Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X‐box promoter motifs

Abstract

DYX1C1, DCDC2, and KIAA0319 are three of the most replicated dyslexia candidate genes (DCGs). Recently, these DCGs were implicated in functions at the cilium. Here, we investigate the regulation of these DCGs by Regulatory Factor X transcription factors (RFX TFs), a gene family known for transcriptionally regulating ciliary genes. We identify conserved X-box motifs in the promoter regions of DYX1C1, DCDC2, and KIAA0319 and demonstrate their functionality, as well as the ability to recruit RFX TFs using reporter gene and electrophoretic mobility shift assays. Furthermore, we uncover a complex regulation pattern between RFX1, RFX2, and RFX3 and their significant effect on modifying the endogenous expression of DYX1C1 and DCDC2 in a human retinal pigmented epithelial cell line immortalized with hTERT (hTERT-RPE1). In addition, induction of ciliogenesis increases the expression of RFX TFs and DCGs. At the protein level, we show that endogenous DYX1C1 localizes to the base of the cilium, whereas DCDC2 localizes along the entire axoneme of the cilium, thereby validating earlier localization studies using overexpression models. Our results corroborate the emerging role of DCGs in ciliary function and characterize functional noncoding elements, X-box promoter motifs, in DCG promoter regions, which thus can be targeted for mutation screening in dyslexia and ciliopathies associated with these genes.—Tammimies, K., Bieder, A., Lauter, G., Sugiaman-Trapman, D., Torchet, R., Hokkanen, M.-E., Burghoorn, J., Castrén, E., Kere, J., Tapia-Páez, I., Swoboda, P. Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor (RF) X transcription factors through X-box promoter motifs.

Differentiation of ciliated human midbrain-derived LUHMES neurons

“…We confirmed the neuronal differentiation and ciliary gene STRT RNA-seq data with an independent method, qRT-PCR normalized against the housekeeping gene GAPDH. Pearson correlation coefficient plots demonstrated effectively identical differential gene expression patterns for a replication group of 17 genes ( Supplementary Figure S2; Supplementary Table S4 ): 4 neuronal differentiation markers (DCX, MAP2, TUBA1A, TUBB3); 2 cilia and ciliopathy genes (CCDC28B, IFT20); 6 cilia and ciliopathy genes with brain or neuron phenotypes (BBS1, BBS2, CC2D2A, IFT81, PDE6D, TCTN2); 2 candidate ciliogenic transcription factor genes (RFX2, RFX5); a ciliary dyslexia candidate gene (DYX1C1/DNAAF4); and 2 neuronal Parkinson’s disease associated genes (MAPT, SNCA) (Tammimies et al, 2016; Reiter and Leroux, 2017; Lauter et al, 2018; Youn and Han, 2018). Ciliogenesis was thus found as a prominent aspect during LUHMES neuronal differentiation.…”

Neuroimaging genetics studies of specific reading disability and developmental language disorder: A review

“…The remaining candidate genes for SRD have received relatively little attention in human neuroimaging studies. Like those of other SRD candidate genes, the protein encoded by DYX1C1 has been linked to neurodevelopmental processes (Currier, Etchegaray, Haight, Galaburda, & Rosen, ; Rosen et al, ; Szalkowski et al, ; Tammimies et al, ; Tarkar et al, ; Threlkeld et al, ; Wang et al, ), and variation on this gene has been associated with reading and spelling abilities in both general population (Bates et al, ; Newbury et al, ; Zhang et al, ) and clinical samples (Lim, Ho, Chou, & Waye, ; Marino et al, ; Venkatesh, Siddaiah, Padakannaya, & Ramachandra, ). With respect to neuroimaging, Darki et al () found a relationship between SNP rs3743204 in DYX1C1 and white matter volume in bilateral temporo‐parietal regions and correlations between white matter volume in these regions and reading scores.…”

Rare variants in dynein heavy chain genes in two individuals withsitus inversusand developmental dyslexia

“…We did not find any other structural variants in regions overlapping with candidate genes. 12 In summary, in individual 2 we identified a common DD-associated haplotype and a rare variant of unknown significance in the outer dynein arm component DNAH11, both inherited from the mother. 13…”

“…Several reports have demonstrated that DD candidate genes have a role in cilia (7,8,11,12,(14)(15)(16)(17)(18). Furthermore, L/R asymmetry defects in the brain have been proposed as an anatomical basis to neurodevelopmental disorders such as schizophrenia and specifically to DD, possibly mediated by ciliary dysfunction (13,27).…”

“…Genetic studies of DD have led to the identification of a number of dyslexia susceptibility genes, reviewed in (6). Interestingly, some of them, namely DYX1C1 (DNAAF4), DCDC2 and KIAA0319, have a reported role in cilia (7)(8)(9)(10)(11)(12)(13). In addition, loss-offunction mutations in DYX1C1 and DCDC2 have been found in patients showing typical ciliary deficits: DYX1C1 in patients with PCD (14) and DCDC2 in patients with nephronophthisis-related ciliopathy, inherited deafness and neonatal sclerosing cholangitis 4 (15)(16)(17)(18).…”