RESUMO
A set of 22 551 unique human NotI flanking sequences (16.2 Mb) was generated. More than 40% of the set had regions with significant similarity to known proteins and expressed sequences. The data demonstrate that regions flanking NotI sites are less likely to form nucleosomes efficiently and resemble promoter regions. The draft human genome sequence contained 55.7% of the NotI flanking sequences, Celera's database contained matches to 57.2% of the clones and all public databases (including non-human and previously sequenced NotI flanks) matched 89.2% of the NotI flanking sequences (identity > or =90% over at least 50 bp, data from December 2001). The data suggest that the shotgun sequencing approach used to generate the draft human genome sequence resulted in a bias against cloning and sequencing of NotI flanks. A rough estimation (based primarily on chromosomes 21 and 22) is that the human genome contains 15 000-20 000 NotI sites, of which 6000-9000 are unmethylated in any particular cell. The results of the study suggest that the existing tools for computational determination of CpG islands fail to identify a significant fraction of functional CpG islands, and unmethylated DNA stretches with a high frequency of CpG dinucleotides can be found even in regions with low CG content.
Assuntos
DNA/metabolismo , Desoxirribonucleases de Sítio Específico do Tipo II/metabolismo , Análise de Sequência de DNA/métodos , Linhagem Celular Transformada , Cromossomos Humanos Par 21/genética , Cromossomos Humanos Par 22/genética , Ilhas de CpG/genética , DNA/química , DNA/genética , Bases de Dados de Ácidos Nucleicos , Genes/genética , Genoma Humano , Humanos , Dados de Sequência Molecular , Sequências Repetitivas de Ácido Nucleico/genéticaRESUMO
We analyzed the interrelation between the efficiency of a gene expression and the nucleotide composition of all protein-coding sequences in 38 unicellular organisms whose complete genomic sequences are known. These organisms comprise 37 prokaryotic (29 eubacteria and eight archaebacteria) and one eukaryotic (yeast) species. We demonstrated that frequency analysis of gene codon composition fails to reflect adequately the gene expression efficiency of all these organisms. We constructed a measure, the elongation efficiency index, that considers simultaneously the information on codon frequencies and the degree of mRNA local self-complementarity. This measure recognizes the ribosome-coding genes as highly expressed in all the unicellular organisms studied. According to our analysis, these species fall into five groups differentiated by the process that makes the key contribution to the elongation rate.
Assuntos
Archaea/genética , Archaea/metabolismo , Bactérias/genética , Bactérias/metabolismo , Expressão Gênica , Elongação Traducional da Cadeia Peptídica/genética , Algoritmos , Archaea/classificação , Proteínas Arqueais/biossíntese , Proteínas Arqueais/genética , Bactérias/classificação , Proteínas de Bactérias/biossíntese , Proteínas de Bactérias/genética , Composição de Bases , Códon/genética , Proteínas Fúngicas/biossíntese , Proteínas Fúngicas/genética , Genes Arqueais , Genes Bacterianos , Modelos Genéticos , RNA Arqueal/genética , RNA Bacteriano/genética , RNA Fúngico/genética , RNA Mensageiro/genética , Proteínas Ribossômicas/biossíntese , Proteínas Ribossômicas/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismoRESUMO
We propose an original program "Evolutionary constructor" that is capable of computationally efficient modeling of both population-genetic and ecological problems, combining these directions in one model of required detail level. We also present results of comparative modeling of stability, adaptability and biodiversity dynamics in populations of unicellular haploid organisms which form symbiotic ecosystems. The advantages and disadvantages of two evolutionary strategies of biota formation--a few generalists' taxa-based biota formation and biodiversity-based biota formation--are discussed.