DamID of Dam::EMR-1 in Caenorhabditis elegans L1 larvae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA520793 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Laminopathies are caused by mutations in components of the nuclear envelope (NE). While most NE components are widely expressed, laminopathies affect only a subset of tissues. However, the understanding of the molecular mechanisms that explain this phenomenon is still elusive. Here we have performed a genome wide DamID analysis in adult C. elegans nematodes comparing the DNA association profile of two components of the NE, Lamin/LMN-1 and Emerin/EMR-1. Although both proteins were associated to silent DNA, EMR-1 showed a predominant role in the anchoring of muscle and neuronal promoters to the nuclear periphery. Deletion of either EMR-1 or LEM-2, another integral NE protein, caused local changes in nuclear architecture with both increased and decreased LMN-1 association. Comparison of Dam::LMN-1 and Dam::EMR-1 DNA assotiation in wild type strains and Dam::LMN-1 DNA association in wild type, lem-2(tm1582) and emr-1(gk119) mutant backgrounds.
2013-12-02 | E-GEOD-44188 | biostudies-arrayexpress
Project description:The execution of developmental programs of gene expression requires an accurate partitioning of the genome into distinct compartments, with heterochromatin enriched at the nuclear periphery. In C. elegans embryonic cells, the methylation of histone H3 lysine 9 (H3K9me) is critical for peripheral anchoring via the chromodomain protein CEC-4, while alternative, H3K9me-independent pathway(s) function in differentiated tissues. An RNAi screen unexpectedly identified the euchromatin factor MRG-1, which binds H3K36me2/me3 domains, as necessary for heterochromatin sequestration in differentiated cells. The data in this submission refer to the identification of chromatin enriched at the nuclear periphery (as measured by interaction with Dam::EMR-1) in intestinal cells of control, singly depleted cec-4 or mrg-1 or doubly depleted cec-4 mrg-1 animals.
2019-04-12 | GSE126028 | GEO
Project description:Laminopathies are caused by mutations in components of the nuclear envelope (NE). While most NE components are widely expressed, laminopathies affect only a subset of tissues. However, the understanding of the molecular mechanisms that explain this phenomenon is still elusive. Here we have performed a genome wide DamID analysis in adult C. elegans nematodes comparing the DNA association profile of two components of the NE, Lamin/LMN-1 and Emerin/EMR-1. Although both proteins were associated to silent DNA, EMR-1 showed a predominant role in the anchoring of muscle and neuronal promoters to the nuclear periphery. Deletion of either EMR-1 or LEM-2, another integral NE protein, caused local changes in nuclear architecture with both increased and decreased LMN-1 association.
2013-12-02 | GSE44188 | GEO
Project description:To adapt RNA polymerase DamID (RAPID) for FLP-mediated spatial control in Caenorhabditis elegans, we inserted a Dam::rpb-6 fusion gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the hsp-16.41 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver to enable basal Dam::rpb-6 expression in the hypodermis. Nematodes were cultured at 20 degrees Celcius to ensure low levels of Dam::RPB-6 expression in the hypodermis and total genomic DNA was purified from L4 larvae. DNA from animals expressing GFP::Dam was used to control for unspecific methylation. The genome-wide association profile of Dam::RPB-6 was determined by deep sequencing, which revealed a list of 2331 protein coding genes with FDR < 0.05. Original RAPID reference: Gomez-Saldivar et al (2020) Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 216, 931–945. doi:10.1534/genetics.120.303774
2022-09-30 | GSE214300 | GEO
Project description:Comparison of DamID profiles and LAD patterning across cell types reveals regions of variable LADs LmnB1 interactions at the nuclear periphery of C57Bl/6 pro-B cells and fibroblasts were identified by DamID in duplicate for both pro-B and fibroblasts (4 samples total). For each sample, Dam-LmnB1/Dam-only Log2 ratios of chromosomes 11 and 12 were calculated, lifted over to mm9, duplicates were normalized and averaged together.
2014-12-16 | E-GEOD-56990 | biostudies-arrayexpress
Project description:DamID of Dam::LMN-1 and Dam::EMR-1 in Caenorhabditis elegans adult worms
| PRJNA189179 | ENA
Project description:We have adapted the DamID protocol for use with high throughput sequencing. We have used DamID to identify the positions within the Drosophila genome where the transcription factor DSX is bound. We sequenced DpnI-digested genomic DNA from fly tissues containing UAS-Dam (control) or UAS-Dam-DsxF or UAS-Dam-DsxM.
2014-10-30 | GSE27269 | GEO
Project description:We have adapted the DamID protocol for use with high throughput sequencing. We have used DamID to identify the positions within the Drosophila genome where the transcription factor DSX is bound. We sequenced DpnI-digested genomic DNA from fly tissues containing UAS-Dam (control) or UAS-Dam-DsxF or UAS-Dam-DsxM. We have performed DamID-seq on adult male and female fatbody and on ovary. We used two biological replicates for each tissue and sex.
2014-10-30 | E-GEOD-27269 | biostudies-arrayexpress
Project description:Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. We determined DamID scores for Polycomb, normalized by Dam only control, for Drosophila larval central brain, larval fat bodies and repo+ glial cells of larval central brain. All samples were performed with 2 biological replicates. In case of Dam only control for larval central brain, each biological replicate was performed with 3 technical replicates.
2016-03-17 | E-GEOD-75831 | biostudies-arrayexpress
Project description:DamID, in which a protein of interest is fused to Dam methylase, enables mapping of protein-DNA binding through readout of adenine methylation in genomic DNA. DamID offers a compelling alternative to chromatin immunoprecipitation sequencing (ChIP-Seq), particularly in cases where cell number or antibody availability are limiting. This comes at a cost, however, of high non-specific signal and a lowered spatial resolution of several kb, limiting its application to transcription factor-DNA binding. Here we show that mutations in Dam, when fused to the transcription factor Tcf7l2, greatly reduce non-specific methylation. Combined with a simplified DamID sequencing protocol, we find that these Dam mutants allow for accurate detection of transcription factor binding at a sensitivity and spatial resolution closely matching that seen in ChIP-seq.
2019-01-23 | GSE125447 | GEO