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Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE145092 | GEO | 2021/06/16

REPOSITORIES: GEO

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Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally [ChIP-seq]

Project description: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. Correlation with splicing outcomes demonstrate that these associations are functional. The interactions between 5 splice sites, U1 snRNP, and elongating RNA polymerase II occurs genome-wide. Our findings reveal that during intron synthesis the upstream 5 splice site remains attached to the transcriptional machinery and is thus brought into proximity of the 3 splice site to enable rapid splicing.

2021-06-16 | GSE144874 | GEO

Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally

Project description:Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally

| PRJNA606025 | ENA

Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RIP-seq]

2021-06-16 | GSE144905 | GEO

Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RNA-Seq]

2021-06-16 | GSE144906 | GEO

Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally [ChIP-seq]

Project description:Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally [ChIP-seq]

| PRJNA605197 | ENA

Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RNA-Seq]

Project description:Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RNA-Seq]

| PRJNA605255 | ENA

Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RIP-seq]

Project description:Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RIP-seq]

| PRJNA605252 | ENA

Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA.

Project description:Communication between U1 and U2 snRNPs is critical during pre-spliceosome assembly; yet, direct connections have not been observed. To investigate this assembly step, we focused on Prp5, an RNA-dependent ATPase of the DExD/H family. We identified homologs of Saccharomyces cerevisiae Prp5 in humans (hPrp5) and Schizosaccharomyces pombe (SpPrp5), and investigated their interactions and function. Depletion and reconstitution of SpPrp5 from extracts demonstrate that ATP binding and hydrolysis by Prp5 are required for pre-spliceosome complex A formation. hPrp5 and SpPrp5 are each physically associated with both U1 and U2 snRNPs; Prp5 contains distinct U1- and U2-interacting domains that are required for pre-spliceosome assembly; and, we observe a Prp5-associated U1/U2 complex in S. pombe. Together, these data are consistent with Prp5 being a bridge between U1 and U2 snRNPs at the time of pre-spliceosome formation.

| S-EPMC1271757 | biostudies-literature

Efficient transcription through an intron requires the binding of an Sm-type U1 snRNP with intact stem loop II to the splice donor.

Project description:The mechanism behind the positive action of introns upon transcription and the biological significance of this positive feedback remains unclear. Functional ablation of splice sites within an HIV-derived env cDNA significantly reduced transcription that was rescued by a U1 snRNA modified to bind to the mutated splice donor (SD). Using this model we further characterized both the U1 and pre-mRNA structural requirements for transcriptional enhancement. U1 snRNA rescued as a mature Sm-type snRNP with an intact stem loop II. Position and sequence context for U1-binding is crucial because a promoter proximal intron placed upstream of the mutated SD failed to rescue transcription. Furthermore, U1-rescue was independent of promoter and exon sequence and is partially replaced by the transcription elongation activator Tat, pointing to an intron-localized block in transcriptional elongation. Thus, transcriptional coupling of U1 snRNA binding to the SD may licence the polymerase for transcription through the intron.

| S-EPMC2875018 | biostudies-literature

tRIP-seq reveals repression of premature polyadenylation by co-transcriptional FUS-U1 snRNP assembly.

Project description:RNA processing occurs co-transcriptionally through the dynamic recruitment of RNA processing factors to RNA polymerase II (RNAPII). However, transcriptome-wide identification of protein-RNA interactions specifically assembled on transcribing RNAPII is challenging. Here, we develop the targeted RNA immunoprecipitation sequencing (tRIP-seq) method that detects protein-RNA interaction sites in thousands of cells. The high sensitivity of tRIP-seq enables identification of protein-RNA interactions at functional subcellular levels. Application of tRIP-seq to the FUS-RNA complex in the RNAPII machinery reveals that FUS binds upstream of alternative polyadenylation (APA) sites of nascent RNA bound to RNAPII, which retards RNAPII and suppresses the recognition of the polyadenylation signal by CPSF. Further tRIP-seq analyses demonstrate that the repression of APA is achieved by a complex composed of FUS and U1 snRNP on RNAPII, but not by either one alone. Moreover, our analysis reveals that FUS mutations in familial amyotrophic lateral sclerosis (ALS) that impair the FUS-U1 snRNP interaction aberrantly activate the APA sites. tRIP-seq provides new insights into the regulatory mechanism of co-transcriptional RNA processing by RNA processing factors.

| S-EPMC7202220 | biostudies-literature

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