Specific sequence changes in multiple transcript system DYT3 are associated with X-linked dystonia parkinsonism

Abstract

X-linked dystonia parkinsonism (XDP) is an X-linked recessive adult onset movement disorder characterized by both dystonia and parkinsonism. We report delineation of the disease gene within a 300-kb interval of Xq13.1 by allelic association. Sequencing of this region in a patient revealed five disease-specific single-nucleotide changes (here referred to as DSC) and a 48-bp deletion unique to XDP. One of the DSCs is located within an exon of a not previously described multiple transcript system that is composed of at least 16 exons. There is a minimum of three different transcription start sites that encode four different transcripts. Two of these transcripts include distal portions of the TAF1 gene (TATA-box binding protein-associated factor 1) and are alternatively spliced. Three exons overlap with ING2 (a putative tumor suppressor) and with a homologue of CIS4 (cytokine-inducible SH2 protein 4), both of which are encoded by the opposite strand. Although all DSCs are located within this multiple transcript system, only DSC3 lies within an exon. This exon is used by all alternative transcripts making a pathogenic role of DSC3 in XDP likely. The multiple transcript system is therefore referred to as DYT3 (disease locus in XDP).

Fig. 1.

Genomic delineation and analysis of DYT3.(a) Contig of the initial XDP critical region spanning ≈400 kb (11). The thick upper line indicates the 260 kb sequenced in an XDP patient. (b) The genes assigned to the newly defined critical interval of 300 kb are given in color. Blue, TAF1 (17) (TATA box-binding protein associated factor 1); red, ING2 (18) (inhibitor of growth family member 2); green, OGT (19 -21) (O-linked-N-acetylglucosamine transferase); yellow, CXCR3 (23) [chemokine (C-X-C motif) receptor 3]; black, DYT3 (gene mutated in XDP); orange, ACRC (22) (acidic repeat-containing gene). Orientation of transcription is indicated by arrows. (c) Genomic structure of DYT3. Exons derived from TAF1 (blue) are numbered according to TAF1 nomenclature. Novel exons identified within TAF1 are marked light blue. The first facultative exon of DYT3 is numbered 1, followed by exons 2-5. Exon 2 is highlighted red, because ING2 covers part of its opposite strand. The first exon of OGT is given in green. Potentially relevant CpG islands, putative Pol II promoters, and polyadenylation sites are indicated. (d) Alternative transcripts 1, 2, and 3 were discovered in phage (phage 7/02, phage 3/03, and phage 10/02, respectively). Transcript 2 was extended by RT-PCR by using primer 189510R derived from exon 4 in combination with various TAF1-specific primers. These experiments resulted in the identification of splice variants a-e of transcript 2.

Fig. 2.

Analysis of polymorphic changes in DYT3 critical region. (a) DSCs 1, 2, 3, 10, and 12; SNPs 4 and 5; and the 48-bp deletion in their sequence context. (b) Sequence analysis of DSC3, the only DSC embedded in an exonic DNA sequence in an XDP patient and a Filipino male control.