Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Guanine- and cytosine-rich genes are actively transcribed at the nuclear Lmnb1 compartment

ABSTRACT: Chromatin organization in the mammalian cell nucleus plays a vital role in the regulation of gene expression. The lamina-associated domain at the inner nuclear membrane has been proposed to harbor heterochromatin, while the nuclear interior has been shown to contain most of the euchromatin. Here, we show that a sub-set of actively transcribing genes, marked by RNA Pol II pSer2, are associated with Lmnb1 at the inner nuclear envelop in mESCs and the number of genes proportionally increases upon in vitro differentiation of mESC to olfactory precursor cells. These nuclear periphery-associated actively transcribing genes primarily represent housekeeping genes, and their gene bodies are significantly enriched with guanine and cytosine compared to genes actively transcribed at the nuclear interior. We found the promoters of these gene’s to also be significantly enriched with guanine and to be predominantly regulated by zinc finger protein transcription factors. We provide evidence supporting the emerging notion that the Lmnb1 region is not solely transcriptionally silent.

ORGANISM(S): Mus musculus

PROVIDER: GSE246040 | GEO | 2025/10/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Guanine- and cytosine-rich genes are actively transcribed at the nuclear Lmnb1 compartment

Project description:Guanine- and cytosine-rich genes are actively transcribed at the nuclear Lmnb1 compartment

| PRJNA1031166 | ENA

DamID (LmnB1/Dam) Log2 ratios of C57Bl/6 fibroblasts and RAG2-/- pro-B cells.

Project description:Comparison of DamID profiles and LAD patterning across cell types reveals regions of variable LADs LmnB1 interactions at the nuclear periphery of C57Bl/6 pro-B cells and fibroblasts were identified by DamID in duplicate for both pro-B and fibroblasts (4 samples total). For each sample, Dam-LmnB1/Dam-only Log2 ratios of chromosomes 11 and 12 were calculated, lifted over to mm9, duplicates were normalized and averaged together.

2014-12-16 | E-GEOD-56990 | biostudies-arrayexpress

MicroRNA profiling of mouse embryonic fibroblast Lmnb1D/D and Lmnb1+/+ cells

Project description:Comparison of miRNA profiles of Lmnb1D/D and Lmnb1+/+ cells.

2009-09-10 | E-MEXP-1792 | biostudies-arrayexpress

Transcription profiling of mouse wild type cells vs Lmnb1 knockout cells

Project description:Comparison of gene expression profiles in wild type cells vs Lmnb1 knockout cells.

2007-01-08 | E-MEXP-538 | biostudies-arrayexpress

ChIP-seq of Lmnb1-/- and Lmnb1+/- olfactory lineages

Project description:Lamins, the major components of the nuclear lamina, have diverse functions in many cellular processes. Despite broad expression, lamins have been implicated in cell type-specific roles in development, aging and disease by regulating gene expression. Yet, due to the lack of in depth lineage-specific functional studies, it remains unclear whether or how lamins regulate cell type-specific functions. Using targeted knockout of lamin B1 in the olfactory sensory neuron lineage, we show that lamin B1 is not required for early stages of olfactory sensory neuron differentiation but is needed for formation of mature neurons that properly respond to odor stimulation. Lamin B1 mutant cells exhibited decreased expression of genes involved in mature neuron function, increased expression of genes atypical of the olfactory lineage and clustered nuclear pore distribution. These results demonstrate that the universally expressed lamin B1 regulates cell type-specific gene expression and terminal differentiation.

2017-05-01 | GSE80290 | GEO

RNA-seq of Lmnb1-/- and Lmnb1+/- olfactory lineages

2017-05-01 | GSE80044 | GEO

Genome-wide mapping of RNA Polymerase II binding sites

Project description:Protein coding genes and some of the non-coding RNA genes in eucaryotes are transcribed by RNA Polymerase II. A transcription machinery complex consists of RNA Pol II and many other proteins including transcription factors, activators and repressors of transcription. Pol II binding sites are found in actively transcribing genes and many which are not actively transcribing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of RNA Polymerase II in the genome of K562 & NB4 cells

2008-10-02 | E-GEOD-13008 | biostudies-arrayexpress

Differential features of lamina-associated domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

Project description:The nuclear lamina interacts with the genome through megabase-size lamina-associated domains (LADs). LADs have been identified in proximity labeling assays and recently by chromatin immunoprecipitation-sequencing (ChIP-seq) of A- and B-type lamins. LADs localize mainly to the nuclear periphery, they are gene-poor and largely heterochromatic. Here, we show that the mode of chromatin fragmentation for ChIP, namely either bath sonication (used to date for ChIP of nuclear lamins) or digestion with micrococcal nuclease (MNase) leads to the discovery of distinct sets of lamin-interacting domains (which we refer to as LiDs) with distinct gene content, histone composition enrichment and relationship to lamin B1-interacting domains. We find that total genome coverage by lamin A/C ('LMNA') LiDs identified in sonicated or MNase-digested chromatin is similar (~730 megabases). Over half of these domains, however, are uniquely detected in sonicated or MNase-digested chromatin. Whereas sonication-specific LMNA LiDs are gene-poor and devoid of a broad panel of histone modifications, MNase-specific LMNA LiDs are of higher gene density and are enriched in H3K9me3, H3K27me3 and in histone variant H2A.Z. Analysis of published LMNB1 LADs and of LMNB1 LiDs identified by ChIP-seq further shows that LMNA can associate with 'open' chromatin domains displaying euchromatin features which are not associated with LMNB1. The differential genetic and epigenetic properties of lamin-interacting chromatin domains indicate the existence of distinct LiD populations identifiable in different chromatin contexts, including nuclease-accessible 'open' regions presumably localized in the nuclear interior.

2015-03-24 | GSE57149 | GEO

Genome-wide mapping of RNA Polymerase II binding sites

2008-10-02 | GSE13008 | GEO

Lamin B1 deletion in myeloid neoplasms alters hematopoietic cell fate and causes Pelger-Huët nuclear anomaly

Project description:The most common cytogenetic abnormality found in complex karyotype high risk MDS/AML is del5q. Disease is often identified through visual inspection and recognition of abnormalities such as pseudo-Pelger-Huet anomaly (PPHA), which presents as deviations of normal neutrophil nuclear morphology. The link between PPHA and leukemia is unknown, but mutations in the lamin B1 receptor (LBR) have been identified as the cause of benign presence in otherwise normal individuals. Lamin B1 (LMNB1) is the ligand for LBR and is important for maintaining nuclear lamina integrity and influencing 3D gene structural changes that impact transcription; the LMNB1 gene locus is also contained with chromosome 5q, so we hypothesized that appearance of PPHA is potentially caused by del5q in MDS/AML containing the LMNB1. To help characterize the potential role of LMNB1 in normal hematopoietic stem and progenitor cells (HSPCs), we infected CD34+ cord blood HSPCs with lentiviruses expressing shRNAs targeting LMNB1 (LB1) and luciferase (C11) as a control and assessed changes in transcription due to LMNB1 disruption via RNSeq and 3D genome structural changes through HiC. Neutrophils were also differentiated from LMNB1 shRNA and control treated CD34+ cord blood HSPCs and transcriptional/structural changes identified via RNAseq and HiC. Additionally, to understand long-term in vivo effects of LMNB1 loss on self-renewal and lineage bias, we engrafted control and LMNB1 shRNA infected CD34+ HSPCs into NSG mice and harvest hCD34+ cells 12 weeks later for scRNAseq.

2022-03-11 | GSE174533 | GEO

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