Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish

Abstract

Alternative splicing is pervasive in mammalian genomes and involved in embryo development, whereas research on crosstalk of alternative splicing and embryo development was largely restricted to mouse and human and the alternative splicing regulation during embryogenesis in zebrafish remained unclear. We constructed the alternative splicing atlas at 18 time-course stages covering maternal-to-zygotic transition, gastrulation, somitogenesis, pharyngula stages, and post-fertilization in zebrafish. The differential alternative splicing events between different developmental stages were detected. The results indicated that abundance alternative splicing and differential alternative splicing events are dynamically changed and remarkably abundant during the maternal-to-zygotic transition process. Based on gene expression profiles, we found splicing factors are expressed with specificity of developmental stage and largely expressed during the maternal-to-zygotic transition process. The better performance of cluster analysis was achieved based on the inclusion level of alternative splicing. The biological function analysis uncovered the important roles of alternative splicing during embryogenesis. The identification of isoform switches of alternative splicing provided a new insight into mining the regulated mechanism of transcript isoforms, which always is hidden by gene expression. In conclusion, we inferred that alternative splicing activation is synchronized with zygotic genome activation and discovered that alternative splicing is coupled with transcription during embryo development in zebrafish. We also unveiled that the temporal expression dynamics of splicing factors during embryo development, especially co-orthologous splicing factors. Furthermore, we proposed that the inclusion level of alternative splicing events can be employed for cluster analysis as a novel parameter. This work will provide a deeper insight into the regulation of alternative splicing during embryogenesis in zebrafish.

Transcriptome analyses reveal key roles of alternative splicing regulation in atlantic salmon during the infectious process of Piscirickettsiosis disease

“…KEGG pathways and GO terms were treated as significant with a Fold Enrichment >2 and an FDR p-value <0.05. In addition, due to the lack of a specific salmonids database of splicing factors (SF), heterogeneous nuclear ribonucleoproteins (hnRNP), and serine-arginine proteins (SR), we used the dataset developed for Zebrafish by Liu et al [ 36 ].…”

miR-430 regulates zygotic mRNA during zebrafish embryogenesis

“…In zebrafish, various RNA-seq-based methods have been used to assign genes in each of these three categories. Notably, single-nucleotide polymorphisms (SNPs) in different parental strains [ 6 ], pull-down of metabolically labeled mRNA followed by sequencing [ 7 , 9 ], intron reads from total RNA-seq [ 4 , 10 ], and analysis of splicing [ 11 , 12 ], 3′UTR [ 13 , 14 ] and 5′UTR [ 15 , 16 ] isoforms have, to some extent, determined the maternal and zygotic components of maternal-zygotic genes. Yet, useful SNPs are only found in ~25% of protein coding genes [ 9 ], and de novo transcription from the maternal allele cannot be distinguished from their maternal mRNA fraction [ 6 ].…”