Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation [RIP-seq]

ABSTRACT: lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

ORGANISM(S): Homo sapiens

PROVIDER: GSE149032 | GEO | 2020/07/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

Project description:Gene programs that control differentiation are regulated through the interplay between DNA, RNA, and protein. Cooperation among these fundamental cellular components can occur through highly structured interactions connecting domains formed by specific sequences of nucleotides, ribonucleotides, and/or amino acids and also through the assembly of biomolecular condensates. Here, we show that endoderm differentiation is regulated through the interaction of the long noncoding (lnc) RNA DIGITand the bromodomain and extra-terminal (BET) domain family protein BRD3. BRD3 forms phase-separated condensates that contain DIGIT, occupies enhancers of endoderm transcription factors, and is required for endoderm differentiation. Purified BRD3 binds to acetylated histone H3 lysine 18 (H3K18ac) in vitro and occupies regions of the genome enriched in H3K18ac during endoderm differentiation, including the key transcription factors that regulate endoderm differentiation. DIGIT is also enriched in regions of H3K18ac, and depletion of DIGIT results in decreased recruitment of BRD3 to these regions. Our findings support a model where cooperation between DIGIT and BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest a broader role for protein-lncRNA phase-separated condensates as regulators of transcription in development.

2020-07-08 | GSE126661 | GEO

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

Project description:lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

| PRJNA522865 | ENA

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation [RIP-seq]

Project description:lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation [RIP-seq]

| PRJNA627192 | ENA

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation.

Project description: Not available

| S-EPMC8008247 | biostudies-literature

DIGIT regulates endoderm differentiation of human embryonic stem cells

Project description:Endoderm differentiation is a critical step leading to development of the gastrointestinal system. We found that DIGIT is a lncRNA that is required for endoderm differentiation. We used directional RNA sequencing (RNA-seq) to globally evaluate the effects of loss of DIGIT expression during endoderm differentiation and chromatin immunoprecipitation and sequencing (ChIP-seq) to define the sites occupied by SMAD3 during endoderm diferentiation.

2016-10-04 | GSE75297 | GEO

Single cell RNA sequencing of adult regenerating mouse digit tips

Project description:Innate regeneration following digit tip amputation is one of the few examples of epimorphic regeneration in mammals. Digit tip regeneration is mediated by the blastema, the same structure invoked during limb regeneration in some lower vertebrates. By genetic lineage analyses in mice, the digit tip blastema has been defined as a population of heterogeneous, lineage restructed progenitor cells. These previous studies, however, do not comprehensively evaluate blastema heterogeneity or address lineage restruction of closely related cell types. Here we report single cell RNA sequencing of over 38,000 cells from mouse digit tip blastemas and unamputated control digit tips and generate an atlas of the cell types participating in digit tip regeneration.

2020-02-24 | GSE143888 | GEO

Digital gene expression tag profiling of digit morphologies in bats

Project description:As the only truly flying mammals, bats use their unique wing formed from elongated digits connected by membranes to power their flight. The forelimb of bats consists of four elongated digits (digits II-V) and one shorter digit (digit I) that is morphologically similar to the hindlimb digits. Elongation of bat forelimb digits is thought to results from changes in the temporal and spatial expression of a number of developmental genes. As a result, comparing gene expression profiles between short and elongated digit morphologies of the fore- and hindlimbs may elucidate the molecular mechanisms underlying digit elongation in bats. Here, we performed a large-scale analysis of gene expression of forelimb digit I, forelimb digits II-V, and all five hindlimb digits in Myotis ricketti using digital gene expression tag profiling approach. Results of this study not only implicate several developmental genes as robust candidates underlying digit elongation in bats, but also provide a better understanding of the genes involved in autopodial development in general. A large-scale analysis of gene expression of 3 different parts of autopods in Myotis ricketti using digital gene expression tag profiling approach.

2010-12-06 | E-GEOD-20038 | biostudies-arrayexpress

Transcription profiling of human primary bronchial/tracheal epithelial cells treated with 10 different sources of cigarette smoke condensates

Project description:Nine cigarette smoke condensates (CSCs) were produced under a standard ISO smoking machine regimen and one was produced by a more intense smoking machine regimen. These CSCs were used to treat primary normal human bronchial epithelial cells for 18 hours. Experiment Overall Design: Primary human bronchial/tracheal epithelial cells were grown in culture and treated with 10 different sources of cigarette smoke condensates.

2009-10-03 | E-GEOD-18235 | biostudies-arrayexpress

Digital gene expression tag profiling of digit morphologies in bats

2010-12-06 | GSE20038 | GEO

BRD3 regulates the inflammatory and stress response in rheu-matoid arthritis synovial fibroblasts

Project description:Individual functions of members of the bromodomain (BRD) and extra-terminal (BET) protein family underlying the anti-inflammatory effects of BET inhibitors in rheumatoid arthritis (RA) are incompletely understood. Here we aimed to analyze regulatory functions of BRD3, an under-studied member of the BET protein family, in RA synovial fibroblasts (FLS). BRD3 was silenced in FLS prior to stimulation with TNF. Alternatively, FLS were treated with I-BET. Transcriptomes were analyzed by RNA sequencing (RNAseq), followed by pathway enrichment analysis. We confirmed results for selective target genes by Real-time PCR, ELISA and Western blotting. BRD3 regulates the expression of several cytokines and chemokines in FLS, and positively correlates with inflammatory scores in the RA synovium. In addition, RNAseq pointed to a profound role of BRD3 in regulating FLS proliferation, metabolic adaption, and response to stress, including oxidative stress, and autophagy. BRD3 acts as an upstream regu-latory factor that integrates the response to inflammatory stimuli and stress conditions in FLS and executes many functions of BET proteins that have previously identified using pan-BET inhibitors.

2023-11-30 | GSE247226 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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