Gene expression in microdissected embryonic regions during mouse axis elongation.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA494804 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This dataset contains spatiotemporal transcriptome information on different axial progenitors throughout mouse axis elongation. Neuromesodermal Progenitors (NMPs), Lateral and Paraxial Mesoderm Progenitors (LPMPs), and Notochord Progenitors (NotoPs) show distinct expression profiles. Extensive similarity exist between NMPs and their immediate mesoderm-committed descendants at each stage investigated. Over time transcriptional changes occur in LPMPs and NMPs, with the major change occurring in NMPs between early somitogenesis and completion of trunk morphogenesis. In contrast, NotoPs contain a more stable transcriptome over time.
2018-10-06 | GSE120870 | GEO
Project description:snRNA-seq of microdissected regions from the axolotl pallium
| PRJEB52503 | ENA
Project description:In order to understand the relationship between cellular diversity and pallium regions, single-nucleus RNA-seq (snRNA-seq) was performed in 3 microdissected regions from the axolotl pallium: medial, dorsal, and lateral.
2022-07-19 | E-MTAB-11662 | biostudies-arrayexpress
Project description:HDAC1 binding regions in mouse embryonic limbs
| PRJNA595550 | ENA
Project description:GLI3 binding regions in mouse embryonic forelimb buds
| PRJNA552300 | ENA
Project description:The CDK12-INTAC Axis Modulates LEO1 Phosphorylation for Processive Transcription Elongation
| PRJNA899509 | ENA
Project description:The coordinated transcription of genes involves the regulated release of RNA polymerase II (RNAPII) from promoter-proximal sites into active elongation. DNA lesions in transcribed strands block elongation and induce a strong transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but this is not sufficient to resume transcription. Through proteomics screens, we find that the TCR-specific CSB protein loads the evolutionary conserved PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. PAF1C is dispensable for TCR-mediated repair, but is essential for recovery of RNA synthesis after UV irradiation, suggesting an uncoupling between DNA repair and transcription recovery. Moreover, we find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress.
2021-01-15 | GSE140930 | GEO
Project description:Epigenetic regulation of chromatin plays a critical role in controlling embryonic stem (ES) cell self-renewal and pluripotency. However, the roles of histone demethylases and activating histone modifications such as trimethylated histone 3 lysine 4 (H3K4me3) in transcriptional events such as RNA polymerase II (RNAPII) elongation and alternative splicing are largely unknown. In this study, we show that KDM5B, which demethylates H3K4me3, plays an integral role in regulating RNAPII occupancy, transcriptional initiation and elongation, and alternative splicing events in ES cells. Depletion of KDM5B leads to altered RNAPII promoter occupancy, and decreased RNAPII initiation and elongation rates at active genes and at genes marked with broad H3K4me3 domains. Moreover, our results demonstrate that spreading of H3K4me3 from promoter to gene body regions, which is mediated by depletion of KDM5B, modulates RNAPII elongation rates and RNA splicing in ES cells. We further show that KDM5B is enriched nearby alternatively spliced exons, and depletion of KDM5B leads to altered levels of H3K4 methylation in alternatively spliced exon regions, which is accompanied by differential expression of these ASEs. Altogether, our data indicate an epigenetic role for KDM5B in regulating RNAPII elongation and alternative splicing, which may support the diverse mRNA repertoire in ES cells.
2017-04-13 | GSE95074 | GEO
Project description:Epigenetic regulation of chromatin plays a critical role in controlling embryonic stem (ES) cell self-renewal and pluripotency. However, the roles of histone demethylases and activating histone modifications such as trimethylated histone 3 lysine 4 (H3K4me3) in transcriptional events such as RNA polymerase II (RNAPII) elongation and alternative splicing are largely unknown. In this study, we show that KDM5B, which demethylates H3K4me3, plays an integral role in regulating RNAPII occupancy, transcriptional initiation and elongation, and alternative splicing events in ES cells. Depletion of KDM5B leads to altered RNAPII promoter occupancy, and decreased RNAPII initiation and elongation rates at active genes and at genes marked with broad H3K4me3 domains. Moreover, our results demonstrate that spreading of H3K4me3 from promoter to gene body regions, which is mediated by depletion of KDM5B, modulates RNAPII elongation rates and RNA splicing in ES cells. We further show that KDM5B is enriched nearby alternatively spliced exons, and depletion of KDM5B leads to altered levels of H3K4 methylation in alternatively spliced exon regions, which is accompanied by differential expression of these ASEs. Altogether, our data indicate an epigenetic role for KDM5B in regulating RNAPII elongation and alternative splicing, which may support the diverse mRNA repertoire in ES cells.
2017-04-13 | GSE94739 | GEO
Project description:Transitions between pluripotent stem cells and differentiated cells are executed by key transcription regulators. Comparative measurements of RNA polymerase distribution over the genomeM-bM-^@M-^Ys primary transcription units in different cell states can identify the genes and steps in the transcription cycle that are regulated during such transitions. To identify the complete transcriptional profiles of RNA polymerases with high sensitivity and resolution, as well as the critical regulated steps upon which regulatory factors act, we used genome-wide, nuclear run-on (GRO-seq) to map the density and orientation of transcriptionally-engaged RNA polymerases in mouse embryonic stem cells (ESCs) and embryonic fibroblasts (MEFs). In both cell types, progression of a promoter-proximal, paused RNA polymerase II (Pol II) into productive elongation is a rate-limiting step in transcription of ~40% of mRNA-encoding genes. Importantly, quantitative comparisons between cell types reveal that transcription is controlled frequently at paused Pol IIM-bM-^@M-^Ys entry into elongation. Furthermore, M-bM-^@M-^\bivalentM-bM-^@M-^] ESC genes (exhibiting both active and repressive histone modifications) bound by Polycomb Group Complexes PRC 1 and PRC2 show dramatically reduced levels of paused Pol II at promoters relative to an average gene. In contrast, bivalent promoters bound by only PRC2 allow Pol II pausing, but it is confined to extremely 5M-bM-^@M-^Y proximal regions. Altogether, these findings identify rate-limiting targets for transcription regulation during cell differentiation. Mapping engaged RNA polymerase density in two cell types by sequencing run-on transcripts. SUPPLEMENTARY FILES: All fastq files have sanger-fastq format q values. Alignments were generated with eland and the mm9 mouse genome assembly. Reads aligning to regions annotated as similar to rRNA by RepeatMasker were then removed. Wiggle files are in units of RPKM (reads per kilobase per million aligned reads) and are broken up by cell type and chromosome to aid in uploading to UCSC. Each file furthermore contains two tracks - one for each strand. As in the published paper, plus strand RPKM densities are in red with positive values and minus strand RPKM densities are in blue with negative values.
2011-04-01 | E-GEOD-27037 | biostudies-arrayexpress