Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping.

Journal Article (Academic article)

To facilitate transcript mapping and to investigate alterations in genomic structure and gene expression in a defined genomic target, we developed a novel microarray-based method to detect transcriptional activity of the human chromosome 4q22-24 region. Loss of heterozygosity of human 4q22-24 is frequently observed in hepatocellular carcinoma (HCC). One hundred and eighteen well-characterized genes have been identified from this region. We took previously sequenced shotgun subclones as templates to amplify overlapping sequences for the genomic segment and constructed a chromosome-region-specific microarray. Using genomic DNA fragments as probes, we detected transcriptional activity from within this region among five different tissues. The hybridization results indicate that there are new transcripts that have not yet been identified by other methods. The existence of new transcripts encoded by genes in this region was confirmed by PCR cloning or cDNA library screening. The procedure reported here allows coupling of shotgun sequencing with transcript mapping and, potentially, detailed analysis of gene expression and chromosomal copy of the genomic sequence for the putative HCC tumor suppressor gene(s) in the 4q candidate region.

Duke Authors

Cited Authors

  • Li, LH; Li, JC; Lin, YF; Lin, CY; Chen, CY; Tsai, SF

Published Date

  • 2004

Published In

Volume / Issue

  • 32 / 3

Start / End Page

  • e27 -

International Standard Serial Number (ISSN)

  • 1362-4962

Conference Location

  • england