Reassociation kinetics of three satellite components of calf thymus DNA.

Using absorption measurements the reassociation kinetics of three satellite DNA components isolated from calf thymus was studied under various conditions. A different method using CsC1 density gradient determinations particularly suited for kinetic analysis of mixtures was also used and shown to give similar results. Reassociation rate constants were corrected for mismatching during strand reassociation using data obtained by kinetic analysis of fractions of the 1.714 g/cm-3 satellite component. The values of corrected as well as uncorrected complexities were calculated and compared with results of other methods. They were shown to be compatible with the concept of sequence repetition at various levels.     

The six hyaluronidase-like genes in the human and mouse genomes.

The human genome contains six hyaluronidase-like genes. Three genes (HYAL1, HYAL2 and HYAL3) are clustered on chromosome 3p21.3, and another two genes (HYAL4 and PH-20/SPAM1) and one expressed pseudogene (HYALP1) are similarly clustered on chromosome 7q31.3. The extensive homology between the different hyaluronidase genes suggests ancient gene duplication, followed by en masse block duplication, events that occurred before the emergence of modern mammals. Very recently we have found that the mouse genome also has six hyaluronidase-like genes that are also grouped into two clusters of three, in regions syntenic with the human genome. Surprisingly, the mouse ortholog of HYALP1 does not contain any mutations, and unlike its human counterpart may actually encode an active enzyme. Hyal-1 is the only hyaluronidase in mammalian plasma and urine, and is also found at high levels in major organs such as liver, kidney, spleen, and heart. A model is proposed suggesting that Hyal-2 and Hyal-1 are the major mammalian hyaluronidases in somatic tissues, and that they act in concert to degrade high molecular weight hyaluronan to the tetrasaccharide. Twenty-kDa hyaluronan fragments are generated at the cell surface in unique endocytic vesicles resulting from digestion by the glycosylphosphatidyl-inositol-anchored Hyal-2, transported intracellularly by an unknown process, and then further digested by Hyal-1. The two beta-exoglycosidases, beta-glucuronidase and beta-N-acetyl glucosaminidase, remove sugars from reducing termini of hyaluronan oligomers, and supplement the hyaluronidases in the catabolism of hyaluronan.     

Reassociation of disk components solubilized with deoxycholate.

Cattle disk membrane was solubilized in 2% deoxycholate in 0.05 m Tris-HCl buffer at pH 8.0. The sedimentation coefficient of rhodopsin in this solvent was 4.4 S. A sedimentation equilibrium study in H₂O-D₂O solvent showed that rhodopsin was mainly associated with deoxycholate and probably free of phospholipid when the deoxycholate concentration was higher than 0.8%. Bleaching of rhodopsin resulted in aggregation of the protein. Reduction of the deoxycholate concentration by dialysis promoted protein-phospholipid interaction in such a way that when the deoxycholate concentration was 0.2%, most of the rhodopsin present in the initial solution formed a soluble protein-phospholipid-deoxycholate complex with a molecular weight of 86,000. The complex, we believe, contains one molecule of rhodopsin, 50 to 55 molecules of phospholipid, and 20 to 25 molecules of deoxycholate.After dialysis against 0.05 m phosphate buffer at pH 6.5 that contained 20 mm MgCl₂ all the material was incorporated into vesicular membranes of diameters from 20 to 500 nm. Such results signify the dominance of rhodopsin-phospholipid interaction over either inter-rhodopsin or inter-phospholipid interactions in the initial decrease of deoxycholate concentration. The protein-phospholipid membrane was then formed by the two-dimensional aggregation of a rhodopsin-phospholipid complex. The presence of at least a part of the sugar moiety of rhodopsin on the outer surface of the vesicles was shown by using ferritin-labeled concanavalin A.     

The scattered distribution of actin genes in the mouse and human genomes.

A hamster actin cDNA probe was used to localize actin genes on the major components of mouse and human DNAs, namely on the four families of fragments forming the bulk of these genomes. Over 20 EcoRI fragments hybridizing the probe could be detected; a different subset of these fragments was found in each component. Since the fragment families forming the major components of the mouse and human DNAs derive from very long chromosomal segments, the isochores , the presence of actin genes on all components provides evidence for their dispersion in both genomes. In situ hybridization of 125I-labeled probe to metaphase chromosomes in the presence of dextran sulfate confirmed this dispersion by showing that the 29-30 actin gene sites so identified are distributed on almost all chromosomes. Moreover, some human actin genes could be mapped on specific chromosomal segments; in particular, one gene was localized on the long arm of the X chromosome. Finally, three different mouse actin genes were isolated from a recombinant DNA library and previously investigated interspersed repeated sequences were identified in the vicinity of these genes.     

Reassociation kinetics of deoxyribonucleic acid in antigen-stimulated mouse-spleen cells.

In order to directly compare the complexity of the genome of lymphoid cells which have been antigenically stimulated, with that of non-immunized and non-lymphoid cells, DNA was pulse labeled and extracted from BALB/c mouse spleen cells at various time intervals after antigenic stimulation in vivo; the reassociation rates of these newly synthesized DNA preparations were compared with those of the total mouse spleen DNA, obtained from same sources and at the same times. DNA labeled for 60 min at 43, 53, or 72 h after antigenic restimulation, reassociated faster than the corresponding total DNA. On the other hand, the ressociation profile of DNA, labeled for 60 min during the first 24 after restimulation did not differ from that of the total DNA extracted at the same time. When labeled thymidine was available for incorporation at a constant concentration over a period of 24 h, reassociation patterns of labeled DNA were identical to those of the corresponding total DNA at all times after restimulation. Newly synthesized nuclear DNA exhibited reassociation profiles identical to those of the corresponding total nuclear DNA at all times tested. Also, no differences between the reassociation rates of nuclear and total cellular DNA were observed. It was concluded that antigenic stimualtion does not induce a major amplification of genes in the stimulated cells, and that the rapidly reassociating DNA species described represent extranuclear (cytoplasmic) DNA.     

Selective constraint in intergenic regions of human and mouse genomes.

We aligned and analyzed 100 pairs of complete, orthologous intergenic regions from the human and mouse genomes (average length approximately 12 000 nucleotides). The alignments alternate between highly similar segments and dissimilar segments, indicating a wide variation of selective constraint. The average number of selectively constrained nucleotides within a mammalian intergenic region is at least 2000. This is threefold higher than within a nematode intergenic region and at least twofold higher than the number of selectively constrained nucleotides coding for an average protein. Because mammals possess only two- to threefold more proteins than Caenorhabditis elegans, the higher complexity of mammals might be primarily because of the functioning of intergenic DNA.     

VH gene segments in the mouse and human genomes

We have examined the mouse genome sequence to determine its VH gene segment repertoire. In all, 141 segments are mapped to a 3 Mb region of chromosome 12. There is evidence that 92 of these are functional in the mouse strain used for the genome sequence, C57BL/6J; 12 are functional in other mouse strains, and 37 are pseudogenes. The mouse VH gene segment repertoire is therefore twice the size of that in humans. The mouse and human loci bear no large-scale similarity to each other. The 104 functional segments belong to one of the 15 known sequence subgroups, which have been further clustered into eight sets here. Seven of these sets, comprising 101 sequences, are related to five of the human VH families and have the same canonical structures in their hypervariable regions. Duplication of members of one set in the distal half of the locus is mainly responsible for the larger size of the mouse repertoire. Phylogenetic analysis of the VH segments indicates that most of the sequences in the human and mouse VH loci have arisen subsequent to the divergence of the two organisms from their common ancestor.     

Reassociation kinetics of DNA from x-irradiated ascites hepatoma cells of the rat.

The kinetics of the reassociation fo DNA from ascites hepatoma cells has been studied. The curve exhibited three zones corresponding to 'fast', 'intermediate' and 'slow' speeds of DNA reassociation. The difference was observed in the DNA reassociation curves of the control and irradiated (1500 rad) cells which was particularly expressed in the 'slow' zone (10(2) less than C0t less than 10(4). The same dose, however, does not qualitatively effect the secondary DNA structure, which was estimated by the method of thermal elution from the hydroxyapatite column.     

Model genomes: the benefits of analysing homologous human and mouse sequences.

The human genome initiative has provided the motivating force for launching sequencing projects suitable for testing various DNA-sequencing strategies, as well as motivating the development of mapping and sequencing technologies. In addition to projects targeting selected regions of the human genome, other projects are based on model organisms such as yeast, nematode and mouse. The sequencing of homologous regions of human and mouse genomes is a new approach to genome analysis, and is providing insights into gene evolution, function and regulation which could not be determined so easily from the analysis of just one species.     

Comparative analysis of processed pseudogenes in the mouse and human genomes

Pseudogenes are important resources in evolutionary and comparative genomics because they provide molecular records of the ancient genes that existed in the genome millions of years ago. We have systematically identified approximately 5000 processed pseudogenes in the mouse genome, and estimated that approximately 60% are lineage specific, created after the mouse and human diverged. In both mouse and human genomes, similar types of genes give rise to many processed pseudogenes. These tend to be housekeeping genes, which are highly expressed in the germ line. Ribosomal-protein genes, in particular, form the largest sub-group. The processed pseudogenes in the mouse occur with a distinctly different chromosomal distribution than LINEs or SINEs - preferentially in GC-poor regions. Finally, the age distribution of mouse-processed pseudogenes closely resembles that of LINEs, in contrast to human, where the age distribution closely follows Alus (SINEs).     

Substitution pattern of the CArG element in human and mouse genomes

cis-Elements CArG bound by serum response factor (SRF) are presently being intensively studied, but little is known about the substitution pattern of functional CArG elements. Here, we have performed the first evolutionary analysis of CArGome in the human and mouse genome through bioinformatic methods and statistical tests. We calculated the substitution rate at each site of the functional CArG elements. The results showed that the core sites of the functional CArG elements evolved faster than did the background DNA, indicating that these sites were likely to evolve under positive selection. Moreover, a strong TATA "motif" was evident in the core region within the functional CArG elements in both human and mouse promoters. This motif could probably be a major contribution to the formation of the spatial structure, which was important for CArG-SRF recognition. Thus, the study further revealed the sequence character and substitution pattern of CArG elements and provided useful information for the study of the SRF-binding efficiencies of CArG promoters in functional assays.     

The molar ratio of the two major polypeptide components of human high density lipoprotein.

Human high density lipoprotein (HDL) and its subfractions (HDL2 and HDL3) were separated by ultracentrifugation and the molar ratio of the two major polypeptide chains apo-Gln-I and apo-Gln-II was determined by fluorescence tagging of sodium dodecyl sulfate-denatured proteins combined with polyacrylamide disc gel electrophoresis. Using purified apo-Gln-I and apo-Gln-II standards, it was found that holo HDL, holo HDL2, and holo HDL3 from all plasma samples contained a molar ratio of apo-Gln-I to the disulfide-bound dimer of apo-Gln-II of 2:1, that is a 1:1 ratio in terms of each species of polypeptide chain. The method described is useful for making repeated and rapid measurements on microgram quantities of intact lipoproteins.     

Density peaks of paralog pairs in human and mouse genomes

Paralog gene trees, which reflect the increase of genomic complexity in the evolution, can be complicated and ambiguous. A simpler complementary approach is analysis of density distribution of paralog pairs. It can reveal general features of genome evolution, which may be hidden in the forest of gene trees. It is known that distribution of human paralog pairs along the axis of protein divergence between pair members forms two main peaks. Here I show that there are three main peaks in the mouse genome. Thus, the multimodality of paralog pair distribution seems to be a fundamental feature of mammalian genomes. Despite the great diversity of domains presented in small amounts or in multidomain architectures with a few predominant domains, both in human and mouse the first peak consists mostly of gene pairs with zinc finger domains or olfactory receptor domain. In the mouse the olfactory receptor predominates, which stipulates the three-peak distribution (since in the olfactory receptors the second peak is closer to the first peak than in other genes). The mammalian-wide zinc finger orthologs are biased towards the second peak. Thus, the marsupial orthologs are nearly absent in the first peak of human and mouse. The gene pairs in the first peak show a lower ratio of nonsynonymous to synonymous substitutions, which suggests that their evolution is more constrained. The plausible explanation is that they are in subfunctionalization state (partition of initial function of ancestral gene), whereas the second peak contains gene pairs that are already in neofunctionalization state (acquiring of novel functions). These data suggest that the adaptive radiation of mammals was accompanied by a burst of duplication of zinc finger genes, which are located in the first (most recent) peak of paralog pairs.     

Computational comparison of two mouse draft genomes and the human golden path

Background  

The availability of both mouse and human draft genomes has marked the beginning of a new era of comparative mammalian genomics. The two available mouse genome assemblies, from the public mouse genome sequencing consortium and Celera Genomics, were obtained using different clone libraries and different assembly methods.     

An analysis on gene architecture in human and mouse genomes

A comparative genome analysis on exon-intron distribution profiles is performed for human and mouse genomes to deduce similarities and differences between them. Interestingly, both in human and mouse genomes, the total length in introns and intergenic DNA on each chromosome is significantly correlated to the chromosome size. The results presented provide a framework for understanding the nature and patterns of exon-intron length distributions, the constraints on them and their role in genome design and evolution.