Subcellular sequence tracking of RNA maturation during neuronal differentiation [smallRNA]
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ABSTRACT:
PROVIDER: PRJNA671174 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Subcellular sequence tracking of RNA maturation during neuronal differentiation
| PRJNA671492 | ENA
Project description:We developed an extensive resource of RNAseq data to track mRNA maturation across subcellular locations in multiple cell types. Mouse embryonic stem cells, neuronal progenitor cells, and post-mitotic neurons were separated into chromatin-associated, soluble nucleoplasmic and cytoplasmic fractions, with RNA from each fraction isolated as both polyadenylated, total rRNA-depleted pools, and small RNA pools and sequenced. Genes exhibit disparate patterns of RNA enrichment between subcellular fractions, with some genes maintaining more polyadenylated RNA in the chromatin fraction than in the cytoplasm. These chromatin-associated poly(A)+ RNAs are often incompletely spliced and we devise a simple metric to identify introns whose excision is posttranscriptional. X-means clustering and deep learning methods identified intron groups with four defined regulatory behaviors, including complete cotranscriptional splicing, and complete retention in the cytoplasmic RNA. Two groups display intermediate levels of retention in the RNA in the nucleus but are fully spliced in the cytoplasm. These groups include previously described sets of retained introns, but extend to many new introns, including introns repressed by polypyrimidine track binding protein 1 (PTBP1). We find that the PTBP1 regulated Gabbr1 transcript is highly expressed in mESC without expression of Gabbr1 protein. The bulk of Gabbr1 RNA is incompletely spliced and remains sequestered on chromatin similar to certain long noncoding RNAs. Only after neuronal differentiation does Gabbr1 RNA become fully processed and released to the cytoplasm as mRNA. Thus, splicing repression and the chromatin anchoring of RNA provide a combined mechanism of posttranscriptional regulation over development. Our datasets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.
2020-11-18 | GSE159971 | GEO
Project description:Subcellular sequence tracking of RNA maturation during neuronal differentiation [Total]
| PRJNA670929 | ENA
Project description:Subcellular sequence tracking of RNA maturation during neuronal differentiation [Poly]
| PRJNA670896 | ENA
Project description:We developed an extensive resource of RNAseq data to track mRNA maturation across subcellular locations in multiple cell types. Mouse embryonic stem cells, neuronal progenitor cells, and post-mitotic neurons were separated into chromatin-associated, soluble nucleoplasmic and cytoplasmic fractions, with RNA from each fraction isolated as both polyadenylated, total rRNA-depleted pools, and small RNA pools and sequenced. Genes exhibit disparate patterns of RNA enrichment between subcellular fractions, with some genes maintaining more polyadenylated RNA in the chromatin fraction than in the cytoplasm. These chromatin-associated poly(A)+ RNAs are often incompletely spliced and we devise a simple metric to identify introns whose excision is posttranscriptional. X-means clustering and deep learning methods identified intron groups with four defined regulatory behaviors, including complete cotranscriptional splicing, and complete retention in the cytoplasmic RNA. Two groups display intermediate levels of retention in the RNA in the nucleus but are fully spliced in the cytoplasm. These groups include previously described sets of retained introns, but extend to many new introns, including introns repressed by polypyrimidine track binding protein 1 (PTBP1). We find that the PTBP1 regulated Gabbr1 transcript is highly expressed in mESC without expression of Gabbr1 protein. The bulk of Gabbr1 RNA is incompletely spliced and remains sequestered on chromatin similar to certain long noncoding RNAs. Only after neuronal differentiation does Gabbr1 RNA become fully processed and released to the cytoplasm as mRNA. Thus, splicing repression and the chromatin anchoring of RNA provide a combined mechanism of posttranscriptional regulation over development. Our datasets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.
2020-11-18 | GSE159944 | GEO
Project description:We developed an extensive resource of RNAseq data to track mRNA maturation across subcellular locations in multiple cell types. Mouse embryonic stem cells, neuronal progenitor cells, and post-mitotic neurons were separated into chromatin-associated, soluble nucleoplasmic and cytoplasmic fractions, with RNA from each fraction isolated as both polyadenylated, total rRNA-depleted pools, and small RNA pools and sequenced. Genes exhibit disparate patterns of RNA enrichment between subcellular fractions, with some genes maintaining more polyadenylated RNA in the chromatin fraction than in the cytoplasm. These chromatin-associated poly(A)+ RNAs are often incompletely spliced and we devise a simple metric to identify introns whose excision is posttranscriptional. X-means clustering and deep learning methods identified intron groups with four defined regulatory behaviors, including complete cotranscriptional splicing, and complete retention in the cytoplasmic RNA. Two groups display intermediate levels of retention in the RNA in the nucleus but are fully spliced in the cytoplasm. These groups include previously described sets of retained introns, but extend to many new introns, including introns repressed by polypyrimidine track binding protein 1 (PTBP1). We find that the PTBP1 regulated Gabbr1 transcript is highly expressed in mESC without expression of Gabbr1 protein. The bulk of Gabbr1 RNA is incompletely spliced and remains sequestered on chromatin similar to certain long noncoding RNAs. Only after neuronal differentiation does Gabbr1 RNA become fully processed and released to the cytoplasm as mRNA. Thus, splicing repression and the chromatin anchoring of RNA provide a combined mechanism of posttranscriptional regulation over development. Our datasets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.
2020-11-18 | GSE159919 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-11-18 | GSE159990 | GEO
Project description:We performed a SLAMseq Metabolic RNA Labeling on neuronal subcellular compartments, e.g. neurites and soma, derived from Ascl1-induced neurons (iNeurons). This experimental approach provides a snapshot of mRNA kinetics which allows to estimate the half-lives of mRNAs. These data was used to investigate the influence of mRNA degradation machinery in both neuronal compartments.
2023-07-12 | E-MTAB-9400 | biostudies-arrayexpress
Project description:MBD1 activates neuronal developmental genes through modulating chromatin structure during neuronal maturation
| PRJNA386939 | ENA