Genomic structure of a Y-specific ribonucleic acid binding motif-containing gene: a putative candidate for a subset of male infertility.

The genetic basis of infertility remains unclear in a majority of infertile men. Deletion mapping studies suggest that genes on the long arm of the Y-chromosome (Yq) may be important in the spermatogenic process and may play a pathogenetic role in a subset of infertile men. Complementary DNA sequences of two Y-specific genes that contain ribonucleic acid binding motifs and, therefore, referred to as RBM genes (previously named YRRM) were published recently. To develop a PCR-single strand conformation polymorphism strategy for detection of point mutations in the RBM gene(s) in infertile men, we determined the genomic structure and flanking sequences at the intron-exon junctions. Two separate strategies were used in parallel to isolate the genomic fragment bearing the RBM gene. The first strategy employed screening of a P1 genomic library using PCR primers corresponding to the sequences in the 5'- and 3'-ends of the published RBM-1 complementary DNA sequence. The second strategy used subcloning of the YAC clone 925D10 (that contained the RBM gene described here) into cosmids. The P1 and cosmid clones were further restriction mapped and subcloned for DNA sequencing. Because the sequences contained in the P1 and cosmid clones were identical, the sequence information was pooled. A 15-kilobase genomic segment includes the entire RBM gene. The genomic structure of this RBM gene is characterized by 12 exons and 11 introns. There is considerable homology among exons VII, VIII, IX, and X; each encodes one of the SRGY boxes. Several introns also have a high degree of homology among them (introns VI, VII, VIII, and IX). Eleven of the 12 exons have complete sequence homology with the RBM-1 sequence. There is 1 base difference in exon IV at position 495 (a T in the previously published DNA sequence vs. an A in the sequence reported here). The exonic sequences of this gene are distinct from that of the RBM-2 gene. The flanking sequences at the exon-intron junctions were also determined and are reported. Reverse transcription-PCR analysis, using human testis ribonucleic acid suggests that this gene is either not expressed in the testis or, more likely, the single base difference from RBM1 represents a polymorphism in the YAC clone. A high degree of homology between intronic and exonic sequences within the same gene and between different members of the RBM gene family (data not reported in this paper) suggests origin from common ancestral sequences; this also indicates that development of a single strand conformation polymorphism approach for detection of point mutations is likely to prove difficult for some of the exons of this gene.