High-throughput transcriptome sequencing reveals the key stages of cardiovascular development in zebrafish embryos

Abstract

Background The cardiovascular developmental process is a tightly regulated network involving multiple genes. The current understanding of the molecular mechanism behind cardiovascular development is insufficient and requires further research. Results Transcriptome sequencing of three developmental stages in zebrafish embryos was performed and revealed three key cardiovascular developmental stages. Then, the differentially expressed genes (DEGs) involved in cardiovascular development were screened out. The three developmental stages were 18 (T1), 24 (T2), and 42 h post fertilization (hpf) (T3), and the three stages were confirmed by detecting differences in expression between cardiomyocyte and endothelial marker genes (cmlc2, fli1) using in situ hybridization, which represents the characteristics of cardiovascular development. Thousands of DEGs were identified using transcriptome analysis. Of them, 2605 DEGs were in T1-vs-T2, including 2003 up-regulated and 602 down-regulated genes, 6446 DEGs were in T1-vs-T3, consisting of 4608 up-regulated and 1838 down-regulated genes, and 3275 DEGs were in T2-vs-T3, including 2420 up-regulated and 855 down-regulated genes. There were 644 common DEGs and 167 common five-fold higher differentially expressed genes (HDEGs) identified, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Significant differences was observed in the levels of gene expression among different developmental stages in multiple GO terms and KEGG pathways, such as cell migration to the midline involved in heart development, cardiovascular system development, circulatory system process for biological processes of GO terms; and cardiac muscle contraction, adrenergic signaling in cardiomyocytes for KEGG pathways. These results demonstrated that these three stages were important period for the development of the cardiovascular system. Lastly, we used quantitative real-time PCR (qPCR) to validate the reliability of RNA-sequencing by selecting 21 DEGs. Conclusions These results demonstrated that these three stages represented the important periods for cardiovascular system development of zebrafish and some candidate genes was obtained and provided a solid foundation for additional functional studies of the DEGs.

Identification of a hippocampal lncRNA-regulating network in a natural aging rat model

“…All DE genes were mapped to terms in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database ( http://www.genome.jp/kegg/pathway.html ) and the Gene Ontology database ( http://www.geneontology.org/ ). GO terms and KEGG pathways with P < 0.05 were deemed as significantly enriched GO terms and KEGG terms [ 22 ].…”

“…org/). GO terms and KEGG pathways with P < 0.05 were deemed as significantly enriched GO terms and KEGG terms [22].…”

asb5a/asb5b Double Knockout Affects Zebrafish Cardiac Contractile Function

“…Based on the expression level of genes/transcripts in different samples, the distances between genes/transcripts or samples were calculated, and then iterative methods were used to cluster genes or samples. GO enrichment analysis was performed using Goatools software (https://github.com/ tanghaibao/GOatools, version 0.6.9, accessed on 25 July 2023) [12], and when corrected p values (FDR) < 0.05, they were considered to be significantly enriched, and sufficient for GO function. KEGG PATHWAY enrichment analysis was performed using R language.…”

“…Using morpholino interference technology [10], we successfully obtained the asb5a −/− :asb5b-ATGmo double-knockout zebrafish strain. RNA sequencing [11,12] was used to analyze the transcriptome differences between the asb5a −/− :asb5b-ATGmo double-knockout group and the wild-type (WT) group, as well as the asb5a −/− single-knockout group, respectively. We found that the double-knockout group was significantly enriched in functional items related to cardiac muscle contraction.…”