Identification of U2AF(35)-dependent exons by RNA-Seq reveals a link between 3' splice-site organization and activity of U2AF-related proteins

Nucleic Acids Research
Jana KralovicovaIgor Vorechovsky

Abstract

The auxiliary factor of U2 small nuclear RNA (U2AF) is a heterodimer consisting of 65- and 35-kD proteins that bind the polypyrimidine tract (PPT) and AG dinucleotides at the 3' splice site (3'ss). The gene encoding U2AF35 (U2AF1) is alternatively spliced, giving rise to two isoforms U2AF35a and U2AF35b. Here, we knocked down U2AF35 and each isoform and characterized transcriptomes of HEK293 cells with varying U2AF35/U2AF65 and U2AF35a/b ratios. Depletion of both isoforms preferentially modified alternative RNA processing events without widespread failure to recognize 3'ss or constitutive exons. Over a third of differentially used exons were terminal, resulting largely from the use of known alternative polyadenylation (APA) sites. Intronic APA sites activated in depleted cultures were mostly proximal whereas tandem 3'UTR APA was biased toward distal sites. Exons upregulated in depleted cells were preceded by longer AG exclusion zones and PPTs than downregulated or control exons and were largely activated by PUF60 and repressed by CAPERα. The U2AF(35) repression and activation was associated with a significant interchange in the average probabilities to form single-stranded RNA in the optimal PPT and branch site locations and se...Continue Reading

Associated Datasets

Mar 16, 2015·Marcin Knut, Igor Vorechovsky
May 25, 2018·Marcin Knut, Igor Vorechovsky

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Citations

Sep 16, 2015·Cellular and Molecular Life Sciences : CMLS·Muhammad Sohail, Jiuyong Xie
Aug 28, 2016·Nucleic Acids Research·Jana Kralovicova, Igor Vorechovsky
Sep 23, 2016·Nucleic Acid Therapeutics·Jana KralovicovaIgor Vorechovsky
Dec 8, 2015·PloS One·Stepan DenisovMikhail Gelfand
Jul 20, 2017·International Journal of Cancer. Journal International Du Cancer·Bin WangJer-Tsong Hsieh
Jul 5, 2019·EMBO Reports·Manel TariAlexandre Maucuer
Sep 12, 2020·International Journal of Molecular Sciences·Tatiana KováčováLucie Grodecká
Apr 25, 2017·The Journal of Clinical Investigation·Bon Ham YipJacqueline Boultwood
Dec 1, 2019·Genome Biology·Sébastien LemaireDidier Auboeuf
May 23, 2018·Nucleic Acids Research·Jana KrálovicováIgor Vorechovský
Feb 8, 2021·Nucleic Acids Research·Jana KrálovičováIgor Vořechovský
Jul 3, 2021·International Journal of Molecular Sciences·Cristina Martínez-ValienteAlejandra Sanjuan-Pla
Aug 22, 2021·Cellular Microbiology·Che Julius NgwaGabriele Pradel
Sep 15, 2021·The FEBS Journal·Asaki KobayashiAlexandre Maucuer

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Datasets Mentioned

BETA
E-MTAB-2682

Methods Mentioned

BETA
transfections
RNA-Seq
PCR
transfection
footprinting
3′-seq
deubiquitination

Software Mentioned

MEME
MISO
Cufflinks
RNAfold
R
TopHat
DAVID
Browser
CummeRbund
DEXSeq

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