Compositional differences within and between eukaryotic genomes

Abstract

Eukaryotic genome similarity relationships are inferred using sequence information derived from large aggregates of genomic sequences. Comparisons within and between species sample sequences are based on the profile of dinucleotide relative abundance values (The profile is * XY ‫؍‬ f* XY ͞f* X f* Y for all XY, where f* X denotes the frequency of the nucleotide X and f* XY denotes the frequency of the dinucleotide XY, both computed from the sequence concatenated with its inverted complement). Previous studies with respect to prokaryotes and this study document that profiles of different DNA sequence samples (sample size >50 kb) from the same organism are generally much more similar to each other than they are to profiles from other organisms, and that closely related organisms generally have more similar profiles than do distantly related organisms. On this basis we refer to the collection { * XY } as the genome signature. This paper identifies * XY extremes and compares genome signature differences for a diverse range of eukaryotic species. Interpretations on the mechanisms maintaining these profile differences center on genome-wide replication, repair, DNA structures, and context-dependent mutational biases. It is also observed that mitochondrial genome signature differences between species parallel the corresponding nuclear genome signature differences despite large differences between corresponding mitochondrial and nuclear signatures. The genome signature differences also have implications for contrasts between rodents and other mammals, and between monocot and dicot plants, as well as providing evidence for similarities among fungi and the diversity of protists.Local and global compositional heterogeneity is recognized on many scales in eukaryotic genomes, including variation in GϩC content (e.g., isochore compartments, coding vs. noncoding), mobile insertion elements, characteristic centromeric satellite and telomeric repeats, CpG (ϭCG) suppression in vertebrates, and methylation patterns. Our recent studies of genomic sequence data have demonstrated that (i) the dinucleotide relative abundance values (defined below) of different sequence samples of DNA from the same organism are generally much more similar to each other than they are to sequence samples from different organisms and (ii) related organisms generally have more similar dinucleotide relative abundance values than do distantly related organisms (1). Dinucleotide relative abundance values are equivalent to the ''general designs'' derived from biochemical nearest-neighbor frequency analysis (2, 3). These highly stable DNA doublet forms suggest that there may be genome-wide factors, such as functions of the replication and repair machinery, contextdependent mutation rates, DNA modifications, and base-step conformational tendencies that impose limits on the compositional and structural patterns of a genomic sequence. The set of dinucleotide relative abundance values constitutes a ''genomic signature'' (1, 4) that may reflect the influence o...

Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes

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Targeting of High Mobility Group-14/-17 Proteins in Chromatin Is Independent of DNA Sequence

“…Multiple alignments were done using Clustal W (version 1.74). Di-and trinucleotide frequency analysis was done as described by others (18). The average roll angle, tilt angle, and twist angle of each cloned DNA sequence predicted from the di-and trinucleotide frequency were calculated using available software DNA tools (19,20).…”

Start/stop Codon-like Trinucleotides (CLTs) and Extended Clusters as New Language of DNA

“…Previously, the pattern of dinucleotides and trinucleotides in noncoding sequences was extensively studied. [15][16][17][18][19][20][21][22][23][24] Two classes of alpha satellites are shown here: the poly-T class (with dominant TT dinucleotides), and the poly-A class (with dominant AA). It is seen here that all consensus HOR alpha satellites are of poly-T class, while the monomeric alpha satellites are of poly-A or poly-T class.…”

“…Analysis of frequencies of trinucleotides in alpha satellite HORs is performed for consensus HORs in human chromosomes 1,4,5,7,8,9,10,11,17,19, X, and Y (Table 1 and Supplementary tables S1 and S3). As an illustration, ten most frequent trinucleotides in 16mer alpha satellite HORs in human chromosome 7 are shown in Table 2, in comparison to previously computed ten most frequent trinucleotides in the genome of C. elegans 34 as comparison between evolutionary distant genomes.…”