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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE62685 | GEO | 2015/03/09

SECONDARY ACCESSION(S): PRJNA264798

REPOSITORIES: GEO

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Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells.

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 evaluate whether lamins are necessary for the LAD organization in murine embryonic stem cells. Surprisingly, removal of essentially all lamins does not have any detectable effect on the genome-wide interaction pattern of chromatin with emerin, a marker of the inner nuclear membrane. This suggests that other components of the lamina mediate these interactions.

| S-EPMC4428043 | biostudies-literature

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

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

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. 2 samples, each with a biological replicate: wt mESC, B type lamin null (dKO) dKO mESC

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

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

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 | GSE62684 | GEO

Mouse B-type lamins are required for proper organogenesis but not by embryonic stem cells.

Project description:B-type lamins, the major components of the nuclear lamina, are believed to be essential for cell proliferation and survival. We found that mouse embryonic stem cells (ESCs) do not need any lamins for self-renewal and pluripotency. Although genome-wide lamin-B binding profiles correlate with reduced gene expression, such binding is not directly required for gene silencing in ESCs or trophectoderm cells. However, B-type lamins are required for proper organogenesis. Defects in spindle orientation in neural progenitor cells and migration of neurons probably cause brain disorganizations found in lamin-B null mice. Thus, our studies not only disprove several prevailing views of lamin-Bs but also establish a foundation for redefining the function of the nuclear lamina in the context of tissue building and homeostasis.

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Role of Fft3 in nuclear organization

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-03-02 | E-GEOD-58013 | biostudies-arrayexpress

Wash regulates lamin-dependent nuclear genome organization

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-03-10 | GSE59854 | GEO

TSA-Seq Mapping of Nuclear Genome Organization

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-04-25 | GSE66019 | GEO

Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-08-31 | GSE108801 | GEO

Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells.

Project description:During differentiation, thousands of genes are repositioned toward or away from the nuclear envelope. These movements correlate with changes in transcription and replication timing. Using synthetic (TALE) transcription factors, we found that transcriptional activation of endogenous genes by a viral trans-activator is sufficient to induce gene repositioning toward the nuclear interior in embryonic stem cells. However, gene relocation was also induced by recruitment of an acidic peptide that decondenses chromatin without affecting transcription, indicating that nuclear reorganization is driven by chromatin remodeling rather than transcription. We identified an epigenetic inheritance of chromatin decondensation that maintained central nuclear positioning through mitosis even after the TALE transcription factor was lost. Our results also demonstrate that transcriptional activation, but not chromatin decondensation, is sufficient to change replication timing.

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