Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish
Abstract Background Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefor...
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| Format: | Article |
| Language: | English |
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BMC
2018-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4458-7 |
| _version_ | 1811265159524515840 |
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| author | Wen Chen Xuan Zhang Jing Li Shulan Huang Shuanglin Xiang Xiang Hu Changning Liu |
| author_facet | Wen Chen Xuan Zhang Jing Li Shulan Huang Shuanglin Xiang Xiang Hu Changning Liu |
| author_sort | Wen Chen |
| collection | DOAJ |
| description | Abstract Background Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs’ function and conservation is really intriguing. Results We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts. Conclusions By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human. |
| first_indexed | 2024-04-12T20:17:37Z |
| format | Article |
| id | doaj.art-d273cf1d2593408cb59694f4e697eac7 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T20:17:37Z |
| publishDate | 2018-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-d273cf1d2593408cb59694f4e697eac72022-12-22T03:18:05ZengBMCBMC Genomics1471-21642018-05-0119S2738510.1186/s12864-018-4458-7Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafishWen Chen0Xuan Zhang1Jing Li2Shulan Huang3Shuanglin Xiang4Xiang Hu5Changning Liu6Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesKey Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesKey Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesState Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal UniversityKey Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesAbstract Background Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs’ function and conservation is really intriguing. Results We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts. Conclusions By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.http://link.springer.com/article/10.1186/s12864-018-4458-7LncRNAZebrafishCo-expression networkGene ontologyKEGGConservation |
| spellingShingle | Wen Chen Xuan Zhang Jing Li Shulan Huang Shuanglin Xiang Xiang Hu Changning Liu Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish BMC Genomics LncRNA Zebrafish Co-expression network Gene ontology KEGG Conservation |
| title | Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish |
| title_full | Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish |
| title_fullStr | Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish |
| title_full_unstemmed | Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish |
| title_short | Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish |
| title_sort | comprehensive analysis of coding lncrna gene co expression network uncovers conserved functional lncrnas in zebrafish |
| topic | LncRNA Zebrafish Co-expression network Gene ontology KEGG Conservation |
| url | http://link.springer.com/article/10.1186/s12864-018-4458-7 |
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