Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Research article

A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development

Sarita S Paranjpe1, Ulrike G Jacobi12, Simon J van Heeringen1 and Gert Jan C Veenstra1*

Author Affiliations

1 Radboud University Nijmegen, Dept. of Molecular Developmental Biology, Faculty of Science, Nijmegen Center for Molecular Life Sciences, The Netherlands

2 Current address: Teijin Aramid BV, Research Institute QRI, Arnhem, The Netherlands

For all author emails, please log on.

BMC Genomics 2013, 14:762  doi:10.1186/1471-2164-14-762

Published: 6 November 2013

Abstract

Background

Dynamics of polyadenylation vs. deadenylation determine the fate of several developmentally regulated genes. Decay of a subset of maternal mRNAs and new transcription define the maternal-to-zygotic transition, but the full complement of polyadenylated and deadenylated coding and non-coding transcripts has not yet been assessed in Xenopus embryos.

Results

To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts and putative long non-coding RNAs (lncRNA). These lncRNA transcripts were stringently selected as spliced transcripts generated from independent promoters, with limited coding potential and a codon bias characteristic of noncoding sequences. Many lncRNAs are conserved and expressed in a developmental stage-specific fashion.

Conclusions

These data reveal dynamics of transcriptome polyadenylation and abundance and provides a high-confidence catalogue of novel and long non-coding RNAs.

Keywords:
Xenopus tropicalis; RNA-seq; Maternal and embryonic transcriptome; Polyadenylation; Deadenylation; MBT; Codon bias; Long-noncoding RNAs