Identifying genes within microdissected genomic DNA: isolation of brain expressed genes from a translocation region associated with inherited mental illness

A STS content physical and transcription map across the ky, kyphoscoliosis, nonrecombinant region

The ky mouse mutant exhibits a degenerative muscle disease resulting in chronic deformation of the spinal column. Following a previous report describing the mapping of the ky locus to a small region of mouse chromosome 9 (Skynner et al., 1995, Genomics 25, 207-213), we have now undertaken a positional cloning approach to identify candidate genes for ky. A YAC/BAC contig encompassing the ky locus was constructed comprising 48 YAC clones and 48 newly generated STSs. The results from the combined physical and genetic analyses showed that only two overlapping BAC clones, which together do not exceed 260 kb, span the ky nonrecombinant region. A combination of gene hunting methods on the critical BACs has led to the identification of seven coding fragments, which have been tested for expression. The expression analysis and the position of the coding fragments on the contig suggest their grouping in at least four transcription units. One of these transcription units is expressed exclusively in skeletal muscle, making it a suitable candidate for this muscle defect in the ky mouse.

Microdissection of pig chromosomes: dissection of whole chromosomes, arms and bands for construction of paints and libraries

Chromosome microdissection is an important means to efficiently generate a large number of markers from a desired region of a genome. The present study was designed to initiate microdissection and amplification of DNA from whole chromosomes, arms, or bands of porcine chromosomes. The following pig (SSC) chromosomes/segments were scraped: SSC1p, SSC1q26-q2.13, SSC2q11-q14, SSC4q12-q25, SSC13, SSC13q12-q31, SSC13q32-q43, SSC13q32-q43, SSC15, and SSC16q21-q23. After amplification and PCR-labelling, the DNA from the dissected segments were painted back to normal metaphase chromosomes to test their identity. Microdissection of some of the segments (on SSC4, 13 and 15) coincides with the mapping of economically important traits. As a first step towards generation of markers, microcloning of amplified product from SSC1p and SSC15 was carried out. The libraries were screened with a (GT)15 oligonucleotide probe. Future prospects of such a work in farm animals are discussed.

Novel transcribed sequences neighbouring a translocation breakpoint associated with schizophrenia

A 1.3Mb chromosome 11-specific yeast artificial chromosome (YAC) that spans a t(1;11) translocation breakpoint associated with major psychosis has been used to enrich cDNAs that are encoded within it and expressed in the human foetal brain. Database analysis of the selected fragments led to the identification of 54 clones matching alpha-tubulin, 4 fragments matching two anonymous human expressed sequence tags (ESTs) and 8 fragments giving no database matches. The clones matching alpha-tubulin led to the identification of a novel alpha-tubulin locus located approximately 250 kb proximal to the translocation breakpoint. Extensive sequence and expression analysis of this locus suggests that this is a processed pseudogene, although a long open reading frame is maintained and the possibility that an abnormally acting protein may be expressed in a highly tissue or developmental specific manner cannot be discounted. The novel cDNA fragments map up to 700 kb proximal to the translocation breakpoint and are associated with potential CpG islands. Reverse transcriptase polymerase chain reaction (RT-PCR) expression analysis and high resolution genomic mapping suggest that they may comprise up to three novel genes. No major disruption of the identified fragments could be detected in the genomic DNA of translocation carriers. The psychosis associated with this translocation may therefore be due to position effects on the transcription of these genes or an involvement of translocated chromosome 1 sequences.