Chamber Specific Gene Expression Landscape of the Zebrafish Heart

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.

Endothelial TGF-β signaling instructs smooth muscle development in the cardiac outflow tract

“…B) Gene ontology bar plot, showing the most overrepresented cellular compartments up- or down-regulated in the inhibitor treated embryos compared to controls. C) Venn diagram depicting the genes downregulated (log2FC < −0.585) in Alk5 inhibitor treated embryonic hearts, exclusively expressed in the adult zebrafish BA (Singh et al, 2016), and part of the zebrafish matrisome (Nauroy et al, 2018). The 5 genes in the intersection are listed in the box.…”

“…In order to identify extracellular proteins that might function in the signaling between ECs and SMCs, we compared the list of downregulated genes with the secreted factor genes from the zebrafish matrisome (Nauroy et al, 2018) (Figure 5C). Among the 82 genes identified, 5 of them were specifically expressed in the OFT in adult zebrafish (Singh et al, 2016), with fbln5 being the most downregulated one upon Alk5 inhibition (Figure 5C, S4C). Fbln5 is an ECM protein which mediates cell-to-matrix adhesion and has several functions, including the inhibition of EC proliferation in vitro and the organization of the elastic lamina (Sullivan et al, 2007; Yanagisawa et al, 2009).…”

Identification, characterization, and expression of sarcomeric tropomyosin isoforms in zebrafish

“…It is worth mentioning that the expression of TPM4-2a in Fugu fish is primarily in skeletal muscle (Toramoto et al, 2004). To our defense, we would like to point out that Singh et al (2016) reported the expression TPM4-2 in bulbus arteriosus of zebrafish. In their study, these researchers using RNA sequencing data FIG URE 12 Fluorescence image of quail myotubes transfected with YFP fused zebrafish and TPM1-2m.…”

“…It is worth mentioning that the expression of TPM4‐2α in Fugu fish is primarily in skeletal muscle (Toramoto et al, ). To our defense, we would like to point out that Singh et al () reported the expression TPM4‐2 in bulbus arteriosus of zebrafish. In their study, these researchers using RNA sequencing data generation and subsequent alignment technology showed that TPM‐1 and TPM4b (TPM4‐2) are expressed primarily in bulbus arteriosus but not in other heart chambers like atrium and ventricle.…”

“…In their study, these researchers using RNA sequencing data generation and subsequent alignment technology showed that TPM‐1 and TPM4b (TPM4‐2) are expressed primarily in bulbus arteriosus but not in other heart chambers like atrium and ventricle. Singh et al () using one of the most modern technologies, however, failed to detect the expression of a cardiac specific tropomyosin isoform like TPM4‐1α in any of the zebrafish heart chambers, which is puzzling since TPM4‐1α has been reported to be an essential tropomyosin isoform for beating zebrafish heart (Zhao et al, ).…”