Lamina Associated Domains dependent of chromatin state and A-type lamins
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA380656 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12162920.fastq.gz | Fastqsanger.gz | |||
| SRR12162921.fastq.gz | Fastqsanger.gz | |||
| SRR12162922.fastq.gz | Fastqsanger.gz | |||
| SRR12162923.fastq.gz | Fastqsanger.gz | |||
| SRR12162924.fastq.gz | Fastqsanger.gz |
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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
Project description:B-type lamins (Lamin B1 and B2) are key components of the nuclear lamina and play essential roles in three-dimensional (3D) chromatin organization by anchoring Lamina-Associated Domains (LADs). Recent studies have indicated that abnormal gene expression resulting from B-type lamin loss occurs in both LAD and non-LAD regions; however, the underlying molecular mechanisms remain unclear. In this study, we demonstrate that the majority of differentially expressed genes (DEGs) in B-type lamin-depleted cells are predominantly located in non-LAD regions, which are characterized by a constitutive association with nuclear speckles. Through RNA-Seq combined with SC35 Tyramide Signal Amplification Sequencing (TSA-Seq) analysis, we find that aberrant gene regulation is closely associated with the repositioning of chromatin either toward or away from nuclear speckles. The absence of B-type lamins causes a global reorganization of chromatin rather than changes in its fine structure, leading to the disruption of constitutive Speckle-Associated Domains (cSPADs). Additionally, the loss of B-type lamins results in euchromatin deactivation and heterochromatin de-repression, which impairs cell viability by increasing apoptotic signaling and causes defective mRNA splicing. Our data reveal a novel role for B-type lamins in regulating transcriptional activity by conserving genome architecture between the nuclear lamina and nuclear speckles.
2026-04-08 | GSE275661 | GEO
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
Project description:B-type lamins (Lamin B1 and B2) are key components of the nuclear lamina and play essential roles in three-dimensional (3D) chromatin organization by anchoring Lamina-Associated Domains (LADs). Recent studies have indicated that abnormal gene expression resulting from B-type lamin loss occurs in both LAD and non-LAD regions; however, the underlying molecular mechanisms remain unclear. In this study, we demonstrate that the majority of differentially expressed genes (DEGs) in B-type lamin-depleted cells are predominantly located in non-LAD regions, which are characterized by a constitutive association with nuclear speckles. Through RNA-Seq combined with SC35 Tyramide Signal Amplification Sequencing (TSA-Seq) analysis, we find that aberrant gene regulation is closely associated with the repositioning of chromatin either toward or away from nuclear speckles. The absence of B-type lamins causes a global reorganization of chromatin rather than changes in its fine structure, leading to the disruption of constitutive Speckle-Associated Domains (cSPADs). Additionally, the loss of B-type lamins results in euchromatin deactivation and heterochromatin de-repression, which impairs cell viability by increasing apoptotic signaling and causes defective mRNA splicing. Our data reveal a novel role for B-type lamins in regulating transcriptional activity by conserving genome architecture between the nuclear lamina and nuclear speckles.
2026-04-08 | GSE275659 | GEO
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
Project description:Three-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.
2020-03-27 | GSE124205 | GEO
Project description:Three-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.
2020-03-27 | GSE97092 | GEO
Project description:Lamins are the major structural components of the nuclear lamina (NL) beneath the inner nuclear membrane. Although lamins are believed to regulate genome organization and transcription, how they perform these functions remains poorly understood. Combining Hi-C with fluorescence in situ hybridization (FISH) and Histone and Lamina landscape (HiLands) analyses of chromatin domains, we show that lamins differentially regulate the NL-associated HiLands-P and -B domains in mouse ES cells (mESCs). Lamin loss leads to HiLands-P expansion at the NL, detachment of HiLands-B from the NL, and genome-wide changes of 3D chromatin interactions in NL-associated and interior HiLands in mESCs. Further epigenome and transcriptome analyses show that lamins can function from the NL to maintain the boundaries of active and repressive chromatin domains, thereby influencing gene expression throughout the genome. These findings should provide the basis to further understand how changes in the NL-associated chromatin influence transcription in development and NL-associated diseases.
2017-11-01 | GSE89520 | GEO
Project description:Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to lamin B1, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, lamin B1 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin. Examination of LaminA, LaminB and Lap2a DNA binding in Lap2alpha +/+ and Lap2a -/- cells and according changes in Histone modifications and gene expression
2016-01-19 | E-GEOD-70148 | biostudies-arrayexpress
Project description:Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to Lamin B11, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, Lamin B11 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin. Examination of Lamin A/C, Lamin B1 and Lap2a DNA binding in Lap2alpha +/+ and Lap2a -/- cells and according changes in Histone modifications and gene expression
2016-01-19 | E-GEOD-70147 | biostudies-arrayexpress