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Series GSE232141 Query DataSets for GSE232141
Status Public on May 14, 2023
Title The Upstream Sequence Transcription Complex Dictates Nucleosome Positioning and Promoter Accessibility at piRNA Genes in the C. elegans germ line [ChIP-Seq]
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The piRNA pathway is a conserved germline-specific small RNA pathway that ensures genomic integrity and continued fertility. In C. elegans and other nematodes, Type-I piRNA precursor transcripts are expressed from >10,000 small, independently regulated genes clustered within two discrete domains of 1.5 and 3.5 MB on Chromosome IV. These large domains likely play a significant role in promoting germline-specific expression of piRNAs, but the underlying mechanisms are unclear. By examining the chromatin environment specifically in isolated germ nuclei, we demonstrate that piRNA clusters are located in closed chromatin, and confirm the enrichment for the inactive histone modification H3K27me3. The piRNA biogenesis factor USTC (Upstream Sequence Transcription Complex) plays two roles – it promotes a strong association of nucleosomes throughout the domain, and it organizes the local nucleosome environment to direct the exposure of individual piRNA genes. Overall, this work reveals new insight into how chromatin state coordinates transcriptional regulation over large genomic domains, which has implications for understanding global genome organization in the germ line.
 
Overall design Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27me3, H3K36me3, and H3K9me3 as well as Native ChIP-seq of H3 of isolated germline nuclei in C. elegans.
 
Contributor(s) Sanchez N, Gonzalez L, Reinke V
Citation(s) 37215016
Submission date May 10, 2023
Last update date Aug 08, 2023
Contact name Valerie Reinke
E-mail(s) valerie.reinke@yale.edu
Phone 203-785-5228
Organization name Yale University School of Medicine
Department Genetics
Lab Reinke lab
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platforms (1)
GPL26672 Illumina NovaSeq 6000 (Caenorhabditis elegans)
Samples (36)
GSM7316359 Isolated germ nuclei wild-type H3K36me3 rep 1
GSM7316360 Isolated germ nuclei prde-1(mj207)V H3K36me3 rep 1
GSM7316361 Isolated germ nuclei wild-type input for H3K36me3 rep 1
This SubSeries is part of SuperSeries:
GSE232143 The Upstream Sequence Transcription Complex Dictates Nucleosome Positioning and Promoter Accessibility at piRNA Genes in the C. elegans germ line
Relations
BioProject PRJNA971123

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
GSE232141_H3K27me3_WT_zscore.bw 4.9 Mb (ftp)(http) BW
GSE232141_H3K27me3_prde1_zscore.bw 4.9 Mb (ftp)(http) BW
GSE232141_H3K36me3_WT_zscore.bw 3.1 Mb (ftp)(http) BW
GSE232141_H3K36me3_prde1_zscore.bw 3.1 Mb (ftp)(http) BW
GSE232141_H3K9me3_WT_zscore.bw 3.2 Mb (ftp)(http) BW
GSE232141_H3K9me3_prde1_zscore.bw 3.7 Mb (ftp)(http) BW
GSE232141_H3_highsalt_WT_RPM.bw 14.4 Mb (ftp)(http) BW
GSE232141_H3_highsalt_prde1_RPM.bw 14.7 Mb (ftp)(http) BW
GSE232141_H3_lowsalt_WT_RPM.bw 15.0 Mb (ftp)(http) BW
GSE232141_H3_lowsalt_prde1_RPM.bw 15.2 Mb (ftp)(http) BW
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