Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Promoter-proximal transcription-translation coupling controls early transcription in Escherichia coli

ABSTRACT: Promoter-proximal transcription-translation coupling controls early transcription in Escherichia coli

PROVIDER: PRJNA951054 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Promoter-proximal transcription-translation coupling controls early transcription in Escherichia coli

Project description:We report a new but determining pathway of mRNA quality control by transcription-translation coupling (TTC), which inhibits the generation of untranslatable mRNAs from the promoter-proximal region when transcription is decoupled from translation. Single-molecule mRNA FISH shows that the 5’ end-proximal regions of mRNA, of which amount reflects transcription initiation, are not generated without translation. The decoupling between transcription and translation results in the occupancy of RNAPs only within 250 base pairs from the transcription start site. It is further supported by the observation that RNAP decoupled with translation elongates mRNA only 80-90 bp on average in vivo. We show that the length of RNAP elongation before coupling with the ribosome (i.e., 5’-UTR length) determines the mRNA expression level. Our results demonstrate that the ribosome-coupling near the promoter-proximal region, within 100 bp from the transcription start site, functions as an mRNA-quality control, critical for the efficient synthesis of translatable mRNAs by RNAPs. The limited processivity of RNAP before coupling with ribosome provides a potential explanation of the natural distribution of 5’-UTR lengths in E. coli, where longer than 100 bp 5’-UTRs are rare.

2025-09-12 | GSE228686 | GEO

Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition

Project description:Metazoan gene transcription by RNA polymerase (Pol) II is regulated in the promoter-proximal region. Pol II can undergo termination in the promoter-proximal region, but whether this can contribute to transcription regulation in cells remains unclear. Here, we extend our previous multi-omics analysis to quantify changes in transcription kinetics during a human cell type transition event. We observe that upregulation of transcription involves an increase in initiation frequency and, at a set of genes, a decrease in promoter-proximal termination. In turn, downregulation of transcription involves a decrease in initiation frequency and an increase in promoter-proximal termination. Thus, promoter-proximal termination of Pol II contributes to the regulation of human gene transcription.

2025-02-10 | GSE235181 | GEO

The histone deacetylase SIRT6 restrains transcription elongation via promoter-proximal pausing

Project description:The histone deacetylase SIRT6 restrains transcription elongation via promoter-proximal pausing

| PRJNA540991 | ENA

The Integrator complex terminates promoter-proximal transcription at protein-coding genes

Project description:The Integrator complex terminates promoter-proximal transcription at protein-coding genes

| PRJNA471515 | ENA

SPT5 licenses transition into productive transcription elongation by regulating promoter-proximal Pol II stability

Project description:An acute protein depletion system coupled with proteomic and genomic analyses reveal how SPT5 regulates promoter-proximal Pol II stability in eukaryotic cells, linking transcriptional initiation to productive elongation.

2021-02-04 | MSV000086806 | MassIVE

A CSB-PAF1 axis activates RNA polymerase II from promoter-proximal sites and restores efficient transcription elongation after DNA damage repair

Project description:The coordinated transcription of genes involves RNA polymerase II enzymes (RNAPII), which pull DNA through their active sites. DNA lesions in transcribed strands block RNAPII elongation and induce a strong transcriptional arrest. The transcription-coupled repair (TCR) pathway ensures the efficient removal of transcription-blocking DNA lesions, but this is not sufficient to overcome this arrest and 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 specifically in response to DNA damage. PAF1C is dispensable for TCR-mediated repair,but is essential to resume RNA synthesis after UV irradiation, suggesting an unexpected uncoupling between DNA repair and transcription restart. Moreover, we find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation waves 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.

2021-02-28 | PXD016198 | Pride

Pervasive promoter-proximal regulation in archaea

Project description:Pervasive promoter-proximal regulation in archaea

| PRJNA593004 | ENA

S.cerevisiae INO80 is required for promoter proximal nucleosome remodeling.

Project description:During transcription, nucleosomes are evicted from regulatory and coding regions yet chromatin structure is stable. Restoration of chromatin structure involves concerted action of chromatin modifying activities. Our analysis demonstrates a genome wide function of the INO80 remodeling complex for stable repositioning of the nucleosome immediately proximal to the transcription initiation site. INO80 dependent remodeling of the promoter proximal nucleosomes has a global repressive role. Recruitment of INO80 to proximal nucleosomes overlaps with the elongating Polymerase II complex assembly. The amount of associated Polymerase II at start sites correlates with INO80 recruitment for inducible and constantly transcribed genes. Furthermore, at highly inducible promoters INO80 is required for repression of bidirectional transcription. Therefore, we suggest a function for INO80 after transcription initiation to achieve Polymerase II dependent reassembly of promoter proximal nucleosomes.

2016-12-24 | E-MTAB-1810 | biostudies-arrayexpress

The histone deacetylase SIRT6 controls transcription elongation via promoter-proximal pausing (PRO-Seq)

Project description:The histone deacetylase SIRT6 controls transcription elongation via promoter-proximal pausing (PRO-Seq)

| PRJNA540994 | ENA

The histone deacetylase SIRT6 controls transcription elongation via promoter- proximal pausing (ChIP-Seq)

Project description:The histone deacetylase SIRT6 controls transcription elongation via promoter- proximal pausing (ChIP-Seq)

| PRJNA540993 | ENA