Construction of a High-Resolution 2.5-Mb Transcript Map of the Human 6p21.2–6p21.3 Region Immediately Centromeric of the Major Histocompatibility Complex

Abstract

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.

Mechanism of Ca2+-mediated Regulation of NDR Protein Kinase through Autophosphorylation and Phosphorylation by an Upstream Kinase

“…We originally cloned this kinase from a human fetal brain cDNA library using Caenorhabditis elegans expressed sequence tag clone cm11b8 (1). Later, it was mapped to chromosome 6p21 next to the major histocompatibility complex class I gene cluster (2). Recently, we isolated a second NDR isoform, termed NDR2, which is localized on chromosome 12p11 next to the K-ras gene.…”

Molecularly defined interstitial tandem duplication 6p case with mild manifestations

“…The PACs dJ180E22, dJ261G23, dJ75E20, dJ202121, dJ207H1, dJ288E7, dJ97D16, dJ103C14, dJ126C21, dJ8G21, dJ217E5, and dJ59B16 were selected from the Sanger Centre database due to their reported cytogenetic location and/or de®ned genetic marker content (see Table I). The clones dJ50J22, dJ178D20, and dJ99J17 and the BAC clone b121L5 are taken from Tripodis et al [2000]. PAC clone dJ45P21 was reported by Lauer et al [1997].…”

Methods for Large-Scale Mining of Networks of Human Genes

“…The gene WISP2 is co-regulated with PPARD [3] but in PubGene it is found at infinite PubGene distance from PPARD. Among the SCI neighbours of PPARD we also found a large number of genes that are found in the same chromosomal region as PPARD [15], and these genes are found at various PubGene distances, see Table 4. Examples of genes localised close to the PPARD gene are the MAPK11 and TULP1 genes that are found at PubGene distance 2 from PPARD, the ZNF76 and WNT2B genes at PubGene distance 3, while the SFRS3 and RPL10A genes cannot be found by traversing links in the PubGene network.…”

“…Of the 187 genes identified, only 6 (3%) were found at PubGene distance 1 from PPARD. For PPARA, which has two original articles 15 , an identical procedure was used to identify 119 SCI neighbours. Figure 4 shows how the 187 SCI neighbours of PPARD and the 119 SCI neighbours of PPARA are distributed over PubGene distance from PPARD and PPARA, respectively.…”