Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

ABSTRACT: Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

PROVIDER: PRJNA263022 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1503230.fastq.gz	Fastqsanger.gz
	SRR1503231.fastq.gz	Fastqsanger.gz
	SRR1503232.fastq.gz	Fastqsanger.gz
	SRR1503233.fastq.gz	Fastqsanger.gz
	SRR1503234.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Project description:Sequencing of 5' ends of RNA molecules from control and exosome-depleted HeLa-S3 cells. CAGE library construction from RNA extracted from control and exosome-depleted cells.

2014-07-02 | E-GEOD-58991 | biostudies-arrayexpress

Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-10-04 | E-GEOD-62047 | biostudies-arrayexpress

Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-10-04 | GSE62047 | GEO

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Project description:Sequencing of 5' ends of RNA molecules from control and exosome-depleted HeLa-S3 cells.

2014-07-02 | GSE58991 | GEO

Homo sapiens

Project description:Nuclear stability and transcriptional directionality separate functionally distinct RNA species

| PRJNA254060 | ENA

Gene architecture directs splicing outcome in separate nuclear spatial regions

Project description:Gene architecture directs splicing outcome in separate nuclear spatial regions

| PRJNA729741 | ENA

DNA molecular combing-based replication fork directionality profiling

Project description:DNA molecular combing-based replication fork directionality profiling

| PRJNA689720 | ENA

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

Project description:Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-coding genes is limited by unknown mechanisms. In particular, although RNA polymerase II (RNAPII) initiates divergently from most active gene promoters, productive elongation occurs primarily in the sense-coding direction. Here we show in mouse embryonic stem cells that asymmetric sequence determinants flanking gene transcription start sites control promoter directionality by regulating promoter-proximal cleavage and polyadenylation. We find that upstream antisense RNAs are cleaved and polyadenylated at poly(A) sites (PASs) shortly after initiation. De novo motif analysis shows PAS signals and U1 small nuclear ribonucleoprotein (snRNP) recognition sites to be the most depleted and enriched sequences, respectively, in the sense direction relative to the upstream antisense direction. These U1 snRNP sites and PAS sites are progressively gained and lost, respectively, at the 5' end of coding genes during vertebrate evolution. Functional disruption of U1 snRNP activity results in a dramatic increase in promoter-proximal cleavage events in the sense direction with slight increases in the antisense direction. These data suggest that a U1-PAS axis characterized by low U1 snRNP recognition and a high density of PASs in the upstream antisense region reinforces promoter directionality by promoting early termination in upstream antisense regions, whereas proximal sense PAS signals are suppressed by U1 snRNP. We propose that the U1-PAS axis limits pervasive transcription throughout the genome. 3' end sequencing of poly (A) + RNAs in mouse ES cells with and without U1 snRNP inhibition using antisense morpholino oligonucleotides (AMO). Each with two biological replicates.

2013-06-28 | E-GEOD-46433 | biostudies-arrayexpress

Genome-wide replication fork directionality measured by strand-specific sequencing of Okazaki fragments in chicken lymphoma cells (DT40).

Project description:Genome-wide replication fork directionality measured by strand-specific sequencing of Okazaki fragments in chicken lymphoma cells (DT40).

2022-02-18 | GSE196761 | GEO

Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 (RBBP6_POINT-Seq)

Project description:RNA polymerase II (RNAPII) transcription initiates bidirectionally at many human protein-coding genes. Sense transcription usually dominates and leads to messenger RNA production, whereas antisense transcription rapidly terminates. The basis for this directionality is not fully understood. Here, we show that sense transcriptional initiation is more efficient and focused than in the antisense direction. After transcription begins, directionality is maintained by the opposing functions of Integrator (INTS11) and cyclin-dependent kinase 9 (CDK9). INTS11 terminates antisense transcription, whereas sense transcription is protected from this attenuation by CDK9. However, INTS11 terminates transcription in both directions upon CDK9 inhibition, and the engineered recruitment of CDK9 abrogates attenuation by INTS11. Therefore, transcriptional initiation and the asymmetric activities of CDK9 and INTS11 explain the attenuation of antisense transcription, the more extensive nature of sense transcription, and promoter directionality.

2024-03-19 | GSE243265 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data