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DamID-based chromatin profiling of dHey in Kc cells

ABSTRACT: Chromatin binding profiling showed that dHey binds to enhancers in order to maintain EC identity, and co-regulates nuclear organization by governing a switch in the expression of nuclear lamins. Moreover, like dHey loss, de-regulated expression of lamins override identity programs. Thus, a single TF concomitantly orchestrates chromatin state, enhancer activity, and nuclear organization safeguarding differentiated cell identity Chromatin profiling using Dam-dHey shows preferential recruitment to enhancers and transcriptionally active regions. Manuscript title: Specification and maintenance of enterocyte identity requires dHey and nuclear lamins

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE87895 | GEO | 2019/07/15

REPOSITORIES: GEO

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Transcriptome analysis of dHey knock down and control enterocytes, as well as isolated enteroblasts

Project description:Gene expression analses of adult female gut and purified gut cells. Using the adult Drosophila gut, we found that the transcription factor dHey is a critical identity coordinator of differentiated enterocytes (EC`combined expression analyses with chromatin binding profiling showed that dHey determines activity of enhancers in order to maintain EC identity, and co-regulates nuclear organization by governing a switch in the expression of nuclear lamins. Moreover, like dHey loss, de-regulated expression of lamins overrode identity programs. Thus, a single TF concomitantly orchestrates chromatin state, enhancer activity, and nuclear organization safeguarding differentiated cell identity. Conditional dHey knock down in enterocytes (EC) results in loss of the differnetated identity of entrocytes and impacts gut homeostasis. In addtion Using purified Enteroblast (EB) we mappaed the changes in gene expression during EB to EC differentiation, and the impact of dhey on the gene expression of EBs. Manuscript title: Specification and maintenance of enterocyte identity requires dHey and nuclear lamins

2019-07-15 | GSE87894 | GEO

RNAseq analysis of whole Guts over expressing LaminDm0 or GFP in Enterocytes

Project description:A hallmark of aging-related disease such as neurodegeneration, metabolic disorders, and cancer is the inability of differentiated cells to maintain their identity. In a search for identity regulators, we found that transcription factor Hey supervises the identity of differentiated enterocytes (ECs) in the adult Drosophila midgut. Lineage tracing of ECs established that Hey-deficient ECs lose differentiated identity, are unable to maintain their unique nuclear organization, and exhibit pathological reprograming. Orchestrating this organization, Hey specifies and maintains enhancer activity and nuclear lamins expression, remodeling nuclear architecture from a stem-cell configuration into a differentiated one. Moreover, maintaining this configuration of nuclear lamins is key for cell identity, and lamin misexpression overrides cell identities. At the tissue level, loss of Hey or expression of stem cell-related lamin (LamDm0) in ECs resulted in mis-differentiation, impaired epithelial integrity, and reduced organismal survival. Thus, a single transcription factor concomitantly supervises chromatin and nuclear organization, safeguarding cell identity

2019-07-15 | GSE112640 | GEO

Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells [DamID]

Project description:In mammals, the nuclear lamina interacts with hundreds of large genomic regions, termed lamina-associated domains (LADs) that are generally in a transcriptionally repressed state. Lamins form the major structural component of the lamina and have been reported to bind DNA and chromatin. Here we systematically evaluated whether lamins are necessary for the peripheral localization of LADs in murine embryonic stem cells. Surprisingly, removal of essentially all lamins did not have any detectable effect on the genome-wide interaction pattern of chromatin with the inner nuclear membrane. This suggests that other components of the inner nuclear membrane mediate these interactions.

2015-03-10 | GSE62683 | GEO

The nuclear envelope protein Net39 is essential for muscle nuclear integrity and chromatin organization

Project description:Lamins and transmembrane proteins within the nuclear envelope regulate nuclear structure and chromatin organization. Nuclear Envelope Transmembrane Protein 39 (Net39) is muscle nuclear envelope protein whose functions in vivo have not been explored. We show that mice lacking Net39 succumb to severe myopathy and juvenile lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression and metabolism. These abnormalities resemble those of Emery-Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type Lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings highlight the role of Net39 at the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and its potential contribution to the molecular etiology of EDMD.

2020-11-23 | GSE154850 | GEO

The nuclear envelope protein Net39 is essential for nuclear integrity, chromatin organization, and muscle growth (ATAC-Seq)

Project description:Lamins and transmembrane proteins within the nuclear envelope are regulators of nuclear structure and chromatin organization. Nuclear Envelope Transmembrane Protein 39 (Net39) is a muscle-restricted nuclear envelope protein. We show that mice lacking Net39 succumb to severe myopathy and neonatal lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression and metabolism. These abnormalities resemble those of Emery-Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type Lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings reveal an intimate role for the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and highlight the importance of Net39 in these processes and in the molecular etiology of EDMD.

2020-11-24 | GSE154847 | GEO

The nuclear envelope protein Net39 is essential for nuclear integrity, chromatin organization, and muscle growth (RNA-Seq)

2020-11-24 | GSE154849 | GEO

The nuclear envelope protein Net39 is essential for nuclear integrity, chromatin organization, and muscle growth (ChIP-Seq)

2020-11-24 | GSE154848 | GEO

EDD: a program for detection of wide genomic enrichment domains robust against local variations [RNA-Seq]

Project description:Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome-wide. We disclose a novel algorithm, Enriched Domain Detector (EDD), for analysis of broad enrichment domains from ChIP-seq data. EDD enables discovery of genomic domains interacting with broadly distributed chromatin-associated proteins such as lamins. The main advantage of EDD over existing broad peak callers is sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations. EDD is downloadable from http://github.com/eivindgl/edd. RNA-seq experiments in human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs).

2014-04-25 | E-GEOD-54333 | biostudies-arrayexpress

EDD: a program for detection of wide genomic enrichment domains robust against local variations [ChIP-Seq]

Project description:Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome-wide. We disclose a novel algorithm, Enriched Domain Detector (EDD), for analysis of broad enrichment domains from ChIP-seq data. EDD enables discovery of genomic domains interacting with broadly distributed chromatin-associated proteins such as lamins. The main advantage of EDD over existing broad peak callers is sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations. EDD is downloadable from http://github.com/eivindgl/edd. LMNA ChIP-seq experiments in human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs).

2014-04-25 | E-GEOD-54332 | biostudies-arrayexpress

Lamin binding profiles in the ENCODE regions

Project description:A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the biological processes in which chromatin remodeling proteins participate we globally mapped binding regions for several components of the SWI/SNF complex throughout the human genome using ChIP-Seq. SWI/SNF components were found to lie near regulatory elements integral to transcription (e.g. 5’ ends, RNA Polymerases II and III and enhancers) as well as regions critical for chromosome organization (e.g. CTCF, lamins and DNA replication origins). To further elucidate the association of SWI/SNF subunits with each other as well as with other nuclear proteins we also analyzed SWI/SNF immunoprecipitated complexes by mass spectrometry. Individual SWI/SNF factors are associated with their own family members as well as with cellular constituents such as nuclear matrix proteins, key transcription factors and centromere components implying a ubiquitous role in gene regulation and nuclear function. We find an overrepresentation of both SWI/SNF-associated regions and proteins in cell cycle and chromosome organization. Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated. ChIP-chip analysis of lamin A/C and lamin B in HeLa S3 cells

2011-01-10 | E-GEOD-24382 | biostudies-arrayexpress

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