Compositional Mapping of Mouse Chromosomes and Identification of the Gene-Rich Regions

Abstract

The mouse genome is a mosaic of isochores, consisting of long (> 300 kb), compositionally homogeneous DNA segments that can be divided into two GC-poor families, L1 and L2, representing 56% of the genome, and two GC-rich families, H1 and H2, representing 26% and 7% of the genome, respectively, the remaining 11% being formed by satellite and ribosomal DNAs. (GC is the molar fraction of guanine + cytosine in DNA.) The mouse genome differs from the human genome (which is representative of most mammalian genomes) because it shows a narrower compositional spectrum of isochores and it has a karyotype formed exclusively by acrocentric chromosomes. The chromosomal distribution of the four isochore families, as investigated here by in situ hybridization of single-copy sequences from compositional DNA fractions, has shown that G(lemsa) bands are essentially composed of GC-poor isochores, whereas R(everse) bands comprise three subsets of bands: R' bands, containing GC-poor isochores and GC-rich isochores of the H1 family, and T and T' bands, containing all H2 isochores (in addition to other isochores), the former containing a higher proportion of H2 isochores than the latter. Mouse T and T' bands are generally syntenic with, and are compositionally related to, human T and T' bands and have the highest gene concentrations. These findings indicate that the distribution of isochore families and genes in chromosomal bands is basically similar in mouse and in human genomes, in spite of their remarkable differences and their extremely large phylogenetic distance.

Purification of the Aldehyde Oxidase Homolog 1 (AOH1) Protein and Cloning of the AOH1 and Aldehyde Oxidase Homolog 2 (AOH2) Genes

“…The Grafit version 4.0 (Erythacus Software Ltd., Staines, UK) was used for data analysis. Chromosome Preparation and in Situ Hybridization-Mouse metaphase chromosomes were prepared as previously described (23). In situ hybridizations were performed using the following biotin-or digoxigenin-labeled probes: the ϳ3-kb AOH1 cDNA fragment contained in AOH1-24/1 (12); the ϳ2-kb AOH2 cDNA fragment contained in AA79991 (12); the AOH1-containing PAC 2 DNA; the AOH2 containing PAC3 DNA; and the AO containing lambda phage DNA 9m (12).…”

The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density

“…In general, the H3 + and L1 + chromosomal bands are not contiguous along the metaphase chromosome, and are typically separated by the compositionally intermediate H3 -and L1 -bands IHGSC 2004). This type of chromosome organization is highly conserved evolutionarily, and has been described not only in mammalian and avian species (Saccone et al 1997;Andreozzi et al 2001;Federico et al 2004;, but also in reptiles and amphibians (Federico et al 2006). The non-contiguity, in a chromosome, of the GC-richest H3 + and the GC-poorest L1 + bands, emphasises the very different location in nuclei of these two types of band.…”

Defining specificity of transcription factor regulatory activities

“…There is an uneven organization of protein-coding genes found in the genomes of higher eukaryotes, which contain gene-rich and gene-poor regions. Moreover, it has been found that many co-regulated genes are clustered (Mishiro et al, 2009;Saccone et al, 1997;Saccone et al, 1999;Tang et al, 2008;Tschopp et al, 2009). Whether the different enhancers found in a cluster are required for gene regulation because they have diverse roles, or redundant but quantitatively additive roles, still remains to be established (Visel et al, 2009).…”