Single-cell nascent transcription is sparse and heterogeneous, revealing cellular plasticity [EU_seq]
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ABSTRACT:
PROVIDER: PRJNA1168886 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Single-cell nascent transcription is sparse and heterogeneous, revealing cellular plasticity [single_cell]
| PRJNA1168887 | ENA
Project description:Single-cell nascent transcription is sparse and heterogeneous, revealing cellular plasticity [pro-seq]
| PRJNA1168888 | ENA
Project description:Single-cell nascent RNA sequencing is essential for understanding how a genome drives cell diversity. We developed scFLUENT-seq, a single-cell method that captures genome-wide transcription with brief metabolic labeling. Our analysis shows that only 3~6% of the genome is transcribed per cell in a 10-minute window, compared to over 80% in bulk, revealing significant variability in how individual cells interpret the genome. Notably, substantial transcription occurs in intergenic regions, particularly in heterochromatin, with high stochasticity. Moreover, promoter-associated antisense and genic sense transcription rarely co-occur in the same cell. Distal intergenic transcription correlates poorly with gene activity but links to increased genome-wide transcriptional diversity, which marks cellular plasticity and may precede cell-state shifts. Furthermore, mRNA synthesis and decay are uncoupled at the single-cell level, unlike intergenic ncRNA, suggesting specialized mechanisms counteracting stochastic noncoding production. In summary, scFLUENT-seq captures the full transcriptional spectrum, revealing the heterogeneity and regulatory complexity underlying cellular plasticity.
2024-10-09 | GSE278777 | GEO
Project description:Single-cell nascent RNA sequencing is essential for understanding how a genome drives cell diversity. We developed scFLUENT-seq, a single-cell method that captures genome-wide transcription with brief metabolic labeling. Our analysis shows that only 3~6% of the genome is transcribed per cell in a 10-minute window, compared to over 80% in bulk, revealing significant variability in how individual cells interpret the genome. Notably, substantial transcription occurs in intergenic regions, particularly in heterochromatin, with high stochasticity. Moreover, promoter-associated antisense and genic sense transcription rarely co-occur in the same cell. Distal intergenic transcription correlates poorly with gene activity but links to increased genome-wide transcriptional diversity, which marks cellular plasticity and may precede cell-state shifts. Furthermore, mRNA synthesis and decay are uncoupled at the single-cell level, unlike intergenic ncRNA, suggesting specialized mechanisms counteracting stochastic noncoding production. In summary, scFLUENT-seq captures the full transcriptional spectrum, revealing the heterogeneity and regulatory complexity underlying cellular plasticity.
2024-10-09 | GSE278775 | GEO
Project description:Single-cell nascent RNA sequencing is essential for understanding how a genome drives cell diversity. We developed scFLUENT-seq, a single-cell method that captures genome-wide transcription with brief metabolic labeling. Our analysis shows that only 3~6% of the genome is transcribed per cell in a 10-minute window, compared to over 80% in bulk, revealing significant variability in how individual cells interpret the genome. Notably, substantial transcription occurs in intergenic regions, particularly in heterochromatin, with high stochasticity. Moreover, promoter-associated antisense and genic sense transcription rarely co-occur in the same cell. Distal intergenic transcription correlates poorly with gene activity but links to increased genome-wide transcriptional diversity, which marks cellular plasticity and may precede cell-state shifts. Furthermore, mRNA synthesis and decay are uncoupled at the single-cell level, unlike intergenic ncRNA, suggesting specialized mechanisms counteracting stochastic noncoding production. In summary, scFLUENT-seq captures the full transcriptional spectrum, revealing the heterogeneity and regulatory complexity underlying cellular plasticity.
2024-10-09 | GSE278776 | GEO
Project description:Revealing nascent RNA processing dynamics with nano-COP
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Project description:Experience-dependent synaptic plasticity refines brain circuits during development. To uncover protein synthesis-dependent mechanisms contributing to experience-dependent plasticity, we performed quantitative proteomic analysis of the nascent proteome using improved bio-orthogonal metabolic labeling (BONCAT) to identify candidate plasticity proteins (CPPs) that undergo differential protein synthesis in response to visual conditioning (VC) in Xenopus optic tectum. We identified 83 CPPs that formed strongly connected networks and were annotated to a variety of biological functions, including RNA splicing, protein translation, and chromatin remodeling. Functional analysis of select CPPs using translation blocking morpholinos revealed the requirement of eukaryotic initiation factor 3 subunit A (eIF3A), fused in sarcoma (FUS), and ribosomal protein s17 (RPS17) in experience-dependent structural plasticity of tectal neurons. These results demonstrate that the nascent proteome is dynamic in response to VC and that de novo synthesis of the machinery that regulates gene expression and protein translation is required for experience-dependent structural plasticity.
2017-11-21 | MSV000081728 | MassIVE
Project description:Collateral Responses to Classical Cytotoxic Chemotherapies are Heterogeneous and Sensitivities are Sparse
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Project description:miRNAs are key post-transcriptional regulators of gene expression. However, it is still poorly understood how miRNAs themselves are regulated, mainly due to the sparse annotation of miRNA transcription start sites (TSSs). Here, we developed a novel method for identifying active miRNA TSSs from nascent transcriptomes generated by nuclear run-on sequencing. With the least data requirement, our method demonstrated better performance than existing methods. Moreover, it provided ways not only to recognize miRNA TSSs but also to quantify primary miRNA expression in one experiment, which is very useful for revealing miRNAs directly regulated by the regulator(s) of interest.
2017-04-20 | GSE97143 | GEO
Project description:During maturation, eukaryotic precursor RNAs undergo processing events including intron splicing, 3’-end cleavage, and polyadenylation. Here, we describe nanopore analysis of CO-transcriptional Processing (nano-COP), a method for probing the timing and patterns of RNA processing. An extension of native elongating transcript sequencing (NET-seq), which quantifies transcription genome-wide through short-read sequencing of nascent RNA 3’ ends, nano-COP uses long-read nascent RNA sequencing to observe global patterns of RNA processing. First, nascent RNA is stringently purified through a combination of 4-thiouridine metabolic labeling and cellular fractionation. In contrast to cDNA or short-read–based approaches relying on reverse transcription or amplification, the sample is sequenced directly through nanopores to reveal the native context of nascent RNA. nano-COP identifies both active transcription sites and splice isoforms of single RNA molecules during synthesis, providing insight into patterns of intron removal and the physical coupling between transcription and splicing. The nano-COP protocol yields data within 3 days.
2021-01-06 | GSE154079 | GEO