An Integrated Map with Cosmid/PAC Contigs of a 4-Mb Down Syndrome Critical Region

Osoegawa, Kazutoyo; Susukida, Rie; Okano, Satoshi; Kudoh, Jun; Minoshima, Shinsei; Shimizu, Nobuyoshi; Jong, Pieter J. de; Groet, Jürgen; Ives, Jane H.; Lehrach, Hans; Nižetić, Dean; Soeda, Eiichi

doi:10.1006/geno.1996.0132

Cited by 39 publications

(23 citation statements)

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“…3A), and human male lymphocyte DNA (supplied by Pieter J. de Jong, Roswell Park Cancer Institute, Buffalo, NY) ( Fig. 3A) (8). PCR screening and physical mapping followed the protocol provided by Research Genetics and Osoegawa et al (8).…”

Section: Methodsmentioning

confidence: 99%

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Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region

Shiina

Tamiya

Oka

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

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129

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The intensely studied MHC has become the paradigm for understanding the architectural evolution of vertebrate multigene families. The 4-Mb human MHC (also known as the HLA complex) encodes genes critically involved in the immune response, graft rejection, and disease susceptibility. Here we report the continuous 1,796,938-bp genomic sequence of the HLA class I region, linking genes between MICB and HLA-F. A total of 127 genes or potentially coding sequences were recognized within the analyzed sequence, establishing a high gene density of one per every 14.1 kb. The identification of 758 microsatellite provides tools for high-resolution mapping of HLA class I-associated disease genes. Most importantly, we establish that the repeated duplication and subsequent diversification of a minimal building block, MIC-HCGIX-3.8 -1-P5-HCGIV-HLA class I-HCGII, engendered the present-day MHC. That the currently nonessential HLA-F and MICE genes have acted as progenitors to today's immune-competent HLA-ABC and MICA͞B genes provides experimental evidence for evolution by ''birth and death,'' which has general relevance to our understanding of the evolutionary forces driving vertebrate multigene families.

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Section: Methodsmentioning

confidence: 99%

“…3A) (8). PCR screening and physical mapping followed the protocol provided by Research Genetics and Osoegawa et al (8). Two YAC clones, 745D12 with a 590-kb insert and 960H11 with a 1,600-kb insert (Fig.…”

Section: Methodsmentioning

confidence: 99%

Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region

Shiina

Tamiya

Oka

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

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162

129

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“…Large insert yeast and bacterial clones were isolated by polymerase chain reaction (PCR)-based screening of the human CEPH (Centre d'études du Polymorphisme Humain) YAC library (Chumakov et al 1992), a PAC library constructed from human lymphocyte DNA (Genome Systems Inc.), PAC and BAC libraries derived from human male lymphocyte DNA by Dr. Pieter J. de Jong (RPCI 4 and 5 series, and 11 series, respectively) (Osoegawa et al 1996), and a BAC library constructed from the B cell line 978SK (Research Genetics). To construct a physical map of the 1q21-q22 region, 12 locus/ gene-specific primer pairs were designed based on published sequences (Table 1), 18 STS primer pairs were selected from 70 markers positioned on the Whitehead Institute (http:// carbon.wi.mit.edu: 8000/cgi-bin/contig/phys_map) WC1.16 contig map from WI-8369 (most centromeric) to UTR6608 (most telomeric), in the NCBI (http://www.…”

Section: Construction Of a Yac Bac And Pac Contig And Physical Mappingmentioning

confidence: 99%

“…PCR analyses were performed using these PCR primers with YAC, PAC, and BAC DNAs as a template. PCR screening and physical mapping followed the protocol provided by Research Genetics and Osoegawa et al (1996). Chromosomal mapping and chimerism of these BAC and PAC clones were checked by FISH, and the order of the clones within a contig was confirmed using fiberFISH as described previously (Takahashi et al 1990(Takahashi et al , 1991Mizuki et al 1996;Suto et al 1996).…”

Section: Construction Of a Yac Bac And Pac Contig And Physical Mappingmentioning

confidence: 99%

Genomic Anatomy of a Premier Major Histocompatibility Complex Paralogous Region on Chromosome 1q21–q22

Shiina¹,

Andõ²,

Suto³

et al. 2001

Genome Res.

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Human chromosomes 1q21-q25, 6p21.3-22.2, 9q33-q34, and 19p13.1-p13.4 carry clusters of paralogous loci, to date best defined by the flagship 6p MHC region. They have presumably been created by two rounds of large-scale genomic duplications around the time of vertebrate emergence. Phylogenetically, the 1q21-25 region seems most closely related to the 6p21.3 MHC region, as it is only the MHC paralogous region that includes bona fide MHC class I genes, the CD1 and MR1 loci. Here, to clarify the genomic structure of this model MHC paralogous region as well as to gain insight into the evolutionary dynamics of the entire quadriplication process, a detailed analysis of a critical 1.7 megabase (Mb) region was performed. To this end, a composite, deep, YAC, BAC, and PAC contig encompassing all five CD1 genes and linking the centromeric +P5 locus to the telomeric KRTC7 locus was constructed. Within this contig a 1.1-Mb BAC and PAC core segment joining CD1D to FCER1A was fully sequenced and thoroughly analyzed. This led to the mapping of a total of 41 genes (12 expressed genes, 12 possibly expressed genes, and 17 pseudogenes), among which 31 were novel. The latter include 20 olfactory receptor (OR) genes, 9 of which are potentially expressed. Importantly, CD1, SPTA1, OR, and FCERIA belong to multigene families, which have paralogues in the other three regions. Furthermore, it is noteworthy that 12 of the 13 expressed genes in the 1q21-q22 region around the CD1 loci are immunologically relevant. In addition to CD1A-E, these include SPTA1, MNDA, AIM2, BL1A, FY and FCERIA. This functional convergence of structurally unrelated genes is reminiscent of the 6p MHC region, and perhaps represents the emergence of yet another antigen presentation gene cluster, in this case dedicated to lipid/glycolipid antigens rather than antigen-derived peptides.

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“…Long range mapping is also an ongoing and well-established component of the Japanese sequencing program, carried out by E. Soeda (Tsukuba, Japan), Y. Sakaki and N. Shimizu. E. Soeda reported a 4-Mb contig in 21q22.22 (Osoegawa et al, 1996), and a 7-Mb high resolution map from SOD1 to ETS2. The contigs that are being sequenced are generally displayed on the servers of the corresponding sequencing centers (for Germany, maps are also displayed in ACEdb format at http://chr21.rz-berlin.mpg.de).…”

Section: Sequence-ready Mapsmentioning

confidence: 99%

Report of the seventh international workshop on human chromosome 21 mapping 1997

Korenberg

Aaltonen

Brahe

et al. 1998

Cytogenet Genome Res

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An Integrated Map with Cosmid/PAC Contigs of a 4-Mb Down Syndrome Critical Region

Cited by 39 publications

References 0 publications

Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region

Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region

Genomic Anatomy of a Premier Major Histocompatibility Complex Paralogous Region on Chromosome 1q21–q22

Report of the seventh international workshop on human chromosome 21 mapping 1997

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