Dynamic Transcriptional Landscape of the Early Chick Embryo

Junxiao Ren; Congjiao Sun; Michael Clinton; Ning Yang

doi:10.3389/fcell.2019.00196

Dynamic Transcriptional Landscape of the Early Chick Embryo

Front Cell Dev Biol. 2019 Sep 12:7:196. doi: 10.3389/fcell.2019.00196. eCollection 2019.

Authors

Junxiao Ren^{1

2}, Congjiao Sun^{1

2}, Michael Clinton³, Ning Yang^{1

2}

Affiliations

¹ Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
² National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China.
³ Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom.

Abstract

Defining the dynamic transcriptome of the early embryo at high resolution would assist greatly in understanding vertebrate development. Here, we describe the dynamic transcription landscape of early chick embryo development using advanced single-molecule long-read isoform sequencing (Iso-Seq) and RNA-Seq technology. Our transcriptomic profiling reflected the time course of chicken embryonic development from day 1 to day 8 of incubation, a period encompassing gastrulation, somitogenesis, and organogenesis. This analysis identified transcriptional isoforms, alternative splicing (AS) events, fusion transcripts, alternative polyadenylation (APA) sites, and novel genes. Our results showed that intron retention (IR) represented the most abundant AS type and displayed distinct features and dynamic modulation during development. Moreover, we constructed a high-resolution expression profile across embryonic development. Our combined expression dataset correlates distinct gene clusters with specific morphological changes, and provides the first framework for the molecular basis of early chicken embryogenesis. Analysis of gene expression in the developing chicken embryo highlighted the dynamic nature and complexity of the chicken transcriptome and demonstrated that dramatically increased IR events are associated with distinct gene sets.

Keywords: Iso-Seq; RNA-Seq; chicken; embryonic development; intron retention.