Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish
PublisherNature Publishing Group
MetadataShow full item record
AbstractLong intergenic noncoding RNAs (lincRNAs) are increasingly recognized as potential key regulators of heart development and related diseases, but their identities and functions remain elusive. In this study, we sought to identify and characterize the cardiac lincRNA transcriptome in the experimentally accessible zebrafish model by integrating bioinformatics analysis with experimental validation. By conducting genome-wide RNA sequencing profiling of zebrafish embryonic hearts, adult hearts, and adult muscle, we generated a high-confidence set of 813 cardiac lincRNA transcripts, 423 of which are novel. Among these lincRNAs, 564 are expressed in the embryonic heart, and 730 are expressed in the adult heart, including 2 novel lincRNAs, TCONS-00000891 and TCONS-00028686, which exhibit cardiac-enriched expression patterns in adult heart. Using a method similar to a fetal gene program, we identified 51 lincRNAs with differential expression patterns between embryonic and adult hearts, among which TCONS-00009015 responded to doxorubicin-induced cardiac stress. In summary, our genome-wide systematic identification and characterization of cardiac lincRNAs lays the foundation for future studies in this vertebrate model to elucidate crucial roles for cardiac lincRNAs during heart development and cardiac diseases. Copyright 2017 The Author(s).
SponsorsThis work was supported by the National Institutes of Health (P30CA134274 to the University of Maryland Baltimore; HL81753 and HL107304 to X.X.) and the Mayo Foundation (to X.X.). Funding for open access charge: National Institutes of Health.
Keywordlong intergenic noncoding RNAs
Gene Expression Profiling
Heart--growth & development
Identifier to cite or link to this itemhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85018965799&doi=10.1038%2fs41598-017-00823-3&partnerID=40&md5=d512ba1e97f65cde94f135f1e1c5376a; http://hdl.handle.net/10713/11258
- Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
- Authors: Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A, Schier AF
- Issue date: 2012 Mar
- Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss).
- Authors: Wang J, Fu L, Koganti PP, Wang L, Hand JM, Ma H, Yao J
- Issue date: 2016 Apr
- Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution.
- Authors: Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP
- Issue date: 2011 Dec 23
- Genome-wide identification and characterization of long intergenic noncoding RNAs and their potential association with larval development in the Pacific oyster.
- Authors: Yu H, Zhao X, Li Q
- Issue date: 2016 Feb 10
- Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing.
- Authors: Billerey C, Boussaha M, Esquerré D, Rebours E, Djari A, Meersseman C, Klopp C, Gautheret D, Rocha D
- Issue date: 2014 Jun 19