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U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [PAC-seq]

ABSTRACT: U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [PAC-seq]

PROVIDER: PRJNA902391 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22315427_1.fastq.gz	Fastqsanger.gz
	SRR22315427_2.fastq.gz	Fastqsanger.gz
	SRR22315428_1.fastq.gz	Fastqsanger.gz
	SRR22315428_2.fastq.gz	Fastqsanger.gz
	SRR22315429_1.fastq.gz	Fastqsanger.gz

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U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [PAC-seq]

Project description:The expansion of introns within mammalian genomes poses a challenge for the production of full-length messenger RNAs (mRNA)s, with increasing evidence that these long AT-rich sequences present obstacles to transcription. Here, we investigate RNAPII elongation in mammalian cells at high resolution and demonstrate that RNAPII transcribes faster across introns. Moreover, we find that this acceleration is mediated by the association of U1 snRNP (U1) with the elongation complex at 5’ splice sites. The direct stimulation of elongation rate through introns by U1 reduces the occurrence of both premature termination and transcriptional arrest, thereby dramatically increasing RNA production. We further show that changes in RNAPII elongation rate due to AT-content and U1 binding explain previous reports of pausing or termination at splice junctions and the edge of CpG islands. We propose that this role for U1 has evolved to mitigate the risks that long, AT-rich intronic sequences pose to transcript completion.

2023-03-24 | GSE218134 | GEO

U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [PRO-seq]

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U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [TT-Seq]

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U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [ChIP-Seq]

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U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [RNA-Seq]

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U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes

Project description:U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes

| PRJNA902389 | 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

U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [PRO-seq]

Project description:U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [PRO-seq]

| PRJNA902384 | ENA

U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [ChIP-Seq]

Project description:U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [ChIP-Seq]

| PRJNA902383 | ENA

U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [TT-Seq]

Project description:U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [TT-Seq]

| PRJNA902382 | ENA