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A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development
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-codi...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907017/ https://www.ncbi.nlm.nih.gov/pubmed/24195446 http://dx.doi.org/10.1186/1471-2164-14-762 |
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author | Paranjpe, Sarita S Jacobi, Ulrike G van Heeringen, Simon J C Veenstra, Gert Jan |
author_facet | Paranjpe, Sarita S Jacobi, Ulrike G van Heeringen, Simon J C Veenstra, Gert Jan |
author_sort | Paranjpe, Sarita S |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3907017 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-39070172014-01-31 A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development Paranjpe, Sarita S Jacobi, Ulrike G van Heeringen, Simon J C Veenstra, Gert Jan BMC Genomics Research Article 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. BioMed Central 2013-11-06 /pmc/articles/PMC3907017/ /pubmed/24195446 http://dx.doi.org/10.1186/1471-2164-14-762 Text en Copyright © 2013 Paranjpe et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Paranjpe, Sarita S Jacobi, Ulrike G van Heeringen, Simon J C Veenstra, Gert Jan A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development |
title | A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development |
title_full | A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development |
title_fullStr | A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development |
title_full_unstemmed | A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development |
title_short | A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development |
title_sort | genome-wide survey of maternal and embryonic transcripts during xenopus tropicalis development |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907017/ https://www.ncbi.nlm.nih.gov/pubmed/24195446 http://dx.doi.org/10.1186/1471-2164-14-762 |
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