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Singh AR, Sivadas A, Sabharwal A, Vellarikal SK, Jayarajan R, Verma A, Kapoor S, Joshi A, Scaria V, Sivasubbu S. Chamber Specific Gene Expression Landscape of the Zebrafish Heart. PLoS One 2016; 11:e0147823. [PMID: 26815362 PMCID: PMC4729522 DOI: 10.1371/journal.pone.0147823] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/08/2016] [Indexed: 01/01/2023] Open
Abstract
The organization of structure and function of cardiac chambers in vertebrates is defined by chamber-specific distinct gene expression. This peculiarity and uniqueness of the genetic signatures demonstrates functional resolution attributed to the different chambers of the heart. Altered expression of the cardiac chamber genes can lead to individual chamber related dysfunctions and disease patho-physiologies. Information on transcriptional repertoire of cardiac compartments is important to understand the spectrum of chamber specific anomalies. We have carried out a genome wide transcriptome profiling study of the three cardiac chambers in the zebrafish heart using RNA sequencing. We have captured the gene expression patterns of 13,396 protein coding genes in the three cardiac chambers—atrium, ventricle and bulbus arteriosus. Of these, 7,260 known protein coding genes are highly expressed (≥10 FPKM) in the zebrafish heart. Thus, this study represents nearly an all-inclusive information on the zebrafish cardiac transcriptome. In this study, a total of 96 differentially expressed genes across the three cardiac chambers in zebrafish were identified. The atrium, ventricle and bulbus arteriosus displayed 20, 32 and 44 uniquely expressing genes respectively. We validated the expression of predicted chamber-restricted genes using independent semi-quantitative and qualitative experimental techniques. In addition, we identified 23 putative novel protein coding genes that are specifically restricted to the ventricle and not in the atrium or bulbus arteriosus. In our knowledge, these 23 novel genes have either not been investigated in detail or are sparsely studied. The transcriptome identified in this study includes 68 differentially expressing zebrafish cardiac chamber genes that have a human ortholog. We also carried out spatiotemporal gene expression profiling of the 96 differentially expressed genes throughout the three cardiac chambers in 11 developmental stages and 6 tissue types of zebrafish. We hypothesize that clustering the differentially expressed genes with both known and unknown functions will deliver detailed insights on fundamental gene networks that are important for the development and specification of the cardiac chambers. It is also postulated that this transcriptome atlas will help utilize zebrafish in a better way as a model for studying cardiac development and to explore functional role of gene networks in cardiac disease pathogenesis.
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Affiliation(s)
- Angom Ramcharan Singh
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Ankit Sabharwal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Shamsudheen Karuthedath Vellarikal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Ankit Verma
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Shruti Kapoor
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Adita Joshi
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
- * E-mail: (VS); (SS)
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
- * E-mail: (VS); (SS)
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