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ABSTRACT: Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells

PROVIDER: PRJNA264798 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1623081.fastq.gz	Fastqsanger.gz
	SRR1623082.fastq.gz	Fastqsanger.gz
	SRR1623083.fastq.gz	Fastqsanger.gz
	SRR1623084.fastq.gz	Fastqsanger.gz

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

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Mus musculus

Project description:Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells [RNA-Seq]

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Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

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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

B-type lamins differentially associate with specific genes during differentiation without directly affecting their expression

Project description:B-type lamins, the major structural component of the nuclear lamina, is thought to play a repressive role in the expression of many of its bound genes whose silencing are known to be critical for cell differentiation during early development. Using global mapping of lamin-B-chromatin interaction, we find that the binding to lamin-B indeed correlated with gene silencing in mouse embryonic stem cells (ESC) and ESC-derived trophectoderm (TE) lineage cells. To address whether lamin-B directly suppresses the expression of the bound genes, we have derived ESCs from lamin-B-null mouse blastocysts. Unexpectedly, microarray analyses of ESCs and TE cells show that B-type lamins do not repress the expression of their bound genes. Furthermore, the knockout mice that do not express any B-type lamins can develop to term but exhibit small body size and perinatal lethality. Our studies demonstrate that B-type lamins are not required for cell differentiation during early embryonic development. Instead, they are required for proper late embryonic and perinatal development. The availability of the null ESCs and mice opens the door to further define the functions of B-type lamins.

2011-10-31 | GSE24532 | 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.

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Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells [RNA-Seq]

2015-03-10 | E-GEOD-62684 | biostudies-arrayexpress

Recruitment to the nuclear periphery enhances repression of H3K9me2-marked genes and transposons to shape cell fate [CUT&Run]

Project description:Heterochromatic loci marked by histone H3 lysine 9 dimethylation (H3K9me2) are enriched at the nuclear periphery in metazoans, but the functional importance of this organization is unknown. Both the nuclear lamins and the nuclear membrane protein lamin B receptor (LBR) have been linked to heterochromatin positioning in mammals, yet embryonic stem cells (mESCs) lacking all lamins retain both LBR and H3K9me2 at the nuclear periphery. We ablated LBR in this context and show that heterochromatin detaches from the nuclear periphery in lamin + LBR quadruple knockout (QKO) cells. QKO mESCs sustain naïve pluripotency and maintain H3K9me2 at normal levels across the genome but cannot repress H3K9me2-marked genes or transposons. Further, their capacity to differentiate into epiblast-like cells (EpiLCs) is impaired. While normal EpiLCs expand H3K9me2 across the genome, QKO EpiLCs exhibit abnormal patterning of this mark. QKO cells can exit naïve pluripotency and activate epiblast-stage genes but also express markers of alternative fates including the primitive endoderm. These results establish that recruitment of H3K9me2 to the nuclear periphery controls the spatial position, dynamic remodeling, and repressive capacity of this mark to shape cell fate decisions.

2024-08-09 | GSE264603 | GEO

Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells [RNA-Seq]

2015-03-10 | GSE62684 | GEO

DamID-based chromatin profiling of dHey in Kc cells

Project description: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

2019-07-15 | GSE87895 | GEO

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