The RNA-binding proteins CELF1 and ELAVL1 cooperatively control RNA isoform production

Abstract

Corresponding authors: LP (Tel +33 22323 4473, luc.paillard@univ-rennes1.fr); and YA (Tel +33 22323 4475, yann.audic@univ-rennes1.fr).Running title CELF1, ELAVL1, and splice isoform production 1 5 10 15 20 ABSTRACT ELAVL1 and CELF1 are RNA-binding proteins that are involved in alternative splicing control. To explore their functional relationship, we looked for mRNAs that are differentially spliced following the depletion of CELF1, ELAVL1, or both. We found that these proteins control the usage of their target exons in the same direction. Double depletion has a greater effect than individual depletions, showing that CELF1 and ELAVL1 exert additive control. To confirm these results, we carried out RT-PCR on the alternative cassette exons of several mRNAs, including CD44, WNK1, PHACTR2, MICAL3, SPTBN1, and PPP3CB. Using FRET, we found that CELF1 and ELAVL1 directly interact in cell nuclei. We demonstrated that the combined levels of CELF1 and ELAVL1 are a valuable biomarker in several cancers, even when their individual levels may yield very limited information. CD44 alternative splicing probably accounts in part for the effects of CELF1 and ELAVL1 levels on patient survival. These data point to strong functional interactions between CELF1 and ELAVL1 in the control of mRNA isoform production, resulting in significant impacts on human pathology.

An Alzheimer’s disease pathway uncovered by functional omics: the risk gene CELF1 regulates KLC1 splice variant E expression, which drives Aβ pathology

“…CELF1 plays a role in cardiac development, myotonic dystrophy, and cancer 12,13 , but its function in AD has not been elucidated, even though the CELF1 locus has been associated with AD 6,7,8,9 . We found a direct relationship between CELF1 and KLC1 in data obtained by integrating two omics studies that we previously conducted 14,15 . First, transcriptomics data from HeLa cells showed that three of the ten exons most strongly altered by CELF1 knockdown were KLC1 exons (Fig.…”

“…As neuronal splicing is especially complex 38 , factors other than CELF1 may also regulate KLC1 splicing, and further studies are needed to fully understand the KLC1 splicing mechanism. In a similar example, the relationship between CELF1 expression and cancer patient survival is variable in different cancer types 14 . When conducting functional genomics for disease research, it is important to confirm the final conclusion of the functional expression analysis at the site of the disease lesion, which in the case of AD is the brain.…”

“…We have previously described the results of exon array experiments using Agilent (Santa Clara, California, USA) SurePrint G3 human exon array probes. Hybridized RNA was extracted from HeLa cells previously treated with siRNAs to repress CELF1, ELAVL , or both proteins or a control siRNA 14 . We examined the control siRNA and CELF1 siRNA datasets to identify the most highly differentially expressed exons.…”

GWAS-Top Polymorphisms Associated With Late-Onset Alzheimer Disease in Brazil: Pointing Out Possible New Culprits Among Non-Coding RNAs

“…The CELF1 ( CUGBP Elav-like family member 1 ) gene encodes CELF1 protein, a RNA-binding protein related to the regulation of different post-transcriptional events and alternative splicing, mRNA translation, and mRNA stability ( Beisang et al, 2012 ; Bateman et al, 2017 ). During alternative RNA processing, the protein can select the splicing target site by binding to U/G-rich elements in the transcript sequence, leading to mRNA decay and controlling translation efficiency (preprint David et al, 2020 ). The rs10838725 polymorphism has been associated with LOAD in a GWAS ( Lambert et al, 2013 ; Karch et al, 2016 ; Marioni et al, 2018 ).…”