Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

Specific Patterns in Correlations of Super-Short Tandem Repeats (SSTRs) with G+C Content, Genic and Intergenic Regions, and Retrotransposons on All Human Chromosomes

The specific characteristics of k-mer words (2 ≤ k ≤ 11) regarding genomic distribution and evolutionary conservation were recently found. Among them are, in high abundance, words with a tandem repeat structure (repeat unit length of 1 bp to 3 bp). Furthermore, there seems to be a class of extremely short tandem repeats (≤12 bp), so far overlooked, that are non-random-distributed and, therefore, may play a crucial role in the functioning of the genome. In the following article, the positional distributions of these motifs we call super-short tandem repeats (SSTRs) were compared to other functional elements, like genes and retrotransposons. We found length- and sequence-dependent correlations between the local SSTR density and G+C content, and also between the density of SSTRs and genes, as well as correlations with retrotransposon density. In addition to many general interesting relations, we found that SINE Alu has a strong influence on the local SSTR density. Moreover, the observed connection of SSTR patterns to pseudogenes and -exons might imply a special role of SSTRs in gene expression. In summary, our findings support the idea of a special role and the functional relevance of SSTRs in the genome.

Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes

Dinucleotides are known as determinants for various structural and physiochemical properties of DNA and for binding affinities of proteins to DNA. These properties (e.g., stiffness) and bound proteins (e.g., transcription factors) are known to influence important biological functions, such as transcription regulation and 3D chromatin organization. Accordingly, the question arises of how the considerable variations in dinucleotide contents of eukaryotic chromosomes could still provide consistent DNA properties resulting in similar functions and 3D conformations. In this work, we investigate the hypothesis that coupled dinucleotide contents influence DNA properties in opposite directions to moderate each other's influences. Analyzing all 2478 chromosomes of 155 eukaryotic species, considering bias from coding sequences and enhancers, we found sets of correlated and anti-correlated dinucleotide contents. Using computational models, we estimated changes of DNA properties resulting from this coupling. We found that especially pure A/T dinucleotides (AA, TT, AT, TA), known to influence histone positioning and AC/GT contents, are relevant moderators and that, e.g., the Roll property, which is known to influence histone affinity of DNA, is preferably moderated. We conclude that dinucleotide contents might indirectly influence transcription and chromatin 3D conformation, via regulation of histone occupancy and/or other mechanisms.

Eukaryotic Genomes Show Strong Evolutionary Conservation of k-mer Composition and Correlation Contributions between Introns and Intergenic Regions

Several strongly conserved DNA sequence patterns in and between introns and intergenic regions (IIRs) consisting of short tandem repeats (STRs) with repeat lengths <3 bp have already been described in the kingdom of Animalia. In this work, we expanded the search and analysis of conserved DNA sequence patterns to a wider range of eukaryotic genomes. Our aims were to confirm the conservation of these patterns, to support the hypothesis on their functional constraints and/or the identification of unknown patterns. We pairwise compared genomic DNA sequences of genes, exons, CDS, introns and intergenic regions of 34 Embryophyta (land plants), 30 Protista and 29 Fungi using established k-mer-based (alignment-free) comparison methods. Additionally, the results were compared with values derived for Animalia in former studies. We confirmed strong correlations between the sequence structures of IIRs spanning over the entire domain of Eukaryotes. We found that the high correlations within introns, intergenic regions and between the two are a result of conserved abundancies of STRs with repeat units ≤2 bp (e.g., (AT)n). For some sequence patterns and their inverse complementary sequences, we found a violation of equal distribution on complementary DNA strands in a subset of genomes. Looking at mismatches within the identified STR patterns, we found specific preferences for certain nucleotides stable over all four phylogenetic kingdoms. We conclude that all of these conserved patterns between IIRs indicate a shared function of these sequence structures related to STRs.

Immunological pathways of macrophage response to Brucella ovis infection

As the molecular mechanisms of Brucella ovis pathogenicity are not completely clear, we have applied a transcriptome approach to identify the differentially expressed genes (DEGs) in RAW264.7 macrophage infected with B. ovis. The DEGs related to immune pathway were identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) functional enrichment analysis. Quantitative real-time PCR (qRT-PCR) was performed to validate the transcriptome sequencing data. In total, we identified 337 up-regulated and 264 down-regulated DEGs in B. ovis-infected group versus mock group. Top 20 pathways were enriched by KEGG analysis and 20 GO by functional enrichment analysis in DEGs involved in the molecular function, cellular component, and biological process and so on, which revealed multiple immunological pathways in RAW264.7 macrophage cells in response to B. ovis infection, including inflammatory response, immune system process, immune response, cytokine activity, chemotaxis, chemokine-mediated signaling pathway, chemokine activity, and CCR chemokine receptor binding. qRT-PCR results showed Ccl2 (ENSMUST00000000193), Ccl2 (ENSMUST00000124479), Ccl3 (ENSMUST00000001008), Hmox1 (ENSMUST00000005548), Hmox1 (ENSMUST00000159631), Cxcl2 (ENSMUST00000075433), Cxcl2 (ENSMUST00000200681), Cxcl2 (ENSMUST00000200919), and Cxcl2 (ENSMUST00000202317). Our findings firstly elucidate the pathways involved in B. ovis-induced host immune response, which may lay the foundation for revealing the bacteria–host interaction and demonstrating the pathogenic mechanism of B. ovis.

Whole-Genome k-mer Topic Modeling AssociatesBacterial Families

Alignment-free k-mer-based algorithms in whole genome sequence comparisons remainan ongoing challenge. Here, we explore the possibility to use Topic Modeling for organismwhole-genome comparisons. We analyzed 30 complete genomes from three bacterial families bytopic modeling. For this, each genome was considered as a document and 13-mer nucleotiderepresentations as words. Latent Dirichlet allocation was used as the probabilistic modeling of thecorpus. We where able to identify the topic distribution among analyzed genomes, which is highlyconsistent with traditional hierarchical classification. It is possible that topic modeling may be appliedto establish relationships between genome's composition and biological phenomena.

COMBinatorial Oligonucleotide FISH (COMBO-FISH) with Uniquely Binding Repetitive DNA Probes

During the last decade, genome sequence databases of many species have been more and more completed so that it has become possible to further develop a recently established technique of FISH (Fluorescence In Situ Hybridization) called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to standard FISH techniques, COMBO-FISH makes use of a bioinformatic search in sequence databases for probe design, so that it can be done for any species so far sequenced. In the original approach, oligonucleotide stretches of typical lengths of 15-30 nucleotides were selected in such a way that they only co-localize at the given genome target. Typical probe sets of about 20-40 stretches were used to label about 50-250 kb specifically. The probes of different lengths can be composed of purines and pyrimidines, but were often restricted to homo-purine or homo-pyrimidine probe sets because of the experimental advantage of using a protocol omitting denaturation of the target strand and triple strand binding of the probes. This allows for a better conservation of the 3D folding and arrangement of the genome. With an improved, rigorous genome sequence database analysis and sequence search according to statistical frequency and uniqueness, a novel family of probes repetitively binding to characteristic genome features like SINEs (Short Interspersed Nuclear Elements, e.g., ALU elements), LINEs (Long Interspersed Nuclear Elements, e.g., L1), or centromeres has been developed. These probes can be synthesized commercially as DNA or PNA probes with high purity and labeled by fluorescent dye molecules. Here, new protocols are described for purine-pyrimidine probes omitting heat treatment for denaturation of the target so that oligonucleotide labeling can also be combined with immune-staining by specific antibodies. If the dyes linked to the oligonucleotide stretches undergo reversible photo-bleaching (laser-induced slow blinking), the labeled cell nuclei can be further subjected to super-resolution localization microscopy for complex chromatin architecture research.

Genome sequence comparison under a new form of tri-nucleotide representation based on bio-chemical properties of nucleotides

Genetic sequence analysis, classification of genome sequence and evolutionary relationship between species using their biological sequences, are the emerging research domain in Bioinformatics. Several methods have already been applied to DNA sequence comparison under tri-nucleotide representation. In this paper, a new form of tri-nucleotide representation is proposed for sequence comparison. The comparison does not depend on the alignment of the sequences. In this representation, the bio-chemical properties of the nucleotides are considered. The novelty of this method is that the sequences of unequal lengths are represented by vectors of the same length and each of the tri-nucleotide formed out of the given sequence has its unique representation. To validate the proposed method, it is verified on several data sets related to mammalians, viruses and bacteria. The results of this method are further compared with those obtained by methods such as probabilistic method, natural vector method, Fourier power spectrum method, multiple encoding vector method, and feature frequency profiles method. Moreover, this method produces accurate phylogeny in all the cases. It is also proved that the time complexity of the present method is less.