GEO DataSets

(Submitter supplied) 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. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL24676 GPL24247

10 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL13112 GPL24676

52 Samples

Download data

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Other

Platforms:

GPL13112 GPL24247

17 Samples

Download data: BEDGRAPH

(Submitter supplied) 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. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL24676 GPL24247

10 Samples

Download data: BEDGRAPH

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: BEDGRAPH

(Submitter supplied) 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. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

12 Samples

Download data: BEDGRAPH

(Submitter supplied) Regulation of RNA polymerase II (Pol II) elongation is a critical step in gene regulation. Here, we report that U1 snRNP recognition and transcription pausing at stable nucleosomes are linked through premature polyadenylation signal (PAS) termination. By generating RNA exosome conditional deletion mouse embryonic stem cells, we identified a large class of polyadenylated short transcripts in the sense direction destabilized by the RNA exosome. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

4 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19057

20 Samples

Download data: BW

(Submitter supplied) Regulation of RNA polymerase II (Pol II) elongation is a critical step in gene regulation. Here, we report that U1 snRNP recognition and transcription pausing at stable nucleosomes are linked through premature polyadenylation signal (PAS) termination. By generating RNA exosome conditional deletion mouse embryonic stem cells, we identified a large class of polyadenylated short transcripts in the sense direction destabilized by the RNA exosome. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

12 Samples

Download data: BW, TXT

(Submitter supplied) Regulation of RNA polymerase II (Pol II) elongation is a critical step in gene regulation. Here, we report that U1 snRNP recognition and transcription pausing at stable nucleosomes are linked through premature polyadenylation signal (PAS) termination. By generating RNA exosome conditional deletion mouse embryonic stem cells, we identified a large class of polyadenylated short transcripts in the sense direction destabilized by the RNA exosome. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: BW, TXT

(Submitter supplied) Pervasive transcription in the mammalian genome produces thousands of long noncoding RNAs (lncRNAs) and promoter- or enhancer-associated unstable transcripts. They preferentially locate to chromatin, at which some regulate chromatin structure, transcription and RNA processing. While several RNA sequences responsible for nuclear localization have been identified, such as repeats in the lncRNA Xist and Alu-like elements for long RNAs, how lncRNAs as a class are enriched on chromatin remains elusive. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21273

112 Samples

Download data: BED, BW, TXT

(Submitter supplied) RNA subcellular localization often correlates with its function and regulation. For many long noncoding RNAs (lncRNAs) and some isoforms of coding genes, their transcripts are preferentially retained on the chromatin. However, the mechanisms controlling the chromatin retention of lncRNAs and mRNA transcripts remain largely unknown. We hypothesize that embedded RNA sequences and interacting proteins may be the cis and trans regulators governing RNA subcellular localization, respectively. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL20795 GPL21273

12 Samples

Download data: TXT

(Submitter supplied) Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis in human cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL21697

48 Samples

Download data: BW, GTF

(Submitter supplied) Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was performed to generate genome-wide binding maps of two U1-snRNP proteins: U1C and U1-70K in Trypanosoma brucei.

Organism:

Trypanosoma brucei

Type:

Other

Platforms:

GPL16563 GPL16562 GPL16561

5 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: BEDGRAPH, BW, TXT

(Submitter supplied) In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: TXT

(Submitter supplied) In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

7 Samples

Download data: BW

(Submitter supplied) In eukaryotes, U1 small nuclear ribonucleoprotein (snRNP) forms spliceosomes in equal stoichiometry with U2, U4, U5 and U6 snRNPs; however, its abundance in human far exceeds that of the other snRNPs. Here we used antisense morpholino oligonucleotide to U1 snRNA to achieve functional U1 snRNP knockdown in HeLa cells, and identified accumulated unspliced pre-mRNAs by genomic tiling microarrays. In addition to inhibiting splicing, U1 snRNP knockdown caused premature cleavage and polyadenylation in numerous pre-mRNAs at cryptic polyadenylation signals, frequently in introns near (<5 kilobases) the start of the transcript. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL4914

3 Samples

Download data: BAR, CEL

(Submitter supplied) Full-length transcription in the majority of human genes depends on U1 snRNP (U1) to co-transcriptionally suppress transcription-terminating premature 3’-end cleavage and polyadenylation (PCPA) from cryptic polyadenylation signals (PASs) in introns. However, the mechanism of this U1 activity, termed telescripting, is unknown. Here, we captured a complex, comprising U1 and CPA factors (U1–CPAFs), that binds intronic PASs and suppresses PCPA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

22 Samples

Download data: BW