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Transient Ddx61-enriched condensates refine heart regeneration programs

ABSTRACT: Transient Ddx61-enriched condensates refine heart regeneration programs

PROVIDER: PRJNA1033659 | ENA |

REPOSITORIES: ENA

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Transient Ddx61-enriched condensates refine heart regeneration programs

Project description:Gene regulatory mechanisms that underlie tissue regeneration have been largely studied at the level of transcription. Here, proximity labeling methods identified enhanced presence of Processing body (P-body) marker, Ddx61, in zebrafish heart muscle cells induced to divide by injury or mitogenic stimulation. We found that Ddx61-containing condensates emerge and develop complex, transient structures in cardiomyocytes during cardiogenic settings in adult zebrafish, developing mice, and human stem cell-derived myocardium. Mutations in zebrafish ddx61 disrupted cardiomyocyte cycling and differentiation after cardiac injury or mitogen presence, and DDX61 knockdown in human cardiomyocytes inhibited similar parameters under maturation conditions in vitro. RNA affinity and proteomic profiling implicated mRNAs preferentially associating with Ddx61 during regeneration, and induced transgenic expression of one of these mRNAs, encoding the BMP signaling inhibitor, Chordin, disrupted indicators of heart regeneration after cardiac injury. Our experiments provide evidence that mRNA sorting by specialized context-dependent condensates can modulate gene expression and impact tissue regenerative capacity.

2025-08-26 | GSE246577 | GEO

Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA-sequencing

Project description:Here, we apply differential transcriptome analysis on microscopically isolated cell populations, to define five transcriptional programs that represent each transient embryonic zone and the progression between these zones. The five transcriptional programs contain largely uncharacterized genes in addition to transcripts necessary for stem cell maintenance, neurogenesis, migration, and differentiation. Additionally, we found intergenic transcriptionally active regions that possibly encode novel zone-specific transcripts. Finally, we present a high-resolution transcriptome map of transient zones in the embryonic mouse forebrain. mRNAseq performed after laser microdissection of cells from transient embryonic zones in the mouse cortex

2011-08-22 | E-GEOD-30765 | biostudies-arrayexpress

Light induced targeting enables proteomics on endogenous condensates

Project description:Endogenous condensates with transient constituents are notoriously difficult to study with common biological assays like mass-spectrometry and other proteomics profiling. Here we report a method for light-induced targeting of endogenous condensates (LiTEC) in living cells. LiTEC combines the identification of molecular zip codes that target the endogenous condensates with optogenetics to enable controlled and reversible partitioning of an arbitrary cargo, such as enzymes commonly used in proteomics, into the condensate in a blue light dependent manner. We demonstrate a proof of concept by combining LiTEC with proximity-based biotinylation (BioID) and uncover putative components of transcriptional condensates in mouse embryonic stem cells. Our approach opens the road to genome-wide functional studies of endogenous condensates.

2024-10-18 | GSE270770 | GEO

Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA-sequencing

2011-08-22 | GSE30765 | GEO

Light-induced targeting enables proteomics on endogenous condensates

2024-10-25 | PXD049054 | Pride

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

Refine regulatory elements across the genome

Project description:Refine regulatory elements across the genome

| PRJNA627176 | ENA

WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity [Nanog_WT_R153A_RNAseq]

Project description:WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity [Nanog_WT_R153A_RNAseq]

| PRJNA1267032 | ENA

HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs [RNA-Seq]

Project description:HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs [RNA-Seq]

| PRJNA1168539 | ENA

Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in HEK-293T Cells

Project description:Phase separation of biomolecules into condensates is a key mechanism in the spatiotemporal organization of biochemical processes in cells. We systematically engineered light-inducible transcription factor condensates with different material properties and analyzed their influence on transcription activation. When transcription factor condensates were transformed into solid-like gels, we observed a reduced activation of gene expression. We wanted to evaluate the impact that the condensate formation of the transcription factor RelA had on its endogenous promoters using expression data. To this aim, HEK-293T cells were transfected either with empty vector (1-3) or eGFP-RelA (4-6) or eGFP-RelA, Cry2olig-mCh-FUSN-NLS-NbGFP and Cry2olig-mCh-FUSN-NLS, along with an NF-κB-responsive SEAP reporter (7-9). In each of the three groups of transfected cells, 8 h after transfection, 3 samples were kept in the dark (D) and 3 under blue light illumination (BL, 5 μmol m-² s-1) for 24 h prior to RNA extraction. RNA-seq libraries from the 18 samples were sequenced by BGI on a DNBSEQ platform using paired-end chemistry with a read length of 100 base pairs each. Each strand was sequenced across two separate lanes (L03, L04), generating a total of 4 FASTQ files per sample.

2024-04-01 | E-MTAB-13905 | biostudies-arrayexpress

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