Systematics for types and effects of DNA variations

Systematic errors in annotations of truncations, loss-of-function and synonymous variants

Description of genetic phenomena and variations requires exact language and concepts. Vast amounts of variation data are produced with next-generation sequencing pipelines. The obtained variations are automatically annotated, e.g., for their functional consequences. These tools and pipelines, along with systematic nomenclature, mainly work well, but there are still some problems in nomenclature, organization of some databases, misuse of concepts and certain practices. Therefore, systematic errors prevent correct annotation and often preclude further analysis of certain variation types. Problems and solutions are described for presumed protein truncations, variants that are claimed to be of loss-of-function based on the type of variation, and synonymous variants that are not synonymous and lead to sequence changes or to missing protein.

Individual Genetic Heterogeneity

Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.

Evaluation of alternations in DNA methylation of CYP3A4 gene upstream regulatory elements in gastric cancer and in response to Diazinon treatment

BACKGROUND

Little is known about cytochrome P450 3A4 (CYP3A4) DNA methylation and transcription alterations in gastric cancer.

OBJECTIVE

In this paper, we initially aimed to address the effect of diazinon pesticide on DNA methylation and transcription changes of the CYP3A4 gene in a human gastric cell line. In the next step, we studied the methylation differences of CpG sites within the upstream regulatory regions of the CYP3A4 gene among human gastric cancerous and healthy tissues.

METHODS

For the in vitro assay, the methylation changes of the C/EBP response element and transcript level of the CYP3A4 gene were studied following treatment of the AGS cell line with various concentrations of diazinon pesticide. In the next phase, the methylation percentages of 24 CpG sites within or around the upstream regulatory elements including near promoter, C/EBP binding site, XREM, and CLEM4 in 11 specimens of human gastric cancer tissue were compared to their adjacent healthy tissues.

RESULTS

Treatment with 10 µM Diazinon significantly increased the CYP3A4 gene transcription by approximately 27-fold, which was correlated with the hypermethylation of 3 CpGs in C/EBP binding sites including -5998, -5731 and -5725 (p<0.001 for all comparisons). Results of bisulfite sequencing revealed that the CpG sites which are located in -1521 (p=0.003), -1569 (p=0.027), -10813 (p=0.003), -10851 (p=0.001) and -10895 (p=0.0) bp from transcription start site, were significantly hypermethylated in cancerous tissues comparing to their healthy cohort.

CONCLUSION

Hypermethylation of CLEM4 and a region near the core promoter may have a significant association with gastric cancer incidence.

Mapping OMIM Disease-Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes

Human genome resequencing projects provide an unprecedented amount of data about single-nucleotide variations occurring in protein-coding regions and often leading to observable changes in the covalent structure of gene products. For many of these variations, links to Online Mendelian Inheritance in Man (OMIM) genetic diseases are available and are reported in many databases that are collecting human variation data such as Humsavar. However, the current knowledge on the molecular mechanisms that are leading to diseases is, in many cases, still limited. For understanding the complex mechanisms behind disease insurgence, the identification of putative models, when considering the protein structure and chemico-physical features of the variations, can be useful in many contexts, including early diagnosis and prognosis. In this study, we investigate the occurrence and distribution of human disease–related variations in the context of Pfam domains. The aim of this study is the identification and characterization of Pfam domains that are statistically more likely to be associated with disease-related variations. The study takes into consideration 2,513 human protein sequences with 22,763 disease-related variations. We describe patterns of disease-related variation types in biunivocal relation with Pfam domains, which are likely to be possible markers for linking Pfam domains to OMIM diseases. Furthermore, we take advantage of the specific association between disease-related variation types and Pfam domains for clustering diseases according to the Human Disease Ontology, and we establish a relation among variation types, Pfam domains, and disease classes. We find that Pfam models are specific markers of patterns of variation types and that they can serve to bridge genes, diseases, and disease classes. Data are available as Supplementary Material for 1,670 Pfam models, including 22,763 disease-related variations associated to 3,257 OMIM diseases.

Systematics for types and effects of RNA variations

Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.

Poikilosis - pervasive biological variation

Biological systems are dynamic and display heterogeneity at all levels. Ubiquitous heterogeneity, here called for poikilosis, is an integral and important property of organisms and in molecules, systems and processes within them. Traditionally, heterogeneity in biology and experiments has been considered as unwanted noise, here poikilosis is shown to be the normal state. Acceptable variation ranges are called as lagom. Non-lagom, variations that are too extensive, have negative effects, which influence interconnected levels and once the variation is large enough cause a disease and can lead even to death. Poikilosis has numerous applications and consequences e.g. for how to design, analyze and report experiments, how to develop and apply prediction and modelling methods, and in diagnosis and treatment of diseases. Poikilosis-aware new and practical definitions are provided for life, death, senescence, disease, and lagom. Poikilosis is the first new unifying theory in biology since evolution and should be considered in every scientific study.

Poikilosis - pervasive biological variation

Biological systems are dynamic and display heterogeneity at all levels. Ubiquitous heterogeneity, here called for poikilosis, is an integral and important property of organisms and in molecules, systems and processes within them. Traditionally, heterogeneity in biology and experiments has been considered as unwanted noise, here poikilosis is shown to be the normal state. Acceptable variation ranges are called as lagom. Non-lagom, variations that are too extensive, have negative effects, which influence interconnected levels and once the variation is large enough cause a disease and can lead even to death. Poikilosis has numerous applications and consequences e.g. for how to design, analyze and report experiments, how to develop and apply prediction and modelling methods, and in diagnosis and treatment of diseases. Poikilosis-aware new and practical definitions are provided for life, death, senescence, disease, and lagom. Poikilosis is the first new unifying theory in biology since evolution and should be considered in every scientific study.