tobasei R;Paneru B;Salem M
ENCODE项目揭示人类基因组约70%被转录。然而，只有1 - 2%的RNA编码蛋白质，其余的是非编码RNA。长链非编码RNA（lncRNAs）是一类多样的非编码RNA，长度超过200个核苷酸。新出现的证据表明，lncRNAs在包括基因表达调控在内的各种细胞过程中发挥关键作用。lncRNAs呈现出低水平的基因表达和序列保守性，这使得在基因组中通过计算识别它们变得困难。在这项研究中，使用TopHat和Cufflinks软件将超过20亿条Illumina测序读段映射到基因组参考序列上。去除了长度小于200个核苷酸、具有超过83 - 100个氨基酸的开放阅读框（ORF），或者与美国国家生物技术信息中心（NCBI）nr - 蛋白质数据库有显著同源性的转录本。此外，还使用了一个计算流程，基于蛋白质编码分数测试对剩余的转录本进行筛选。根据筛选严格程度的不同，鉴定出了31195到54503个lncRNAs，其中只有421个与其他物种中已知的lncRNAs匹配。一个数字基因表达图谱揭示了2935个组织特异性和3269个普遍表达的lncRNAs。这项研究对虹鳟鱼基因组中的lncRNAs进行了注释，为鲑科鱼类的功能基因组学研究提供了宝贵的资源。
The ENCODE project revealed that ~70% of the human genome is transcribed. While only 1–2% of the RNAs encode for proteins, the rest are non-coding RNAs. Long non-coding RNAs (lncRNAs) form a diverse class of non-coding RNAs that are longer than 200nt. Emerging evidence indicates that lncRNAs play critical roles in various cellular processes including regulation of gene expression. LncRNAs show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult. In this study, more than two billion Illumina sequence reads were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200nt, with more than 83–100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test. Depending on the filtering stringency conditions, between 31,195 and 54,503 lncRNAs were identified, with only 421 matching known lncRNAs in other species. A digital gene expression atlas revealed 2,935 tissue-specific and 3,269 ubiquitously-expressed lncRNAs. This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.