DamID of Dam::LMN-1 and Dam::EMR-1 in Caenorhabditis elegans adult worms
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ABSTRACT: 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.
Project description:We show there is minimal genome-wide chromatin rearrangements (as measured by DNA accessibility) during tissue differentiation in C. elegans transgenic expression of E. coli DAM (DNA Adenine Methyltransferase) from tissue-specific promoters followed by mapping of methylated sites using a procedure that captures 20bp sequences flanking methylated sites for Illumina sequencing PD3994 = transgenic line expressing DAM from myo-3 promoter PD3995 = transgenic line expressing DAM from rol-6 promoter PD3997 = transgenic line expressing DAM from vit-2 promoter N2dam = wildtype (N2) line; its genomic DNA was in vitro DAM-methylated parsed = Solexa reads in which linker sequences were successfully parsed out by the authors WS170DAMtags_ALL.txt = the set of all in_silico-generated DAM tags from C. elegans genome version WS170
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.
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 RNA-Seq analysis in adult C. elegans nematodes comparing gene expression in wild type and single and double mutants of two components of the NE, EMR-1 and LEM-2. Our data confirm that EMR-1 and LEM-2 facilitate gene repression and that both proteins control the expression of mainly muscle and neuronal genes. mRNA profiles of wild type, emr-1(gk119), lem-2(tm1582) and emr-1(RNAi) lem-2(tm1582) young adult worms were generated by deep sequencing, in triplicate for the wild type and duplicates for the other backgrounds, using Illumina GAIIx.
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 RNA-Seq analysis in adult C. elegans nematodes comparing gene expression in wild type and single and double mutants of two components of the NE, EMR-1 and LEM-2. Our data confirm that EMR-1 and LEM-2 facilitate gene repression and that both proteins control the expression of mainly muscle and neuronal genes.
Project description:Comr protein was found to be a major regulator of gene activity in drosophila spermatocytes. We obtained Comr binding profile to determine targets of Comr. Comr binding in drosophila male germ line cells was determined using DamID technique. Comparison of Dam-Comr binding to Dam-alone signal in duplicate for each sample type.
Project description:Genome-wide identification of the binding sites of the Drosophila transcription factors Achaete, Asense, E(spl)m3-HLH and Senseless in wing imaginal cells using DamID profiling. Each Dam-fusion-derived sample is compared to a control Dam-only sample. Two biological replicates were performed for sca-Asense, neur-Asense, sca-Achaete, neur-Achaete, neur-Sens and sca-E(spl)m3-HLH.
Project description:CEH-60 binding profile by comparison of DNA methylation of a C. elegans strain expression ceh-60::dam to a control strain expressing gfp::dam. Sequencing libraries prepared using NEBNext Singleplex oligos for Illumina®. Data analysis performed with GeneDamIDseq (Sharma, Ritler, and Meister 2016).
Project description:LET-418/Mi-2 is an ATP-dependent chromatin remodeler and is part of large complexes like the NuRD complex which are repressive complex and has a role in vulval development in Caenorhabditis elegans. Along with MEP-1, LET-418 also forms the MEC complex which functions in the post embryonic development of the nematode. Earlier studies have shown that there is extensive chromatin remodeling taking place in the intestinal tissue. This study is aimed at deciphering the binding targets of LET-418 and MEP-1 in the intestine using DamID technique. Around 4500 worms were collected from each genotype (let-418::dam, mep-1::dam and gfp::dam) in two replicates. Sequencing and data analysis was performed according to (GOMEZ-SALDIVAR et al. 2021)
Project description:SUUR protein was found to be a major component of three repressive chromatin states named BLACK, BLUE and GREEN chromatins. Here we addressed a question of developmental dynamics of these chromatin states using SUUR as a marker. SUUR binding in larval salivary glands, brains and 12-14 hours embryos was determined using DamID technique. Comparison of Dam-SUUR binding to Dam-alone signal in duplicate for each sample type.
Project description:Paper abstract: The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of isolated these neurons. Their profiles were similarly enriched in cell-type-specific enhancers of genes implicated in neural development. We identified a total of 429 target genes, of which 56 were common to Ab and Kn; these targets included genes necessary to shape dendritic arbors in either or both of the two sensory subtypes. Furthermore, a common target gene, encoding the cell adhesion molecule Ten-m, was expressed more strongly in class I than IV, and this differential was critical to the class-selective directional control of dendritic branch sprouting or extension. Our analyses illustrate how differentiating neurons employ distinct and shared repertoires of gene expression to produce class-selective morphological traits. Each Dam-fusion-derived sample is compared to a control Dam-only sample. Four biological replicates were performed.