Searching for coding sequences in the mammalian genome: the H-2K region of the mouse MHC is replete with genes expressed in embryos.

Abstract

We have searched for expressed genes in 170 kb of cosmid cloned DNA from the H‐2K region of the mouse MHC. This region is known to contain two genes, H‐2K and K2. We identified unique/low copy sequences evenly spaced along the cloned DNA, and used these as probes to search for conserved sequences in Southern blots from a variety of mammalian species. The majority of the unique sequences were found to have homologues and most of these were associated with CpG non‐methylated islands. Northern blot analysis and isolation of clones from 5.5 and 10.5‐day embryo cDNA libraries showed five additional genes encoded in the H‐2K region. Four of these are abundant in embryos; the fifth is exclusively expressed in lymphoid cells. Our data indicate a minimum of seven genes in 170 kb, an unexpectedly high gene density. These results differ from two recent studies where similar lengths of cloned DNA were examined for expressed genes, and only one, or a part of one gene was found. The combined data suggest that the spatial organization of genes in the mammalian genome may not be random.

Downregulation of Ke 6, a novel gene encoded within the major histocompatibility complex, in murine polycystic kidney disease.

“…serum albumin, 7% SDS, 1 mM EDTA, and 0.5 M sodium phosphate, pH 7.0, at 65°C for 16 to 18 h. DNA probes were labeled by a random-primed labeling method (10), cleaned by spin column, and added to the hybridization fluid at 106 cpm/ml. Membranes were washed at 50°C in 2x SSC (lx SSC is 0.15 M NaCl plus 0.015 M sodium citrate)-0.1% SDS, washed in 0.1x SSC-0.1% SDS for approximately 1 h, and then exposed to X-ray film with intensifying screens at -70°C. All of the Northern blots were probed with mouse 3-actin cDNA, protein tyrosine phosphatase (PTP) cDNA, and/or L-ferritin cDNA to check for equal loading.…”

Structure of Human Chromosome 21—For an Understanding of Genetic Diseases Including Down’s Syndrome—

“…However, its nonrandom nature suggests that it reflects some aspect of genome organization of chromosome 21. lt has become increasingly clear that genes are neither randomly nor uniformly distributed throughout the genome, which suggests that two-thirds to three-quarters of genes are located in Giemsa light bands.~·0. [47][48][49][50] Consider the four physical linkage groups within 21q22.3. Together they involve a total of 14 unique sequences, of which seven are cDNAs of identified products (ETS2, MXl, MX2, CBS, COL6Al, COL6A2, and BCEl).…”

Ke 6 Gene

“…Nucleotide sequence and restriction mapping of the Ke 6 genomic locus and Ke 6a and Ke 6b cDNAs reveal that, of these enzymes, only PstI cuts within the Ke 6 gene. The Ke 6a cDNA probe detects an 11-kb EcoRI fragment, a 4.9-kb BamHI fragment, and a 23-kb HindIII fragment as predicted by the restriction map of cosmid 32 (24). Three PstI fragments of sizes 1.5, 1, and 0.45 kb are detected in the genomic blot.…”