Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Distinctive regulatory architectures of ubiquitous, germline and somatic genes

ABSTRACT: Nuclear long RNA-seq was used to profile gene expression in Germline, Neurons, Muscle, Hypodermis and Intestine nuclei from young adult worms.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE141212 | GEO | 2020/03/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Distinctive regulatory architectures of ubiquitous, germline and somatic genes

Project description:Chromatin accessibility in Germline, Neurons, Muscle, Hypodermis and Intestine nuclei from young adult worms.

2020-03-15 | GSE141210 | GEO

Distinctive regulatory architectures of ubiquitous, germline and somatic genes

Project description:Distinctive regulatory architectures of ubiquitous, germline and somatic genes

| PRJNA592698 | ENA

Distinctive regulatory architectures of ubiquitous, germline and somatic genes

Project description:Distinctive regulatory architectures of ubiquitous, germline and somatic genes

| PRJNA592702 | ENA

Distinctive regulatory architectures of ubiquitous, germline and somatic genes

Project description:Distinctive regulatory architectures of ubiquitous, germline and somatic genes

| PRJNA592701 | ENA

Distinctive regulatory architectures of ubiquitous, germline and somatic genes

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-03-15 | GSE141213 | GEO

Distinctive regulatory architectures of germline-active and somatic genes in <i>C. elegans</i>.

Project description:RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory architectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regulatory element activities across five tissues of Caenorhabditis elegans, covering ?90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline, and somatic tissue-specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters have distinct features. Germline-active promoters have well-positioned +1 and -1 nucleosomes associated with a periodic 10-bp WW signal (W = A/T). Somatic tissue-specific promoters lack positioned nucleosomes and this signal, have wide nucleosome-depleted regions, and are more enriched for core promoter elements, which largely differ between tissues. We observe the 10-bp periodic WW signal at ubiquitous promoters in other animals, suggesting it is an ancient conserved signal. Our results show fundamental differences in regulatory architectures of germline and somatic tissue-specific genes, uncover regulatory rules for generating diverse gene expression patterns, and provide a tissue-specific resource for future studies.

| S-EPMC7706728 | biostudies-literature

Intestine-to-germline transmission of epigenetic information transgenerationally ensures systemic stress resistance in C. elegans

Project description:Epigenetic states are metastable and changed throughout life, and their changes play a major role in the regulation of organismal homeostasis, including stress resistance. However, the mechanisms coordinating epigenetic states and systemic stress resistance across tissues remain largely unknown. Here, we identify the intestine-to-germline communication of epigenetic states, which enhances stress resistance transgenerationally in C. elegans. We firstly show that the alteration in epigenetic states by deficiency of the histone H3K4me3 modifier ASH-2 in the intestine or germline increases organismal oxidative stress resistance, which is abrogated by knockdown of the H3K4 demethylase RBR-2 in the same tissue. Remarkably, the increase in stress resistance induced by ASH-2 deficiency in the intestine is abrogated by RBR-2 knockdown in the germline, suggesting the existence of inter-tissue transmission of epigenetic information from intestine to germline. Simultaneously, this intestine-to-germline communication in the parental generation transgenerationally provides the increase in stress resistance of the descendants for over two generations. Further analyses reveal that the inter-tissue communication requires the insulin/IGF-1 signaling effector DAF-16/FOXO in the intestine and is mediated, at least in part, by transcriptional regulation of F08F1.3, one of the intestinal ASH-2 target genes. These results unveil the novel intestine-to-germline communication of epigenetic information that provides the transgenerational regulation of organismal stress resistance. To further investigate the molecular mechanisms underlying intestine-to-germline communication, we sought the gene expression changes in the intestine ash-2 knockdown worms.

2020-09-03 | GSE119917 | GEO

Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells

Project description:Chromatin diminution is the programmed elimination of specific DNA sequences during development. It occurs in diverse species, but the function(s) of diminution and the specificity of sequence loss remain largely unknown. Diminution in the nematode Ascaris suum occurs during early embryonic cleavages and leads to the loss of germline genome sequences and the formation of a distinct genome in somatic cells. We found that M-bM-^HM-<43 Mb (M-bM-^HM-<13%) of genome sequence is eliminated in A. suum somatic cells, including M-bM-^HM-<12.7 Mb of unique sequence. The eliminated sequences and location of the DNA breaks are the same in all somatic lineages from a single individual and between different individuals. At least 685 genes are eliminated. These genes are preferentially expressed in the germline and during early embryogenesis. We propose that diminution is a mechanism of germline gene regulation that specifically removes a large number of genes involved in gametogenesis and early embryogenesis. To profile the tissue expression of all A. suum genes, we used 8 different developmental stages/tissues of A. suum, including testis, ovary, embryo, larvae, intestine, muscle, male carcass and female carcass. In this submission there are 10 samples: 3 for early embryos (24hr, 46hr and 64hr) and the other 7 for testis, ovary, larvae, intestine, muscle, male carcass and female carcass. For each sample, 200 ug of total RNA was used for poly(A) selection and 200 ng of poly(A)+ RNA was used to make the cDNA libraries using standard Illumina protocol.

2012-11-13 | E-GEOD-38470 | biostudies-arrayexpress

Immune reposne of germline-ablated P. pacificus exposed to S. marcescens

Project description:Transcriptional profiling of germline-ablated P. pacificus worms exposed to S. marcescens for 8 hours versus germline-ablated P. pacificus exposed to the control E. coli OP50. First goal was to identify genes that are involved in immune response of germline-ablated P. pacificus when exposed to S. marcescens. Second, this was compared to longevity-regulating genes in germline-deficient animals (see series GSE37331). One-condition experiments. Germline ablated P. pacificus worms exposed to S. marcescens for 8 hours versus germline-ablated P. pacificus exposed to the control E. coli OP50. 4 biological replicates for each condition, including 2 dye-swaps.

2012-04-17 | E-GEOD-37337 | biostudies-arrayexpress

C. elegans germline-ablated (Z2-, Z3-) animals versus intact animals, N2 strain

Project description:Transcriptional profiling of C. elegans germline-ablated worms versus unablated intact animals, N2 strain One-condition experiment. C. elegans germline-ablated versus intact N2. 3 biological replicates, including 1 dye-swap.

2013-03-01 | E-GEOD-44702 | 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