Direct isolation of human transcribed sequences from yeast artificial chromosomes through the application of RNA fingerprinting

Cytogenetic evaluation: a primer for pediatric nurse practitioners

Patients with genetic disorders require specific types of cytogenetic testing for accurate diagnosis and prognosis followed by prompt treatment. This primer will serve as a guide for pediatric nurse practitioners on the use of various cytogenetic testing for the diagnosis of genetic disorders. Knowledge of the latest cytogenetic technologies will facilitate diagnosis and counseling related to genetic abnormalities such as inherited disorders, mental retardation, developmental delay, and autism. This reference will enable pediatric nurse practitioners to help identify patients with various inherited genetic disorders and provide subsequent monitoring and treatment.

Novel expressed sequences obtained by means of a suppression subtractive hybridisation analysis from the 6q21 region that is frequently deleted in gastric cancer

In our search for genomic regions that are involved in the development of gastric cancer, we recently identified a 2-cM minimal region of overlapping heterozygous deletions in 6q16.3-q23.1. Here, we describe an application of the suppression subtraction method (SSH) to search for genes in this small region of the genome, taking advantage of the fact that many human genes present on yeast artificial chromosomes (YACs) are expressed in yeast. Subtraction was performed with two virtually contiguous YACs that cover a region of approximately 2.5 Mb. Combined forward and reversed subtractions resulted in the identification of 12 clones of human origin, all of which could be confirmed by sequence analysis as originating from the 6q21 region. Expression in human tissues could be confirmed by Northern analysis for two of the clones, one of them showing a high level of expression in stomach tissue.

Transcription and proper splicing of a mammalian gene in yeast

The house mouse strain C57BL/6 harbours 64 copies of the multicopy gene Sp100-rs. Three of these are contained in the yeast artificial chromosome (YAC) clone yMm75. Four Sp100-rs transcripts of 3.0, 2.6, 1.6 and 1.3kb were detected by Northern hybridization in the yMm75-harbouring line of Saccharomyces cerevisiae. Additional and less abundant transcripts were detected by RT-PCR. With one exception, the YAC-derived Sp100-rs transcripts were a subset of those found in the C57BL/6 mouse. This indicates transcription and proper splicing of murine pre-mRNAs in yeast. Analysis of the splice sites shows that the yeast splicing machinery accepts splice sites that deviate from the standard yeast consensus sequences. It may be feasible, therefore, at least in a fair proportion of cases, to exploit the mammalian mRNAs present in transgenic yeast for gene recognition of YAC-inserts.

Identification of a novel gene (ADPRTL1) encoding a potential Poly(ADP-ribosyl)transferase protein

Poly(ADP-ribosyl)ation of nuclear proteins plays a significant role in the maintenance of genomic DNA stability. To date, four poly(ADP-ribosyl)ating proteins have been identified in humans. We now report the full-length sequence, expression profile, and chromosomal localization of a novel gene, ADPRTL1, encoding an ADP-ribosyltransferase-like protein. The predicted open reading frame encodes a protein of 1724 amino acids with a molecular mass of 192.8 kDa. The protein contains a region showing homology to the catalytic domains of the nuclear-localized ADP-ribosyltransferase proteins (Adprt), two recently identified Adprt-like proteins (Adprtl2 and Adprtl3), and the telomere-associated protein tankyrase. Key amino acids known to be important for the activity of these enzymes are conserved within this region of the Adprtl1 protein, indicating that Adprtl1 is a functional poly(ADP-ribosyl)transferase. As has been noted for tankyrase, sequence analysis of the Adprtl1 protein suggests that it is not capable of binding DNA directly. Thus, the transferase activity of Adprtl1 may be activated by other factors such as protein-protein interaction mediated by the extensive carboxyl terminus. We have subsequently refined the location of the ADPRTL1 genomic locus to 13q11, close to the recently cloned ZNF198 gene.

Transcription and RNA processing of mammalian genes in Saccharomyces cerevisiae

The recognition of mammalian genes encoded within a mouse yeast artificial chromosome (YAC) by the yeast transcription and RNA processing machinery was investigated. Transcripts from five genes known to be encoded by the YAC were all found in the total yeast RNA. Of 12 mouse introns assayed, six were correctly spliced by the yeast. However, an abnormal transcription of mouse DNA was also observed. Three genes of three tested were transcribed both from their sense and antisense strands and all tested microsatellite, inter-repetitive and anonymous mouse loci were detected in the YAC clone RNA. An RNA transcript from a well defined intergenic region of two head-to-head oriented mouse genes was detected by RT-PCR and by RNase protection assay. These results indicate the presence of multiple yeast-specific transcription sites in the mouse DNA. 3' RACE experiments demonstrated the inability of the yeast to use the mouse polyadenylation signals. Thus, a method for isolation of mammalian exons based on a YAC clone RNA is likely to produce a high background, because the enrichment with mammalian exons in the YAC RNA is low. Nevertheless, YAC clones can serve as in vivo test tubes to study the conservation of RNA processing sequences.