Autism is associated with chromosomal abnormalities such as microduplications, deletions and inversions. The gender bias of autistic disorder suggests an important role of the X-chromosome in the etiology of the disease. Homologous recombination (HR) initiated by double-strand breaks can repair and diversify mammalian genes. Non-allelic homologous recombination can lead to predispositions to disease, for example, by changing gene dosage by duplications or deletions. Regions on chromosomes with high frequency of recombination are called “recombination hotspots.” Recombination hotspots in the human genome have been mapped and a 13-mer motif is found to be present in more than 40% of the hotspots. Notably, some of these hotspots are found to be located close to known disease-causing nonallelic HR hot spots and common mitochondrial deletion hot spots. In this work, autism-associated genes in the X-chromosome are checked for hotspots and five out of fifteen genes (NLGN4X, NLGN3, AFF2, GRPR, and IL1RAPL1) are found to contain them. Moreover, it is shown that some exons of these genes unexpectedly contain perfect or near-perfect matches to the most common 13-mer hotspot motif. Possible effects of the presence of the 13-mer motif matches are predicted based on cell mechanisms and three-dimensional protein structures.
To predict the possible effects of the presence of the 13-mer hotspot motif in exons of autism-associated genes in the X-chromosome.
Recombination hotspots in autism-associated genes were found by overlaying the locations of the hotspots with gene coordinates. The presence of the most common 13-mer motif was detected in exons by alignment of the motif with the individual exons. Protein structural modeling and SNP analyses were used to predict the possible effects of the hotspot motifs.
The alignments showed the presence of 12-mer matches in GRPR at exon2, NLGN4X at exons 2 and 3, NLGN3 at exons 2 and 8 and AFF2 at exons 11, 14, 17 and 21. There is a perfect 13-mer match for GRPR exon3 and AFF2 exon15. No matches were found in IL1RAPL1 exons. On GRPR exon3, the hotspot region is located in the cytoplasm at the C-terminus; and HR is predicted to cause interruption of multiple cellular signal transduction pathways. The 12-mer match on exon2 of GRPR affects the third extracellular domains that are essential for the GRP-ligand specificity. Both exons 2 and 8 of NLGN3 along with exon2 of NLGN4X are known to be involved in binding with Neurexin1. A SNP can convert the 12-mer match to a 13-mer match, and HR is predicted to interrupt the signal transport between NLGN4X/NLGN3 and Neurexin1. On AFF2, both 13-mer motifs on exon15 and 12-mer motifs on exons 17 and 21 can affect translation and transcription, and the ability to bind to guanine-quartets; while the 12-mer motif on exon11 is predicted to interrupt the nuclear localization signals for the FMR2 protein.
Although most recombination hotspots are located far from coding regions of the genome, this study has shown perfect or near-perfect motif matches inside exons of genes associated with autism, with potential disease-causing effects.