Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA174286 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Studies using fluorescence in situ hybridization (FISH) have attempted to determine whether specific gene loci associate with promyelocytic leukemia nuclear bodies (PML NBs). Two drawbacks accompany this approach; the lack of spatial resolution inherent with the technique, and the a priori basis for selecting which genes to probe. To overcome these limitations, we developed a technique, which we call immunoTRAP, which purifies the DNA contacting PML NBs at molecular dimensions. When we combined the immunoTRAP technique with immunoFISH and microarray analysis, not only did we verify a TP53-PML NB association, but were able also to identify novel locus associations such as PML, ABCA7, and TFF1. In addition, we observed that these associations are cell type specific, and induction of significantly higher levels of PML gene expression, as well as other physiological changes brought about by interferon treatment, can lead to a physical association of the PML gene with PML NBs in normal human fibroblasts. Thus, immunoTRAP is a technique capable of identifying the chromatin associations around nuclear subcompartments and is amenable for further downstream applications such as microarray analysis or deep sequencing. Identification of binding (Cy5) to PML vs. to non-specific binding in Jurkat cells (n=5)
2013-03-28 | E-GEOD-40554 | biostudies-arrayexpress
Project description:Studies using fluorescence in situ hybridization (FISH) have attempted to determine whether specific gene loci associate with promyelocytic leukemia nuclear bodies (PML NBs). Two drawbacks accompany this approach; the lack of spatial resolution inherent with the technique, and the a priori basis for selecting which genes to probe. To overcome these limitations, we developed a technique, which we call immunoTRAP, which purifies the DNA contacting PML NBs at molecular dimensions. When we combined the immunoTRAP technique with immunoFISH and microarray analysis, not only did we verify a TP53-PML NB association, but were able also to identify novel locus associations such as PML, ABCA7, and TFF1. In addition, we observed that these associations are cell type specific, and induction of significantly higher levels of PML gene expression, as well as other physiological changes brought about by interferon treatment, can lead to a physical association of the PML gene with PML NBs in normal human fibroblasts. Thus, immunoTRAP is a technique capable of identifying the chromatin associations around nuclear subcompartments and is amenable for further downstream applications such as microarray analysis or deep sequencing.
2013-03-28 | GSE40554 | GEO
Project description:Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin. To address roles of PML bodies in transcriptional regulation, we performed RNA-seq analyses with wild-type and PMK knockout mESCs
2019-08-14 | GSE135557 | GEO
Project description:Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate functional roles of PML bodies in chromatin organization, we conducted ATAC-seq with wild-type and PML KO mESCs.
2019-08-14 | GSE135561 | GEO
Project description:Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate roles of PML bodies in transcriptional regulation, we conducted ChIP-seq analysis for histone modifications, including H3K4me3, H3K27ac, H3K27me3, and H3K9ac with wild-type and PML knockout mESCs.
2019-08-14 | GSE135562 | GEO
Project description:Emerging evidence reveals the critical role of the nuclear RNA-protein meshwork complex, termed nuclear matrix, in stabilizing chromatin architecture. While chromatin associates with transcriptional machinery within nuclear bodies to regulate gene expression through hierarchical architecture formation, how the nuclear matrix mediates chromatin-nuclear body associations and their spatial organization remains unclear. Here, we demonstrate that depletion of nuclear matrix factor SAF-A leads to genome-wide chromatin compaction and enhanced chromatin-speckle associations. Using super-resolution imaging and genomic analyses, we show that these chromatin organizational changes alter the inducibility of speckle-associated genes. Mechanistically, we reveal that nuclear matrix exhibits a layered spatial distribution, forming distinct compartments with RNA polymerase II clusters and chromatin in the perispeckle region. Our findings demonstrate that nuclear matrix maintains chromatin architecture and regulates gene expression through spatial coupling with nuclear bodies, providing new insights into the hierarchical organization of nuclear structure-function relationships.
2025-11-24 | GSE310526 | GEO
Project description:Emerging evidence reveals the critical role of the nuclear RNA-protein meshwork complex, termed nuclear matrix, in stabilizing chromatin architecture. While chromatin associates with transcriptional machinery within nuclear bodies to regulate gene expression through hierarchical architecture formation, how the nuclear matrix mediates chromatin-nuclear body associations and their spatial organization remains unclear. Here, we demonstrate that depletion of nuclear matrix factor SAF-A leads to genome-wide chromatin compaction and enhanced chromatin-speckle associations. Using super-resolution imaging and genomic analyses, we show that these chromatin organizational changes alter the inducibility of speckle-associated genes. Mechanistically, we reveal that nuclear matrix exhibits a layered spatial distribution, forming distinct compartments with RNA polymerase II clusters and chromatin in the perispeckle region. Our findings demonstrate that nuclear matrix maintains chromatin architecture and regulates gene expression through spatial coupling with nuclear bodies, providing new insights into the hierarchical organization of nuclear structure-function relationships.
2025-11-24 | GSE310525 | GEO
Project description:Emerging evidence reveals the critical role of the nuclear RNA-protein meshwork complex, termed nuclear matrix, in stabilizing chromatin architecture. While chromatin associates with transcriptional machinery within nuclear bodies to regulate gene expression through hierarchical architecture formation, how the nuclear matrix mediates chromatin-nuclear body associations and their spatial organization remains unclear. Here, we demonstrate that depletion of nuclear matrix factor SAF-A leads to genome-wide chromatin compaction and enhanced chromatin-speckle associations. Using super-resolution imaging and genomic analyses, we show that these chromatin organizational changes alter the inducibility of speckle-associated genes. Mechanistically, we reveal that nuclear matrix exhibits a layered spatial distribution, forming distinct compartments with RNA polymerase II clusters and chromatin in the perispeckle region. Our findings demonstrate that nuclear matrix maintains chromatin architecture and regulates gene expression through spatial coupling with nuclear bodies, providing new insights into the hierarchical organization of nuclear structure-function relationships.
2025-11-24 | GSE310524 | GEO
Project description:Emerging evidence reveals the critical role of the nuclear RNA-protein meshwork complex, termed nuclear matrix, in stabilizing chromatin architecture. While chromatin associates with transcriptional machinery within nuclear bodies to regulate gene expression through hierarchical architecture formation, how the nuclear matrix mediates chromatin-nuclear body associations and their spatial organization remains unclear. Here, we demonstrate that depletion of nuclear matrix factor SAF-A leads to genome-wide chromatin compaction and enhanced chromatin-speckle associations. Using super-resolution imaging and genomic analyses, we show that these chromatin organizational changes alter the inducibility of speckle-associated genes. Mechanistically, we reveal that nuclear matrix exhibits a layered spatial distribution, forming distinct compartments with RNA polymerase II clusters and chromatin in the perispeckle region. Our findings demonstrate that nuclear matrix maintains chromatin architecture and regulates gene expression through spatial coupling with nuclear bodies, providing new insights into the hierarchical organization of nuclear structure-function relationships.
2025-11-24 | GSE310528 | GEO
Project description:Emerging evidence reveals the critical role of the nuclear RNA-protein meshwork complex, termed nuclear matrix, in stabilizing chromatin architecture. While chromatin associates with transcriptional machinery within nuclear bodies to regulate gene expression through hierarchical architecture formation, how the nuclear matrix mediates chromatin-nuclear body associations and their spatial organization remains unclear. Here, we demonstrate that depletion of nuclear matrix factor SAF-A leads to genome-wide chromatin compaction and enhanced chromatin-speckle associations. Using super-resolution imaging and genomic analyses, we show that these chromatin organizational changes alter the inducibility of speckle-associated genes. Mechanistically, we reveal that nuclear matrix exhibits a layered spatial distribution, forming distinct compartments with RNA polymerase II clusters and chromatin in the perispeckle region. Our findings demonstrate that nuclear matrix maintains chromatin architecture and regulates gene expression through spatial coupling with nuclear bodies, providing new insights into the hierarchical organization of nuclear structure-function relationships.
2025-11-26 | GSE311138 | GEO