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DamID of Dam::LMN-1 and Dam::EMR-1 in Caenorhabditis elegans adult worms

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.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE44188 | GEO | 2013/12/02

SECONDARY ACCESSION(S): PRJNA189179

REPOSITORIES: GEO

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DamID of Dam::LMN-1 and Dam::EMR-1 in Caenorhabditis elegans adult worms

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

Next generation sequencing facilitates quantitative analysis of Caenorhabditis elegans N2 wild type, emr-1(gk119), lem-2(tm1582) and emr-1(RNAi) lem-2(tm1582) transcriptomes.

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.

2013-12-02 | E-GEOD-44682 | biostudies-arrayexpress

Next generation sequencing facilitates quantitative analysis of Caenorhabditis elegans N2 wild type, emr-1(gk119), lem-2(tm1582) and emr-1(RNAi) lem-2(tm1582) transcriptomes.

2013-12-02 | GSE44682 | GEO

DamID: Loss of a heterochromatin anchor rescues altered genome organization and EDMD muscle defects triggered by a laminopathy mutation

Project description:Point mutations in nuclear structural protein laminA produce rare and generally tissue-specific diseases called laminopathies. The introduction of a human Emery Dreifuss Muscular Dystrophy (EDMD)-inducing mutation (laminA-Y45C) into C. elegans lamin (LMN-Y59C), recapitulates many EDMD phenotypes, and results in hyper-sequestration of heterochromatic arrays at the nuclear periphery. Using muscle-specific Emerin Dam-ID we show that the LMN-Y59C mutation also leads to misorganization of endogenous chromatin. We find increased perinuclear anchoring primarily along chromosome arms, and enhanced release of chromosomal cores. Coincidentally, Y59C worms have reduced locomotion and compromised sarcomere integrity. By coupling this mutation with deletion of the perinuclear chromodomain protein CEC-4, which tethers H3K9-methylated chromatin, we rescue the EDMD-like physiology and ultrastructural defects in sarcomeres. It further counteracts the altered spatial organization of chromosomal sequences, particularly along chromosomal arms. 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 muscle cells of L3/L4 control animals or cec-4 mutants expressing either GFP::LMN-1 (wild type lamin) or GFP::LMN-1(Y59C).

2020-12-31 | GSE135850 | GEO

Identification of PP2A-B55 targets in Drosophila uncovers regulation of Emerin during nuclear envelope reassembly

Project description:Entry into mitosis is triggered by mitotic kinases that phosphorylate multiple proteins to induce profound cellular changes including nuclear envelope breakdown, chromosome condensation and spindle assembly. Conversely, mitotic exit requires protein dephosphorylation as cells return to their interphase organization. Protein Phosphatase 2A in complex with its B55/Tws regulatory subunit (PP2A-B55) is known to play a crucial role in this transition. However, the precise events and substrates that it regulates are incompletely understood. We used proteomic approaches in Drosophila to identify proteins that interact with PP2A-B55 and are dephosphorylated in a PP2A-B55 dependent manner. Among several candidates, we identified Otefin (also known as Emerin) as a target of PP2A-B55 in the process of nuclear envelope reformation after mitosis. Emerin is a protein of the inner nuclear membrane that interacts with the DNA-binding protein Barrier-to-Autointegration Factor (BAF) via a LEM domain. Our results indicate that phosphorylation of Emerin at Ser50 and Ser54 near its LEM domain negatively regulates its association with BAF, Lamin and additional Emerin. Using live imaging, we show that dephosphorylation of Emerin at the identified sites determines the timing of nuclear envelope reformation. Genetic rescue experiments indicate that this regulation is required in vivo during embryonic development. Phosphoregulation of the Emerin-BAF complex formation by PP2A-B55 appears as a key event of mitotic exit that is likely to be conserved across species.

2023-08-10 | PXD041030 | Pride

Identification of PP2A-B55 targets in Drosophila uncovers regulation of Emerin during nuclear envelope reassembly

2023-08-10 | PXD041091 | Pride

Identification of PP2A-B55 targets in Drosophila uncovers regulation of Emerin during nuclear envelope reassembly

2023-08-10 | PXD041032 | Pride

RNA-seq: Loss of a heterochromatin anchor rescues altered genome organization and EDMD muscle defects triggered by a laminopathy mutation

Project description:Point mutations in nuclear structural protein lamin A produce rare, tissue-specific diseases called laminopathies. The introduction of a human Emery Dreifuss Muscular Dystrophy (EDMD)-inducing mutation (lamin A-Y45C) into C. elegans lamin (LMN-Y59C), recapitulates many EDMD phenotypes, and correlates with hyper-sequestration of heterochromatic arrays at the nuclear periphery. Using muscle-specific emerin Dam-ID, we also document the misorganization of endogenous chromatin in the LMN-Y59C mutant. We score increased perinuclear positioning along chromosome arms, and enhanced release within chromosomal cores. Coincidentally, Y59C worms have reduced locomotion and compromised sarcomere integrity. By coupling the Y59C mutation with deletion of the perinuclear chromodomain protein CEC-4, which tethers H3K9-methylated chromatin, we rescue the EDMD-like physiology and ultrastructural defects in sarcomeres. Deletion of cec-4 also rescued the Y59C-induced changes in chromatin organization. The promoters of genes that change position in the LMN-Y59C mutant, are enriched for E2F (EFL-1/-2) binding sites, consistent with previous studies implicating the Rb-E2F interaction with lamin A in muscle dysfunction. Gene expression changes provoked by LMN-Y59C are also largely reversed by cec-4 deletion. In summary, the ablation of a perinuclear H3K9me-anchor can counteract the dominant muscle-specific defects provoked by a laminopathic mutation, implicating peripheral chromatin organization in the control of muscle integrity.

2020-12-31 | GSE136576 | GEO

Gene expression analyses in otefin mutant Drosophila ovaries

Project description:LEM Domain proteins are key components of the nuclear lamina. Mutations in LEM-D proteins cause dystrophic diseases associated with compromised adult stem cells, yet it remains unclear how LEM-D proteins support stem cell function. Studies described here use the homologue of the LEM-D protein emerin in Drosophila, Otefin (Ote) as a model to understand LEM-D protein function in adult stem cells. Loss of Ote causes female sterility due to a complex germline stem cell (GSC) phenotype that includes both an early block in germline differentiation followed by GSC death. In vivo cell cycle analysis revealed that ote mutant GSCs display a lengthened S phase.We find that loss of the DNA Damage Response (DDR) Chk2 is able to not only rescue the lengthened S phase, but also GSC death and the block in germline differentiation. Activation of detrimental checkpoint in absence of Ote is conserved in both male and female GSCs and surprisingly occurs independent of detectable canonical DDR triggers, including transposon de-repression and DNA damage. Two defects were found to occur upstream of Chk2 activation: nuclear lamina morphological defects and altered heterochromatin organization. Together, our data identify the primary cause for a compromised adult stem cell population in the absence of a LEM-D protein.

2018-07-03 | GSE95309 | GEO

LEM-2 ChIP-seq to study chromatin anchoring

Project description:Chromatin Immunoprecipitation against the nuclear envelope protein LEM-2 to detect association to the nuclear periphery. LEM-2 ChIP was performed on early embryo fixed extracts for wild-type and two mutants that have altered position of a perinuclear chromatin reporter.

2015-12-11 | GSE74133 | GEO

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