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Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 3'end cleavage factor mPAT

ABSTRACT: mPAT approach was used to determine changes to 3'UTR length in yeast upon mutation of cleavage and polyadenylation factor subunits compared to wild type cells

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE160995 | GEO | 2021/06/25

REPOSITORIES: GEO

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Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 3'end cleavage factors

Project description:PAT-seq approach was used to determine changes to 3'UTR length in yeast upon mutation of the core cleavage and polyadenylation subunits Rna14 (rna14-1), Pcf11 (pcf11-2), Clp1 (clp1-K136A-T137A), Hrp1/Nab4 (Nab4-1), Ysh1 (ysh1-13), Fip1 (fip1-1) and Pap1 (pap1-1) compared to wild type cells

2021-06-25 | GSE160538 | GEO

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment

Project description:mPAT approach using an anchored oligo-dT (TV12VN) primer to determine changes to 3'UTR length in yeast upon cordycepin treatment and new transcription using 4-thiouracil (4tU) labelling of RNA. This appears as a T to C conversion in sequencing reads.

2021-06-25 | GSE160993 | GEO

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment with rpb1 slow mutant

Project description:mPAT approach using an anchored oligo-dT (TV12VN) primer to determine changes to 3'UTR length in yeast with a slow RNA polymerase II mutant rpb1-1, complemented with wild-type RPB1 or a slow rpb1 mutant plasmid, upon cordycepin treatment and new transcription using 4-thiouracil (4tU) labelling of RNA. This appears as a T to C conversion in sequencing reads.

2021-06-25 | GSE160994 | GEO

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - cordycepin treatment

Project description:PAT-seq approach was used to determine changes to 3'UTR length in yeast upon addition of 20µg/ml cordycepin (3'deoxyadenosine) for 0, 5, 10, 20 or 40 minutes

2021-06-25 | GSE160537 | GEO

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - NNS complex

Project description:PAT-seq approach was used to determine changes to 3'UTR length in yeast upon mutation of NNS subunits Nrd1 (nrd1-5), Nab3 (nab3-11) and Sen1 (sen1-1) compared to wild type cells

2021-06-25 | GSE160567 | GEO

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 3'end cleavage factor mPAT

Project description:Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 3'end cleavage factor mPAT

| PRJNA675092 | ENA

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast

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

2021-06-25 | GSE160539 | GEO

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast.

Project description: Not available

| S-EPMC8263057 | biostudies-literature

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 3'end cleavage factors

Project description:Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 3'end cleavage factors

| PRJNA673493 | ENA

Regulation of alternative cleavage and polyadenylation by 3’ end processing and splicing factors

Project description:Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage and polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1, and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly influencing C/P events in 5’ introns and U2 impacting those in efficiently spliced introns. Furthermore, PABPN1 regulates expression of transcripts with pAs near the transcription start site, a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results indicate that the abundance of different C/P factors and splicing factors plays diverse roles in APA, and is relevant to APA regulation in biological conditions. knockdown experiments of 23 C/P factors, 3 splicing factors and U1D in mouse C2C12 myoblast cells

2015-04-01 | E-GEOD-62001 | biostudies-arrayexpress

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