title: Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish.
abstract: Long non-coding RNAs (lncRNA) represent an assorted class of transcripts having little or no protein coding capacity and have recently gained importance for their function as regulators of gene expression. Molecular studies on lncRNA have uncovered multifaceted interactions with protein coding genes. It has been suggested that lncRNAs are an additional layer of regulatory switches involved in gene regulation during development and disease. LncRNAs expressing in specific tissues or cell types during adult stages can have potential roles in form, function, maintenance and repair of tissues and organs. We used RNA sequencing followed by computational analysis to identify tissue restricted lncRNA transcript signatures from five different tissues of adult zebrafish. The present study reports 442 predicted lncRNA transcripts from adult zebrafish tissues out of which 419 were novel lncRNA transcripts. Of these, 77 lncRNAs show predominant tissue restricted expression across the five major tissues investigated. Adult zebrafish brain expressed the largest number of tissue restricted lncRNA transcripts followed by cardiovascular tissue. We also validated the tissue restricted expression of a subset of lncRNAs using independent methods. Our data constitute a useful genomic resource towards understanding the expression of lncRNAs in various tissues in adult zebrafish. Our study is thus a starting point and opens a way towards discovering new molecular interactions of gene expression within the specific adult tissues in the context of maintenance of organ form and function.
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India ; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhavan, New Delhi, India.
authors.forename: Kriti
authors.initials: K
authors.lastname: Kaushik
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India.
authors.forename: Vincent Elvin
authors.initials: VE
authors.lastname: Leonard
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India.
authors.forename: Shamsudheen
authors.initials: S
authors.lastname: Kv
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India.
authors.forename: Mukesh Kumar
authors.initials: MK
authors.lastname: Lalwani
authors.affiliation: G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India ; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhavan, New Delhi, India.
authors.forename: Saakshi
authors.initials: S
authors.lastname: Jalali
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India.
authors.forename: Ashok
authors.initials: A
authors.lastname: Patowary
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India.
authors.forename: Adita
authors.initials: A
authors.lastname: Joshi
authors.affiliation: G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India ; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhavan, New Delhi, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India ; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhavan, New Delhi, India.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Sivasubbu
mesh_terms: D000818:Animals; D001921:Brain / Q000196:embryology / Q000254:growth & development / Q000378:metabolism; D015870:Gene Expression; D020869:Gene Expression Profiling; D008099:Liver / Q000378:metabolism; D009132:Muscles / Q000378:metabolism; D009206:Myocardium / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000097:blood / Q000235:genetics* / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D014018:Tissue Distribution; D015027:Zebrafish / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*
chemical_list: D062085:RNA, Long Noncoding