ZFIN ID: ZDB-PUB-160128-1
Chamber Specific Gene Expression Landscape of the Zebrafish Heart
Singh, A.R., Sivadas, A., Sabharwal, A., Vellarikal, S.K., Jayarajan, R., Verma, A., Kapoor, S., Joshi, A., Scaria, V., Sivasubbu, S.
Date: 2016
Source: PLoS One   11: e0147823 (Journal)
Registered Authors: Angom, Ramcharan Singh, Joshi, Adita, Sivasubbu, Sridhar
Keywords: Zebrafish, Gene expression, Cardiac ventricles, Cardiac atria, Transcriptome analysis, RNA sequencing, Adults, Heart
MeSH Terms:
  • Animals
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Heart Atria/growth & development
  • Heart Atria/metabolism*
  • Heart Ventricles/growth & development
  • Heart Ventricles/metabolism*
  • Humans
  • In Situ Hybridization
  • Sequence Analysis, RNA
  • Transcriptome*
  • Zebrafish/genetics*
  • Zebrafish Proteins/genetics*
PubMed: 26815362 Full text @ PLoS One
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.