DNA sequence comparison of human and mouse retinitis pigmentosa GTPase regulator (RPGR) identifies tissue-specific exons and putative regulatory elements

Abstract

Retinitis pigmentosa 3 (RP3) is a progressive retinal degeneration due to mutations in the X-linked RPGR gene. Transcription studies in human and mouse tissues have revealed ubiquitously expressed transcripts and also an exceptional high number of tissue-specific alternative splice variants. However, regulation of tissue-specific expression and splicing is unclear, but this is of particular interest as mutations in this ubiquitously expressed gene lead to severe retinal degeneration, while other tissues are unaffected. To elucidate the conservation pattern of RPGR and to identify additional tissue-specific exons and putative regulatory elements we performed comparative genomic sequencing of the human and mouse RPGR gene. Each of the genes spans a region of nearly 59 kb, and all previously identified exons are conserved between the two species. DNA sequence comparison identified 28 conserved sequence elements (CSEs) in introns, upstream of exon 1, within the promotor region, and downstream of the most 3' exon. Some of the intronic CSEs flank tissue-specific exons and therefore may represent important regulatory elements for alternative splicing. Comparative northern blot hybridization of ubiquitous and tissue-specific RPGR probes identified high molecular weight transcripts with similar expression patterns in both human and mouse. These transcripts range from 6 to 15 kb in size and suggest the presence of additional transcribed sequences within RPGR. Our cross-species sequence comparison enables us to define candidate regions that may explain these large transcripts and will therefore contribute to the understanding of RPGR expression and splicing.

Clinical and immunohistochemical evidence for an X linked retinitis pigmentosa syndrome with recurrent infections and hearing loss in association with an RPGR mutation

“…Therefore, RPGR functions also may be broader than ciliary trafficking alone. Likewise, ORF15 had been suggested to be a relatively ''retina specific'' sequence; 39 however, by using the MCW27 anti-ORF15 antibodies, we showed highly specific expression of this sequence at least in the epithelial lining of the respiratory tract and in non-ciliated cochlear tissues, which suggests a wider expression of ORF15 and a broader functional role of RPGR than previously recognised. We are unaware of any reported cochlear abnormality or respiratory tract problem either in the RPGR knockout mouse 34 or in the Siberian husky, which harbours naturally occurring RPGR mutations.…”

Identification and characterization of a novel RPGR isoform in human retina

“…In humans, exons ORF15, 15a, and 15b can be included into RPGR transcripts, whereas 14 and 15 are occasionally excluded [Kirschner et al, 1999;Vervoort et al, 2000]. As shown for ORF15, isoform-specific exons can be predominantly expressed in the retina and may even constitute hotspots for RP-associated mutations [Bader et al, 2003;Kirschner et al, 2001;Sharon et al, 2003;Vervoort and Wright, 2002].…”

“…Surprisingly, disease associated sequence variants in exons 1 trough 15 of RPGR have only been found in 20% of all X-linked cases. Many of the remaining XLRP patients carry deletions or insertions in an RPGR exon called ORF15, which is alternatively spliced and found predominantly in retina and brain [Kirschner et al, 2001;Vervoort et al, 2000]. Furthermore, disease-associated sequence variants in humans cluster in ORF15, whereas none have been identified in exons 16 to 19 (for reference, see The Human Gene Mutation Database; www.hgmd.org).…”

“…The existence of not yet identified RPGR exons may explain the remaining RP families that are linked to the RPGR interval but lack disease-associated sequence alterations in known exons. To date, several splice variants of RPGR have been reported [Kirschner et al, 1999[Kirschner et al, , 2001Vervoort et al, 2000]. All isoforms affect the protein composition of the C-terminal part of the protein.…”

Overexpression of RPGR Leads to Male Infertility in Mice Due to Defects in Flagellar Assembly1

“…This domain is thought to be common to the majority of both human and murine RPGR protein isoforms known to date. Mouse and humans share 76.4% and 64% identity at the nucleotide and amino acid level, respectively [13]. The N-terminal RCC1-like domain retains 80% amino acid identity [14].…”