Fractal genome sequences.

The existence of fractal sets of DNA sequences have long been suspected on the basis of statistical analyses of genome data. In this article we identify for the first time explicitly the GA-sequences as a class of fractal genomic sequences that are easy to recognize and to extract, and are scattered densely throughout the chromosomes of a large number of genomes from different species and kingdoms including the human genome. Their existence and their fractality may have significant consequences for our understanding of the origin and evolution of genomes. Furthermore, as universal and natural markers they may be used to chart and explore the non-coding regions.

Outline of a genome navigation system based on the properties of GA-sequences and their flanks.

Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments. Although not integral parts of them, Alu-elements were found immediately upstream of all human and chimpanzee GA-sequences with an upstream poly(A)-segment. The article hypothesizes that genome navigation uses these properties of GA-sequences in the following way. (1) Poly(A) binding proteins interact with the upstream poly(A)-segments and arrange adjacent GA-sequences side-by-side ('GA-ribbon'), while folding the intervening DNA sequences between them into loops ('associated DNA-loops'). (2) Genome navigation uses the GA-ribbon as a search path for specific target genes that is up to 730-fold shorter than the full-length chromosome. (3) As to the specificity of the search, each molecule of a target protein is assumed to catalyze the formation of specific oligomers from a set of transcription factors that recognize tetra-GA-motifs. Their specific combinations of tetra-GA motifs are assumed to be present in the particular GA-sequence whose associated loop contains the gene for the target protein. As long as the target protein is abundant in the cell it produces sufficient numbers of such oligomers which bind to their specific GA-sequences and, thereby, inhibit locally the transcription of the target protein in the associated loop. However, if the amount of target protein drops below a certain threshold, the resultant reduction of specific oligomers leaves the corresponding GA-sequence 'denuded'. In response, the associated DNA-loop releases its nucleosomes and allows transcription of the target protein to proceed. (4) The Alu-transcripts may help control the general background of protein synthesis proportional to the number of transcriptionally active associated loops, especially in stressed cells. (5) The model offers a new mechanism of co-regulation of protein synthesis based on the shared segments of different GA-sequences.

The spectra of point mutations in vertebrate genomes.

In spite of the importance of point mutations for evolution and human diseases, their natural spectrum of incidence in different species is not known. Here I propose to determine these spectra by comparing consecutive sequence periods in stretches of repetitive DNA. The article presents the analysis of more than 51,000 such point mutations identified by this approach in the genomes of human, chimpanzee, rat, mouse, pufferfish, zebrafish, and sea squirt. I propose to explain the observed spectra by auto-mutagenic mechanisms of genome variation involving the inter-conversions of nucleotides, single base-pair inversions and their combinations.

Properties and distribution of pure GA-sequences of mammalian genomes.

The article describes DNA sequences of mammalian genomes that are longer than 50 bases, but consist exclusively of G's and A's ('pure GA-sequences'). Although their frequency of incidence should be 10(-16) or smaller, the chromosomes of human, chimpanzee, dog, cat, rat, and mouse contained many tens of thousands of them ubiquitously located along the chromosomes with a species-dependent density, reaching sizes of up to 1300 [b]. With the exception of a small number of poly-A-, poly-G-, poly-GA-, and poly-GAAA-sequences (combined <0.5%), all pure GA-sequences of the mammals tested were unique individuals, contained several repeated short GA-containing motifs, and shared a common hexa-nucleotide spectrum. At most 2% of the human GA-sequences were transcribed into mRNAs; all others were not coding for proteins. Although this could have made them less subject to natural selection, they contained many [corrected] times fewer point mutations than one should expect from the genome at large. As to the presence of other sequences with similarly restricted base contents, there were approximately as many pure TC-sequences as pure GA-sequences, but many fewer pure AC-, TA, and TG-sequences. There were practically no pure GC-sequences. The functions of pure GA-sequences are not known. Supported by a number of observations related to heat shock phenomena, the article speculates that they serve as genomic sign posts which may help guide polymerases and transcription factors to their proper targets, and/or as spatial linkers that help generate the 3-dimensional organization of chromatin.

Inversions and inverted transpositions as the basis for an almost universal "format" of genome sequences.

In genome duplexes that exceed 100 kb the frequency distributions of their trinucleotides (triplet profiles) are the same in both strands. This remarkable symmetry, sometimes called Chargaff's second parity rule, is not the result of base pairing, but can be explained as the result of countless inversions and inverted transpositions that occurred throughout evolution (G. Albrecht-Buehler, 2006, Proc. Natl. Acad. Sci. USA 103, 17828-17833). Furthermore, comparing the triplet profiles of genomes from a large number of different taxa and species revealed that they were not only strand-symmetrical, but even surprisingly similar to one another (majority profile; G. Albrecht-Buehler, 2007, Genomics 89, 596-601). The present article proposes that the same inversion/transposition mechanism(s) that created the strand symmetry may also explain the existence of the majority profile. Thus they may be key factors in the creation of an almost universal "format" in which genome sequences are written. One may speculate that this universality of genome format may facilitate horizontal gene transfer and, thus, accelerate evolution.

The three classes of triplet profiles of natural genomes.

Based on the huge variety of different genomes, one may expect a correspondingly large variety of the frequency distribution of their trinucleotides ("triplet profiles"). Yet, this article reports the unexpected finding that there are essentially only three kinds of triplet profiles among the large number of genomes examined here. None of the classes included random profiles, all of them contained members from vastly different taxa and species. Since the three classes of genomes do not reflect the phylogeny of their member organisms, I propose that these classes may reflect species-independent mechanisms of genome evolution.

Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions.

Chargaff's second parity rules for mononucleotides and oligonucleotides (CIImono and CIIoligo rules) state that a sufficiently long (> 100 kb) strand of genomic DNA that contains N copies of a mono- or oligonucleotide, also contains N copies of its reverse complementary mono- or oligonucleotide on the same strand. There is very strong support in the literature for the validity of the rules in coding and noncoding regions, especially for the CIImono rule. Because the experimental support for the CIIoligo rule is much less complete, the present article, focusing on the special case of trinucleotides (triplets), examined several gigabases of genome sequences from a wide range of species and kingdoms including organelles such as mitochondria and chloroplasts. I found that all genomes, with the only exception of certain mitochondria, complied with the CIItriplet rule at a very high level of accuracy in coding and noncoding regions alike. Based on the growing evidence that genomes may contain up to millions of copies of interspersed repetitive elements, I propose in this article a quantitative formulation of the hypothesis that inversions and inverted transposition could be a major contributing if not dominant factor in the almost universal validity of the rules.

A long-range attraction between aggregating 3T3 cells mediated by near-infrared light scattering.

At what range can a mammalian cell sense the presence of another cell and through what medium? To approach these questions, the formation of aggregates of a 3T3 cell variant (3T3x cells) grown on solid substrates was studied. Each of the aggregates consisted of cells that, at the time of their seeding, were single and located randomly. Yet somehow they seemed to detect each other within a certain range (R(a)) and move together to form aggregates. The article describes a simple assay to measure the value of R(a). When applied to 3T3x cells with altered intensities of near-infrared light scattering (I(sc)) the assay showed that (i) R(a) was much larger than one cell diameter, and (ii) R(a) was directly related to I(sc). The results suggest that near-infrared light scattering by the cells mediate a long-range attraction between them, which does not require physical contact and enables them to detect each other's presence.

Water structuring centers of mammalian cell surfaces.

Cultured mammalian cells appeared to express specific particles on their surface, which could be detected by their ability to nucleate ice crystals (I-centers) in a newly developed, two-dimensional crystallization assay. Their expression required approximately 24 h independent of cell density, and metabolic energy, and the number and distribution of the I-centers were cell-type specific. Their characteristic ability to nucleate ice crystals was highly sensitive to dehydration, to hyaluronidase and phospholipase C, but not to a number of proteases such as trypsin, chymotrypsin, collagenase, and pronase. However, these proteases, especially pronase, were able to detach the I-centers from the cell surface, without destroying their ability to nucleate ice crystals. I-centers were specific products of live cells, located in relatively small numbers at the cell surface organized in a detachable, sheet-like structure. We propose to consider the ice nucleating ability of I-centers as an expression of their ability to influence the water structure in the surface of cells. Even though their biological function is not known at this time, as water-structuring centers they appear remarkable enough to warrant our attention.