Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the Drosophila genome at the nuclear lamina

ABSTRACT: The nuclear lamina (NL) binds chromatin in vitro and is thought to function in its organisation, but genes that interact with the NL are unknown. Using an in vivo approach we identified 474 Drosophila genes that interact with B–type lamin, Lam. These genes are transcriptionally silent, late replicating, lack active histone marks, and are widely spaced. These factors collectively predict Lamin binding behavior, indicating the NL integrates variant and invariant chromatin features. Consistently, NE proximity is partly conserved between cell types and induction of gene expression or active histone marks reduces Lam binding. Lam target genes cluster in the genome, and these clusters are coordinately expressed during development. This genome-wide analysis gives clear insight into the nature and dynamic behavior of the genome at the NL. Keywords: DamID and expression profiling

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE5089 | GEO | 2006/08/29

SECONDARY ACCESSION(S): PRJNA95393

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Spatially restricted position-dependent implications of lamin A promoter occupancy on gene activity (expression)

Project description:Interactions between the nuclear lamina (NL) and chromatin are thought to occur through large lamin association domains (LADs) and correlate with gene repression in these domains. We show that binding of lamin A/C (LMNA) to promoters occurs on discrete domains that are associated with distinct transcriptional outputs. Chromatin immunoprecipitation identifies thousands of LMNA-bound promoters, primarily linked to signaling functions. LMNA often occupies narrow domains on promoters, yet LMNA-bound promoters are often contiguous. LMNA-bound genes are overall repressed, but repression correlates with co-enrichment in repressive histone marks rather than LMNA occupancy per se. Genes marked by LMNA and H3K4me3 escape LMNA-associated repression in the absence of repressive histone marks. Positioning of LMNA on promoters relative to the TSS correlates with distinct transcriptional outputs: whereas upstream-distal binding can be transcriptionally permissive, TSS occupancy is associated with promoter inactivity. Perturbation in NL organization causes reorganization of lamin promoter occupancy and uncouples LMNA binding from promoter inactivity. Our results show the existence of many spatially restricted LMNA binding events on promoter regions, with distinct position-dependent transcriptional outputs. Total RNA obtained from ASCs and ASCs depleted of LMNA (LMNA-KD) and processed for microarray hybridization.

2013-07-14 | E-GEOD-42523 | biostudies-arrayexpress

The nuclear lamina maintains global spatial organization of chromatin in Drosophila

Project description:The nuclear lamina (NL) is a meshwork of lamins and lamin-associated proteins lining the nuclear envelope (NE). Chromatin adjoining the NL in lamina-associated domains (LADs) is densely packed and contains predominantly silent genes. However, how the NL impacts on global chromatin architecture is poorly understood. Here, we show that NL disruption in Drosophila S2 cells leads to bulk chromatin compactization and repositioning from the NE. This increases the chromatin density in the topologically-associating domains (TADs) harboring active genes, and enhances inter-TAD interactions resulting in the intermingling of active and inactive compartments. Importantly, upon NL disruption, a fraction of TADs strongly overlapping with LADs becomes less compact, whilst resident genes are derepressed. Two-color FISH confirms that a a TAD is more decompacted following its release from the NL. Finally, polymer simulations show that chromatin binding to the NL can per se compact attached TADs. Collectively, our findings demonstrate a dual function of the NL in shaping the 3D genome. Attachment of TADs to the NL makes them more condensed but decreases the overall chromatin density in the nucleus by stretching interphase chromosomes.

2019-02-08 | GSE110082 | GEO

Stochastic genome-nuclear lamina interactions: Modulating roles of Lamin A and BAF

Project description:The nuclear lamina (NL) is a filamentous layer lining the inner-nuclear-membrane (INM) that aids in the organization of the genome in large domains of low transcriptional activity. Recently, it was shown that the single-cell genome-NL interactions are much more dynamic than previously anticipated, which challenges the concept of the NL as a safe guard for transcriptional repressed genes. Here we discuss the role of the NL in light of these new findings and introduce Lamin A and BAF as potential modulators of LAD positioning BAF-chromatin and Lamin B2-chromatin interactions were assayed in human HT1080 by DamID on Nimblegen microarrays, with two biological replicates each, that were hybridized in a dye-swap design.

2014-02-15 | E-GEOD-55066 | biostudies-arrayexpress

Lamins organize the three dimensional genome from nuclear periphery in ES cells

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

Spatially restricted position-dependent implications of lamin A promoter occupancy on gene activity (expression)

2013-07-14 | GSE42523 | GEO

Spatially restricted position-dependent implications of lamin A promoter occupancy on gene activity (ChIPs and MeDips)

2013-07-14 | GSE42522 | GEO

Spatially restricted position-dependent implications of lamin A promoter occupancy on gene activity (ChIPs and MeDips)

Project description:Interactions between the nuclear lamina (NL) and chromatin are thought to occur through large lamin association domains (LADs) and correlate with gene repression in these domains. We show that binding of lamin A/C (LMNA) to promoters occurs on discrete domains that are associated with distinct transcriptional outputs. Chromatin immunoprecipitation identifies thousands of LMNA-bound promoters, primarily linked to signaling functions. LMNA often occupies narrow domains on promoters, yet LMNA-bound promoters are often contiguous. LMNA-bound genes are overall repressed, but repression correlates with co-enrichment in repressive histone marks rather than LMNA occupancy per se. Genes marked by LMNA and H3K4me3 escape LMNA-associated repression in the absence of repressive histone marks. Positioning of LMNA on promoters relative to the TSS correlates with distinct transcriptional outputs: whereas upstream-distal binding can be transcriptionally permissive, TSS occupancy is associated with promoter inactivity. Perturbation in NL organization causes reorganization of lamin promoter occupancy and uncouples LMNA binding from promoter inactivity. Our results show the existence of many spatially restricted LMNA binding events on promoter regions, with distinct position-dependent transcriptional outputs. ChIPs were done from cultured untreated and LMNA-downregulated adipose stem cell (ASC) chromatin. MeDIPs were done from LMNA-downregulated ASCs. ChIP and MeDIP DNA was hybridized onto the aforementioned HG-18 Nimbegen promoter arrays.

2013-07-14 | E-GEOD-42522 | biostudies-arrayexpress

Stochastic genome-nuclear lamina interactions: Modulating roles of Lamin A and BAF

2014-02-15 | GSE55066 | GEO

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha [ChIP-Seq]

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

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha [gene expression]

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data