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Series GSE46277 Query DataSets for GSE46277
Status Public on Jan 02, 2014
Title Transcription in Pronuclei and One- to Four-Cell Embryos Drives Early Development in a Nematode
Organism Ascaris suum
Experiment type Expression profiling by high throughput sequencing
Summary A long-standing view of development is that transcription is silenced in the oocyte until early divisions in the embryo. The point at which major transcription is reactivated varies in different organisms, but is usually after the 2-cell stage. However, this model may not be universal. We used RNA-seq and exploited the protracted development of the parasitic nematode Ascaris suum, to provide a comprehensive time course of mRNA expression, degradation, and translation during early development. Surprisingly, we find that ~4,000 genes are transcribed prior to pronuclear fusion and in the 1-4 cell embryos. Intriguingly, we do not detect maternal contribution of many orthologs of maternal C. elegans mRNAs, but instead find these are newly transcribed in the A. suum zygote prior to pronuclear fusion. Ribosome profiling demonstrates that, in general, early embryonic mRNAs are not stored for subsequent translation, but are directly translated following their synthesis. The role of maternally contributed and zygotically transcribed genes differs between the nematodes A. suum and C. elegans despite the fact that the two nematodes appear to exhibit highly similar morphological patterns during early development. Our study indicates that major transcription can occur immediately after fertilization and prior to pronuclear fusion in metazoa, suggesting that newly transcribed genes appear to drive A. suum early development. Furthermore, the mechanisms used for controlling the timing of the expression of key conserved genes has been altered between the two nematodes, illustrating significant plasticity in the regulatory networks that play important roles in developmental outcomes in nematodes.
 
Overall design A total of 28 samples are used for this study. The RNAs for the library construction are derived from 0.5 – 1 ml of synchronized embryo stages corresponding to a minimum of 0.5 billion embryos derived from > 1,000 female worms. The RNAs for polysome analysis are from pooled fractions of polysome gradient. For each sample, the amount of RNA for all polysome fractions is equivalent to the total RNA from the sample. Thus, the data from polysome profiling and RNA transcriptomes are considered as biological replicates. The level of the RNAs between each neighboring stages during development are considered as the reference for each other. Different sequencing strategies were applied for multiple libraries.
 
Contributor(s) Wang J, Garrey J, Davis RE
Citation(s) 24374308
Submission date Apr 22, 2013
Last update date May 15, 2019
Contact name Jianbin Wang
E-mail(s) Jianbin.Wang@ucdenver.edu
Phone 303-724-3227
Organization name University of Colorado Denver
Department Biochemistry and Molecular Genetics
Lab Richard E. Davis Lab
Street address 12801 East 17th Ave
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
 
Platforms (3)
GPL11672 Illumina Genome Analyzer II (Ascaris suum)
GPL15654 Illumina HiSeq 2000 (Ascaris suum)
GPL17050 Illumina MiSeq (Ascaris suum)
Samples (28)
GSM1128027 oocyte with wall
GSM1128028 zygote1
GSM1128029 zygote2
Relations
BioProject PRJNA198514
SRA SRP021466

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE46277_A_summ_mRNAs_polysomes_RPKM.txt.gz 616.6 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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