ArticleBMC genomics2013
A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
37 citing papers in PubMed, 64 citations in OpenAlex.
- Ribosomal RNA Depletion for Poly(A)-Tail-Independent Quantification of Genome Activation.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions.BMC genomics · 2022Article
- Maternal body condition and season influence RNA deposition in the oocytes of alfalfa leafcutting bees (Frontiers in genetics · 2022Article
- A novel class III endogenous retrovirus with a class I envelope gene in African frogs with an intact genome and developmentally regulated transcripts in Xenopus tropicalis.Retrovirology · 2021Article
- Optimized design of antisense oligomers for targeted rRNA depletion.Nucleic acids research · 2021Article
- Control of zygotic genome activation in Xenopus.Current topics in developmental biology · 2021Review
- The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction.Scientific reports · 2020Article
- Spatiotemporal Patterning of Zygotic Genome Activation in a Model Vertebrate Embryo.Developmental cell · 2019Article
- Article
- The Xenopus animal cap transcriptome: building a mucociliary epithelium.Nucleic acids research · 2018Article
- RNA sequencing of early round goby embryos reveals that maternal experiences can shape the maternal RNA contribution in a wild vertebrate.BMC evolutionary biology · 2018Article
- Article
- Zygotic Genome Activation in Vertebrates.Developmental cell · 2017Review
- Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition.Genome research · 2017Article
- Expanding the genetic toolkit in Xenopus: Approaches and opportunities for human disease modeling.Developmental biology · 2017Review
- A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo.Developmental biology · 2017Article
- Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.Developmental biology · 2017Article
- Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis.Developmental biology · 2017Article
- A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs.Seminars in cell & developmental biology · 2017Review
- Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish,EvoDevo · 2017Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundDynamics 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.
resultsTo 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.
conclusionsThese data reveal dynamics of transcriptome polyadenylation and abundance and provides a high-confidence catalogue of novel and long non-coding RNAs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.