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Series GSE140864 Query DataSets for GSE140864
Status Public on May 05, 2020
Title C. elegans development (Gro-Seq)
Organism Caenorhabditis elegans
Experiment type Other
Summary Despite highly conserved chromatin states and cis-regulatory elements, studies of metazoan genomes reveal that gene organization and the strategies to control mRNA expression can vary widely among animal species. C. elegans gene regulation is often assumed to be similar to that of other model organisms, yet evidence suggests the existence of distinct molecular mechanisms to pattern the developmental transcriptome, including extensive post-transcriptional RNA control pathways, widespread splice leader (SL) trans-splicing of pre-mRNAs, and the organization of genes into operons. Here, we performed ChIP-seq for histone modifications in highly synchronized embryos cohorts representing three major developmental stages, with the goal of better characterizing whether the dynamic changes in embryonic mRNA expression are accompanied by changes to the chromatin state. We were surprised to find that thousands of promoters are persistently marked by active histone modifications, despite a fundamental restructuring of the transcriptome. We employed global run-on sequencing using a long-read nanopore format to map nascent RNA transcription across embryogenesis, finding that the invariant open chromatin regions are persistently transcribed by Pol II at all stages of embryo development, even though the mature mRNA is not produced. By annotating our nascent RNA sequencing reads into directional transcription units, we find extensive evidence of polycistronic RNA transcription genome-wide, suggesting that nearby genes in C. elegans are linked by shared transcriptional regulatory mechanisms. We present data indicating that the sharing of cis-regulatory sequences has constrained C. elegans gene positioning and likely explains the remarkable retention of syntenic gene pairs over long evolutionary timescales.
 
Overall design Nascent Pol II transcription was analyzed by sequencing replicate nascent RNA libraries for gastrula stage and late stage C. elegans embryos; high-quality fastq reads from replicate Gro-seq libraries were combined into a single library representing gastrula or late embryo nascent transcriptomes
 
Contributor(s) Bellush JM, Whitehouse I
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Submission date Nov 22, 2019
Last update date May 07, 2020
Contact name Iestyn Whitehouse
E-mail(s) whitehoi@mskcc.org
Organization name Sloan-Kettering Institute
Department Molecular Biology
Street address 1275 York Avenue
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL26522 MinION (Caenorhabditis elegans)
Samples (2)
GSM4188993 gastrula_GroSeq
GSM4188994 late_emb_GroSeq
This SubSeries is part of SuperSeries:
GSE140865 C. elegans development
Relations
BioProject PRJNA591184
SRA SRP231445

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Supplementary file Size Download File type/resource
GSE140864_RAW.tar 97.1 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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