Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA

ABSTRACT: Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA

PROVIDER: PRJNA1103942 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA

Project description:Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping transcriptomes with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq), enabling efficient transcriptome mapping within a single day (∼12 h), increasing ligation efficiency, abolishing adapter dimers, and reducing sample loss and RNA degradation. Rapid PRO-seq allows for transcriptome mapping using 5,000 cells and is applicable to mouse hematopoietic progenitor cells (mHPCs) as well as mouse neurons. Using acute depletion of INTS11 in neuronal cells, we pinpoint a critical role for INTS11 as a regulator of genes in neurodevelopmental disorders. Taken together, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.

2025-07-24 | GSE264740 | GEO

Nascent RNA sequencing (PRO-seq) after rapid degradation of AID-tagged ZNF143

Project description:Nascent RNA sequencing (PRO-seq) after rapid degradation of AID-tagged ZNF143

| PRJNA523738 | ENA

Nascent RNA sequencing (PRO-seq) after 200nM romidepsin treatment of H9 cells

Project description:Nascent RNA sequencing (PRO-seq) after 200nM romidepsin treatment of H9 cells

2019-12-12 | GSE141843 | GEO

Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis

Project description:Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis

| PRJNA1069100 | ENA

Rapid and scalable profiling of nascent RNA with fastGRO

Project description:Rapid and scalable profiling of nascent RNA with fastGRO

| PRJNA601833 | ENA

Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis

Project description:RNA’s catalytic, regulatory, or coding potential depends on structure formation. Because base-pairing occurs during transcription, early structural states can govern RNA processing events and dictate the formation of functional conformations. These co-transcriptional states remain unknown. Here, we develop CoSTseq, which detects nascent RNA base-pairing within and upon exit from RNA polymerases (Pols) transcriptome-wide in living yeast cells. Monitoring each nucleotide’s base-pairing activity during transcription, CoSTseq reveals predominantly rapid pairing – within 25 bp of transcription after addition to the nascent chain. Moreover, ~23% of rRNA nucleotides attain their final base-pairing state near Pol I, while most other nucleotides must undergo changes in pairing status during later steps of ribosome biogenesis. We show that helicases act immediately to remodel structures across the rDNA locus to facilitate ribosome biogenesis. In contrast, nascent pre-mRNAs attain local structures indistinguishable from mature mRNAs, suggesting that refolding behind elongating ribosomes resembles co-transcriptional folding behind Pol II.

2025-02-21 | GSE254264 | GEO

Mapping DNA methylation and CTCF/cohesin occupancy on nascent chromatin and DNMT-targeted nascent chromatin

Project description:Mapping DNA methylation and CTCF/cohesin occupancy on nascent chromatin and DNMT-targeted nascent chromatin

| PRJNA381638 | ENA

Nascent RNA sequencing (PRO-seq) after estrogen treatment in T47D cells

Project description:Nascent RNA sequencing (PRO-seq) after estrogen treatment in T47D cells

| PRJNA764248 | ENA

Nascent RNA sequencing (PRO-seq) after various treatments in T47D cells

Project description:Nascent RNA sequencing (PRO-seq) after various treatments in T47D cells

| PRJNA1055459 | ENA

Single-cell nascent transcription reveals sparse genome usage and plasticity [pro-seq]

Project description:Single-cell nascent transcription reveals sparse genome usage and plasticity [pro-seq]