A 1.1-Mb Transcript Map of the Hereditary Hemochromatosis Locus
- David A. Ruddy1,
- Gregory S. Kronmal1,3,
- Vincent K. Lee1,3,
- Gabriel A. Mintier1,
- Leah Quintana1,
- Rodolfo Domingo, Jr.1,
- Nicole C. Meyer1,
- Alivelu Irrinki1,
- Erin E. McClelland1,
- Amy Fullan1,
- Felipa A. Mapa1,
- Theodore Moore1,
- Winston Thomas1,
- Deborah B. Loeb1,
- Cyrus Harmon2,
- Zenta Tsuchihashi1,
- Roger K. Wolff1,
- Randall C. Schatzman1, and
- John N. Feder1,4
Abstract
In the process of positionally cloning a candidate gene responsible for hereditary hemochromatosis (HH), we constructed a 1.1-Mb transcript map of the region of human chromosome 6p that lies 4.5 Mb telomeric toHLA-A. A combination of three gene-finding techniques, direct cDNA selection, exon trapping, and sample sequencing, were used initially for a saturation screening of the 1.1-Mb region for expressed sequence fragments. As genetic analysis further narrowed the HH candidate locus, we sequenced completely 0.25 Mb of genomic DNA as a final measure to identify all genes. Besides the novel MHC class 1-like HH candidate geneHLA-H, we identified a family of five butyrophilin-related sequences, two genes with structural similarity to a type 1 sodium phosphate transporter, 12 novel histone genes, and a gene we namedRoRet based on its strong similarity to the 52-kDRo/SSA lupus and Sjogren’s syndrome auto-antigen and theRET finger protein. Several members of the butyrophilin family and theRoRet gene share an exon of common evolutionary origin called B30-2. The B30-2 exon was originally isolated from the HLA class 1 region, yet has apparently “shuffled” into several genes along the chromosome telomeric to the MHC. The conservation of the B30-2 exon in several novel genes and the previously described amino acid homology ofHLA-H to MHC class 1 molecules provide further support that this gene-rich region of 6p21.3 is related to the MHC. Finally, we performed an analysis of the four approaches for gene finding and conclude that direct selection provides the most effective probes for cDNA screening, and that as much as 30% of ESTs in this 1.1-Mb region may be derived from noncoding genomic DNA.
[The sequence data described in this paper have been submitted to GenBank under accession nos.U90543–U90548,U90550–U90552, andU91328.]
