The exceptional genomic word symmetry along DNA sequences

Noether's Theorem as a Metaphor for Chargaff's 2nd Parity Rule in Genomics

In the present note, the genomic compositional rule largely known as 'Chargaff's 2nd parity rule' (asserting equimolarity between Adenine-Thymine and Guanine-Cytosine in any of the two DNA strands) is regarded in association with Noether's theorem linking symmetries with conservation laws in physics. In the case of the genome, the strict physical and mathematical prerequisites of Noether's theorem do not hold. However, we conclude that a metaphor can be established with Noether's theorem, as inter-strand symmetry concerning DNA functionality engenders specific features in genome composition. Inversely, when inter-strand symmetry does not hold, the corresponding quantitative relations fail to appear. This association is also considered from the point of view of the existence of emergent laws and properties in evolutionary genomics.

Slaying (Yet Again) the Brain-Eating Zombie Called the "Isochore Theory": A Segmentation Algorithm Used to "Confirm" the Existence of Isochores Creates "Isochores" Where None Exist

The isochore theory, which was proposed more than 40 years ago, depicts the mammalian genome as a mosaic of long, homogeneous regions that are characterized by their guanine and cytosine (GC) content. The human genome, for instance, was claimed to consist of five compositionally distinct isochore families. The isochore theory, in all its reincarnations, has been repeatedly falsified in the literature, yet isochore proponents have persistently resurrected it by either redefining isochores or by proposing alternative means of testing the theory. Here, I deal with the latest attempt to salvage this seemingly immortal zombie—a sequence segmentation method called isoSegmenter, which was claimed to “identify” isochores while at the same time disregarding the main characteristic attribute of isochores—compositional homogeneity. I used a series of controlled, randomly generated simulated sequences as a benchmark to study the performance of isoSegmenter. The main advantage of using simulated sequences is that, unlike real data, the exact start and stop point of any isochore or homogeneous compositional domain is known. Based on three key performance metrics—sensitivity, precision, and Jaccard similarity index—isoSegmenter was found to be vastly inferior to isoPlotter, a segmentation algorithm with no user input. Moreover, isoSegmenter identified isochores where none exist and failed to identify compositionally homogeneous sequences that were shorter than 100−200 kb. Will this zillionth refutation of “isochores” ensure a final and permanent entombment of the isochore theory? This author is not holding his breath.

Novel look at DNA and life-Symmetry as evolutionary forcing

After explanation of the Chargaff´s first parity rule in terms of the Watson-Crick base-pairing between the two DNA strands, the Chargaff´s second parity rule for each strand of DNA (also named strand symmetry), which cannot be explained by Watson-Crick base-pairing only, is still a challenging issue already fifty years. We show that during evolution DNA preserves its identity in the form of quadruplet A+T and C+G rich matrices based on purine-pyrimidine mirror symmetries of trinucleotides. Identical symmetries are present in our classification of trinucleotides and the genetic code table. All eukaryotes and almost all prokaryotes (bacteria and archaea) have quadruplet mirror symmetries in structural form and frequencies following the principle of Chargaff's second parity rule and Natural symmetry law of DNA creation and conservation. Some rare symbionts have mirror symmetry only in their structural form within each DNA strand. Based on our matrix analysis of closely related species, humans and Neanderthals, we find that the circular cycle of inverse proportionality between trinucleotides preserves identical relative frequencies of trinucleotides in each quadruplet and in the whole genome. According to our calculations, a change in frequencies in quadruplet matrices could lead to the creation of new species. Violation of quadruplet symmetries is practically inconsistent with life. DNA symmetries provide a key for understanding the restriction of disorder (entropy) due to mutations in the evolution of DNA.

Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis

For the ubiquitous phenomenon of strand symmetry, it has been shown that it may persist for higher-order oligonucleotides. However, there is no consensus about to what extent (order of oligonucleotides or length of words) strand symmetry still persists. To determine the extent of strand symmetry in genomic sequences is critically important for the further understanding of the phenomenon. Based on previous studies, we have developed an algorithm for the novel word symmetry distance analysis. We applied it to evaluate the higher-order strand symmetry for 206 archaeal genomes and 2,659 bacterial genomes. Our results show that the new approach could provide a clear-cut criterion to determine the extent of strand symmetry for a group of genomes or individual genomes. According to the new measure, strand symmetry would tend to persist for up to 8-mers in archaeal genomes, and up to 9-mers in bacterial genomes. And the persistence may vary from 6- to 9-mers in individual genomes. Moreover, higher-order strand symmetry would tend to positively correlate with GC content and mononucleotide symmetry levels of genomic sequences. The variations of higher-order strand symmetry among genomes would indicate that strand symmetry itself may not be strictly relevant to biological functions, which would provide some insights into the origin and evolution of the phenomenon.

A pathways-based prediction model for classifying breast cancer subtypes

Breast cancer is highly heterogeneous and is classified into four subtypes characterized by specific biological traits, treatment responses, and clinical prognoses. We performed a systemic analysis of 698 breast cancer patient samples from The Cancer Genome Atlas project database. We identified 136 breast cancer genes differentially expressed among the four subtypes. Based on unsupervised clustering analysis, these 136 core genes efficiently categorized breast cancer patients into the appropriate subtypes. Functional enrichment based on Kyoto Encyclopedia of Genes and Genomes analysis identified six functional pathways regulated by these genes: JAK-STAT signaling, basal cell carcinoma, inflammatory mediator regulation of TRP channels, non-small cell lung cancer, glutamatergic synapse, and amyotrophic lateral sclerosis. Three support vector machine (SVM) classification models based on the identified pathways effectively classified different breast cancer subtypes, suggesting that breast cancer subtype-specific risk assessment based on disease pathways could be a potentially valuable approach. Our analysis not only provides insight into breast cancer subtype-specific mechanisms, but also may improve the accuracy of SVM classification models.