Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enrichment of H3K9me2 on unsynapsed chromatin in C. elegans does not target de novo sites

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Eleanor Maine

PROVIDER: E-GEOD-67030 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Enrichment of H3K9me2 on Unsynapsed Chromatin in Caenorhabditis elegans Does Not Target de Novo Sites.

Guo Yiqing Y Yang Bing B Li Yini Y Xu Xia X Maine Eleanor M EM

G3 (Bethesda, Md.) 20150708 9

Many organisms alter the chromatin state of unsynapsed chromosomes during meiotic prophase, a phenomenon hypothesized to function in maintaining germline integrity. In Caenorhabditis elegans, histone H3 lysine 9 dimethylation (H3K9me2) is detected by immunolabeling as enriched on unsynapsed meiotic chromosomes. Loss of the SET domain protein, MET-2, greatly reduces H3K9me2 abundance and results in germline mortality. Here, we used him-8 mutations to disable X chromosome synapsis and performed a ...[more]

PMID: 26156747

Similar Datasets

Enrichment of H3K9me2 on unsynapsed chromatin in C. elegans does not target de novo sites [ChIP-Seq]

Project description:Characterization of the H3K9me2 distribution in the C. elegans adult hermaphrodite genome using ChIP-Seq Examination of H3K9me2 in two different nematode strains: fer-1 control and fer-1;him-8 mutant, where the X chromosomes are unsynapsed. The fer-1 mutation prevents production of embryos.

2015-09-04 | E-GEOD-67028 | biostudies-arrayexpress

Enrichment of H3K9me2 on unsynapsed chromatin in C. elegans does not target de novo sites [RNA-Seq]

Project description:We sequenced mRNA isolated from adult hermaphrodite met-2;him-8 and him-8 gonads in order to determine the gene expression profile of germ cells with or without H3K9me2. Examination of mRNA profiles in nematode gonad of met-2;him-8 (without H3K9me2) and him-8 (with H3K9me2)

2015-09-04 | E-GEOD-67029 | biostudies-arrayexpress

Enrichment of H3K9me2 on Unsynapsed Chromatin in Caenorhabditis elegans Does Not Target de Novo Sites.

Project description:Many organisms alter the chromatin state of unsynapsed chromosomes during meiotic prophase, a phenomenon hypothesized to function in maintaining germline integrity. In Caenorhabditis elegans, histone H3 lysine 9 dimethylation (H3K9me2) is detected by immunolabeling as enriched on unsynapsed meiotic chromosomes. Loss of the SET domain protein, MET-2, greatly reduces H3K9me2 abundance and results in germline mortality. Here, we used him-8 mutations to disable X chromosome synapsis and performed a combination of molecular assays to map the sites of H3K9me2 accumulation, evaluate H3K9me2 abundance in germline vs. whole animals, and evaluate the impact of H3K9me2 loss on the germline transcriptome. Our data indicate that H3K9me2 is elevated broadly across the X chromosome and at defined X chromosomal sites in him-8 adults compared with controls. H3K9me2 levels are also elevated to a lesser degree at sites on synapsed chromosomes in him-8 adults compared with controls. These results suggest that MET-2 activity is elevated in him-8 mutants generally as well as targeted preferentially to the unsynapsed X. Abundance of H3K9me2 and other histone H3 modifications is low in germline chromatin compared with whole animals, which may facilitate genome reprogramming during gametogenesis. Loss of H3K9me2 has a subtle impact on the him-8 germline transcriptome, suggesting H3K9me2 may not be a major regulator of developmental gene expression in C. elegans. We hypothesize H3K9me2 may have a structural function critical for germline immortality, and a greater abundance of these marks may be required when a chromosome does not synapse.

| S-EPMC4555223 | biostudies-literature

Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics

Project description:We applied a middle-down proteomics strategy for large scale protein analysis during in vivo development of Caenorhabditis elegans. We characterized post-translational modifications (PTMs) on histone H3 N-terminal tails at eight time points during the C. elegans lifecycle, including embryo, larval stages (L1 to L4), dauer and L1/L4 post dauer. Histones were analyzed by our optimized middle-down protein sequencing platform using high mass accuracy tandem mass spectrometry. This allows quantification of intact histone tails and detailed characterization of distinct histone tails carrying co-occurring PTMs. We measured temporally distinct combinatorial PTM profiles during C. elegans development. We show that the doubly modified form H3K23me3K27me3, which is rare or non-existent in mammals, is the most abundant PTM in all stages of C. elegans lifecycle. The abundance of H3K23me3 increased during development and it was mutually exclusive of the active marks H3K18ac, R26me1 and R40me1, suggesting a role for H3K23me3 in to silent chromatin. We observed distinct PTM profiles for normal L1 larvae and for L1-post dauer larvae, or L4 and L4 post-dauer, suggesting that histone PTMs mediate an epigenetic memory that is transmitted during dauer formation. Collectively, our data describe the dynamics of histone H3 combinatorial code during C. elegans lifecycle and demonstrate the feasibility of using middle-down proteomics to study in vivo development of multicellular organisms.

2015-11-02 | PXD002525 | Pride

A new dataset of spermatogenic vs oogenic transcriptomes in the nematode C. elegans

Project description:The nematode Caenorhabditis elegans is an important model for studies of germ cell biology, including specification as sperm or oocyte, the meiotic cell cycle and gamete differentiation. Fundamental to those studies is a genome-level knowledge of the germline transcriptome. Here we use RNA-Seq to identify genes expressed in isolated XX gonads, which are roughly 95% germline and 5% somatic gonadal tissue. We generate data from mutants making either sperm [fem-3(q96)] or oocytes (fog-2), both grown at 22M-BM-0C. Our dataset identifies a total of 10,754 mRNAs in the polyadenylated transcriptome of XX gonads, with 1,723 enriched in spermatogenic gonads, 2,869 enriched in oogenic gonads and the remaining 6,274 not enriched in either. These spermatogenic, oogenic and gender-neutral gene datasets compare well with those of earlier studies, but double the number of genes identified. We also query our RNA-Seq data for differential exon usage and find 351 mRNAs with sex-specific isoforms. We suggest that this new dataset will prove useful for studies focusing on C. elegans germ cell biology. Comparison of spermatogenic vs oogenic transcriptomes

2014-07-29 | E-GEOD-57109 | biostudies-arrayexpress

gonad-only_young_adult_20dC_42hrs_post-L1_N2_tiling_array

Project description:modENCODE_submission_481 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Tissue: Gonad; Developmental Stage: Young Adult 20dC 42 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain N2; Developmental Stage Young Adult 20dC 42 hrs post-L1; Tissue Gonad

2010-08-04 | E-GEOD-23269 | biostudies-arrayexpress

3'UTR sequencing of C.elegans strains

Project description:3'UTR sequencing was performed in indicated C.elegans strains to obtain information about alterations in 3'UTR lengths and alternative polyadenylation events.

2021-09-03 | E-MTAB-9147 | biostudies-arrayexpress

P. pacificus and C. elegans exposed to various pathogens

Project description:This SuperSeries is composed of the following subset Series: GSE36413 : C. elegans young adults : Exposed to Bacillus thuringiensis DB27 vs. E. coli OP50 exposure; 4hours GSE36493: C. elegans young adults: Exposed to Staphylococcus aureus versus exposed to E. coli OP50 : 4 hours GSE36499: C. elegans young adults: Exposed to Serratia marcescens versus exposed to E. coli OP50 : 4 hours GSE36501: C. elegans young adults: Exposed to Xenorhabdus nematophila versus exposed to E. coli OP50 : 4 hours GSE36517: P. pacificus young adults: Exposed to Bacillus thuringiensis DB27 versus exposed to E. coli OP50 : 4 hours GSE36519: P. pacificus young adults: Exposed to Staphylococcus aureus versus exposed to E. coli OP50 : 4 hours GSE36521: P. pacificus young adults: Exposed to Serratia marcescens versus exposed to E. coli OP50 : 4 hours GSE36523: P. pacificus young adults: Exposed to Xenorhabdus nematophila versus exposed to E. coli OP50 : 4 hours Refer to individual Series

2012-03-20 | E-GEOD-36636 | biostudies-arrayexpress

Phosphopeptide enrichment on synthetic libraries and HeLa cells digest

Project description:2 phosphopeptide enrichment methods (TiO2 and Ti-IMAC) were evaluated on synthetic libraries and HeLa cells digest. The resulting peptides were compared to the ones without enrichment with regards to the nature of the phosphorylation site (serine, threonine, tyrosine) and the characteristics of the peptide enriched. It was found that the enrichment methods are unbiased for these properties and that the result of the enrichment reflects the original condition of the sample.

2014-08-11 | PXD000759 | Pride

Microarray of young adults of endu-2(tm4977) loss of function mutant and endu-2(tm4977);Ex[endu-2::EGFP] rescue strain grown up at 25°C

Project description:The poly-U specific endoribonuclease ENDU-2 plays an important role in maintaining germline immortality in C. elegans. The endu-2 loss-of function mutants display a mortal germline phenotype at 20°C but not at 15°C. At 25°C, the mortal germline phenotype is enhanced. In addition, an extrachromosomal endu-2::EGFP transgene rescues the mutant phenotype. In order to investigate the role of ENDU-2 on mRNA abundancy, a microarray analysis was performed via comparing young adults of endu-2(tm4977) loss of function mutant and endu-2(tm4977);Ex[endu-2::EGFP] rescue strain grown up at 25°C. As ENDU-2 affects maternal inheritance, grouped animals for comparison were derived from one grandmother (endu-2(tm4977);Ex[endu-2::EGFP]) to ensure the same maternal inheritance at the parental generation.

2020-10-31 | E-MTAB-7993 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data