N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3'-end processing

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Authors

BARTOŠOVIČ Marek COVELO MOLARES Helena GREGOROVÁ Pavlína HROŠŠOVÁ Dominika KUDLA G. VAŇÁČOVÁ Štěpánka

Year of publication 2017
Type Article in Periodical
Magazine / Source Nucleic Acids Research
MU Faculty or unit

Central European Institute of Technology

Citation
Web https://academic.oup.com/nar/article/45/19/11356/4097621
Doi http://dx.doi.org/10.1093/nar/gkx778
Keywords EMBRYONIC STEM-CELLS; BLOCKED 5' TERMINI; SEX DETERMINATION; COMPREHENSIVE ANALYSIS; NUCLEAR-RNA; METHYLATION; DROSOPHILA; REVEALS; OBESITY; N-6-METHYLADENOSINE
Description N6-methyladenosine (m(6)A) is the most abundant base modification found in messenger RNAs (mRNAs). The discovery of FTO as the first m6A mRNA demethylase established the concept of reversible RNA modification. Here, we present a comprehensive transcriptome-wide analysis of RNA demethylation and uncover FTO as a potent regulator of nuclear mRNA processing events such as alternative splicing and 3' end mRNA processing. We show that FTO binds preferentially to pre-mRNAs in intronic regions, in the proximity of alternatively spliced (AS) exons and poly(A) sites. FTO knockout (KO) results in substantial changes in pre-mRNA splicing with prevalence of exon skipping events. The alternative splicing effects of FTO KO anti-correlate with METTL3 knockdown suggesting the involvement of m(6)A. Besides, deletion of intronic region that contains m(6)A-linked DRACH motifs partially rescues the FTO KO phenotype in a reporter system. All together, we demonstrate that the splicing effects of FTO are dependent on the catalytic activity in vivo and are mediated by m(6)A. Our results reveal for the first time the dynamic connection between FTO RNA binding and demethylation activity that influences several mRNA processing events.
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