We have physically mapped and cloned a 2.5-Mb chromosomal segment flanking the centromeric end of the major histocompatibility complex (MHC). We characterized in detail 27 YACs, 144 cosmids, 51 PACs, and 5 BACs, which will facilitate the complete genomic sequencing of this region of chromosome 6. The contig contains the genes encoding CSBP, p21, HSU09564 serine kinase, ZNF76, TCP-11, RPS10, HMGI(Y), BAK, and the human homolog of Tctex-7 (HSET). The GLO1 gene was mapped further centromeric in the 6p21.2-6p21.1 region toward TCTE-1. The gene order of the GLO1-HMGI(Y) segment in respect to the centromere is similar to the gene order in the mouse t-chromosome distal inversion, indicating that there is conservation in gene content but not gene order between humans and mice in this region. The close linkage of the BAK and CSBP genes to the MHC is of interest because of their possible involvement in autoimmune disease.The 2.5-Mb chromosomal segment flanking the centromeric end of the major histocompatibility complex (MHC) spans the boundary of the 6p21.2 (Giemsa dark) and 6p21.3 (Giemsa light) bands. This segment is of interest because of the association of the MHC with diseases, particularly of autoimmune etiology and the synteny to the mouse tcomplex distal inversion on chromosome 17 (Hamvas et al. 1996). The conservation between the 4-Mb human MHC and the mouse H2 complex is well documented (Hanson and Trowsdale 1991;Amadou et al. 1995), but for the region centromeric to the MHC, it is not well established.The mouse t-complex is an intensively studied region containing genes, which, when mutated or rearranged, cause a number of effects including embryonic lethality, male sterility, recombination suppression, and transmission ratio distortion (Silver 1993b;Foreijt et al. 1994). A part of this complex, within the distal inversion extending from the mouse Hmgi(y) gene to the H2-K region, contains a number of testis-expressed genes (Abe et al. 1988;Yeom et al. 1992). Testis-expressed sequences have been previously identified centromeric to the MHC (Ragoussis et al. 1992).In humans, this region harbors a gene involved in retinitis pigmentosa (ArP14) (Shugart et al. 1995) whereas chromosomal rearrangements with breakpoints within the region are associated with neoplasia (Johansson et al. 1993;Nilbert et al. 1995;Xiao et al. 1997).To investigate the relationship of this human segment to the mouse t-complex distal inversion, we have assembled YAC and bacterial clone contigs and mapped sequences with known homology between mice and humans. We screened a variety of genomic libraries in different cloning vectors to obtain clones, and we used both fingerprinting-and hybridization-based approaches to construct contigs. The resulting contigs have enabled the construction of transcript maps and are a first step toward construction of sequence-ready bacterial clone contigs. GENOME RESEARCH 631Cold Spring Harbor Laboratory Press on May 12, 2018 -Published by genome.cshlp.org Downloaded from RESULTS Construction of a YAC ContigAs a...

We have constructed a 2.5-Mb physical and transcription map that spans the human 6p21.2-6p21.3 region and includes the centromeric end of the MHC, using a combination of techniques. In total 88 transcription units including exons, cDNAs, and cDNA contigs were characterized and 60 were confidently positioned on the physical map. These include a number of genes encoding nuclear and splicing factors (Ndr kinase, HSU09564, HSRP20); cell cycle, DNA packaging, and apoptosis related [p21, HMGI(Y), BAK]; immune response (CSBP, SAPK4); transcription activators and zinc finger-containing genes (TEF-5, ZNF76); embryogenesis related (Csa-19); cell signaling (DIPP); structural (HSET), and other genes (TULP1, HSPRARD, DEF-6, EO6811, cyclophilin), as well as a number of RP genes and pseudogenes (RPS10, RPS12-like, RPL12-like, RPL35-like). Furthermore, several novel genes (a Br140-like, a G2S-like, a FBN2-like, a ZNF-like, and B1/KIAA0229) have been identified, as well as cDNAs and cDNA contigs. The detailed map of the gene content of this chromosomal segment provides a number of candidate genes, which may be involved in several biological processes that have been associated with this region, such as spermatogenesis, development, embryogenesis, and neoplasia. The data provide useful tools for synteny studies between mice and humans, for genome structure analysis, gene density comparisons, and studies of nucleotide composition, of different isochores and Giemsa light and Giemsa dark bands.

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