Identification of a novel gene on chromosome 7q31 that is interrupted by a translocation breakpoint in an autistic individual

Abstract

The results of genetic linkage studies for autism have suggested that a susceptibility locus for the disease is located on the long arm of chromosome 7 (7q). An autistic individual carrying a translocation, t(7;13)(q31.3;q21), with the chromosome 7 breakpoint located in the region of 7q implicated by genetic studies was identified. A novel gene known as "RAY1" (or "FAM4A1") was found to be directly interrupted by the translocation breakpoint. The gene, which was found to be encoded by 16 exons with evidence of alternative splicing, spanned > or =220 kb of DNA at 7q31.3. Mutation screening of the entire coding region in a set of 27 unrelated autistic individuals failed to identify phenotype-specific variants, suggesting that coding region mutations are unlikely to be involved in the etiology of autism. Apparent homologues of RAY1 have also been identified in mouse, rat, pig, chicken, fruit fly, and nematode. The human and mouse genes share similar splicing patterns, and their predicted protein products are 98% identical.

Figure 1

Ideogram of the long arm of chromosome 7 indicating the relative positions of positive linkage results from genome scans for autism and severe speech and language disorder (from Barrett et al. [A]; Fisher et al. [B; for SPCH1]; IMGSAC [C]; Philippe et al. [D]; Ashley-Koch et al. [E]; and Barrett et al. [F]). The position of RAY1 and the translocation breakpoint for t(7;13)(q31.2;q21), relative to neighboring genes and DNA markers, is also shown. RAY1 contains 16 exons and spans two BAC clones and one PAC clone. Exon 7 is alternatively spliced, and alternate 3′ terminal exons (16a or 16b), are employed in different transcripts. The translocation breakpoint probably occurs between exons 9 and 10 (cosmid clone 14c9 is translocated and 172d6 is not translocated). The relative positions of the CpG island, antisense transcript Hs. 131046, and the 139-bp palindrome are also shown. The end sequences of cosmids cos14c9, cos 19d10, cos172d6, and BAC H_NH0032P06 were generated, which allowed them to be aligned to the existing genomic sequence.

Figure 2

Amino acid sequence alignment for cloned human RAY1 (FAM4A1), mouse mray (Fam4a1), and the deduced D. melanogaster (fruit fly) and C. elegans (nematode) genes dray and nray. The D. melanogaster gene was deduced by analysis of genomic clone CDM:10211043 (GenBank accession number AC014350), by use of GENSCAN, and from EST clones (GenBank accession numbers AA438606 and AA949923). The C. elegans gene sequence was deduced by analysis of genomic clone CEF11A10 (GenBank accession number Z68297), by use of FGENES, and from EST sequences (GenBank accession numbers C45487, C40736, C34292 and M80024). 5′ mRNAs (GenBank accession numbers AW360118 and AW436819) for a pig homologue were also identified; taken together, they encode for 241 N-terminal amino acids, which are identical to 240 of the first 242 amino acids of the human sequence. A rat EST clone (GenBank accession number AW141348) encodes the 3′ end of the gene, which is 100% identical to the human C-terminal 120 amino acids.

Figure 3

Multiple-tissue northern blot (Clontech) for human RAY1, for selected tissues: heart (a), brain (b), placenta (c), lung (d), liver (e), skeletal muscle (f), kidney (g), and pancreas (h). A 2.4-kb transcript is abundant in most tissues—in particular, the heart, liver, and pancreas. A less abundant but slightly larger transcript can be seen for brain (∼2.5 kb), and larger transcripts (∼2.8 kb) are also present in the heart and the placenta, in addition to the 2.4-kb transcript.