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

Sievers, Aaron; Wenz, Frederik; Hausmann, Michael; Hildenbrand, Georg

doi:10.3390/genes9100482

Cited by 15 publications

(28 citation statements)

References 38 publications

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“…k-mer analysis has become a popular approach for sequence comparison [32,33]. So far, there are three pivotal previous studies that classified complete genomes by this approach.…”

Section: Resultsmentioning

confidence: 99%

Whole-Genome k-mer Topic Modeling Associates Bacterial Families

Borrayo

May-Canche

Paredes

et al. 2020

Genes

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

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“…k-mer analysis has become a popular approach for sequence comparison [32,33]. So far, there are three pivotal previous studies that classified complete genomes by this approach.…”

Section: Resultsmentioning

confidence: 99%

Whole-Genome k-mer Topic Modeling Associates Bacterial Families

Borrayo

May-Canche

Paredes

et al. 2020

Genes

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“…Compared with first-generation sequencing technology, high-throughput sequencing technology is a milestone in the field of genomics because of lower costs and better opportunity to identify DEGs for further studying the pathogenesis of diseases. 39 – 41 Brucella can be transmitted through contaminated placenta and aerosol, and can enter the host through gastrointestinal and respiratory mucosae. The mucosal immune response is the host’s main defense host against invasive Brucella .…”

Section: Discussionmentioning

confidence: 99%

Immunological pathways of macrophage response to Brucella ovis infection

Zhou

Luo

et al. 2020

Innate Immun

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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.

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“…The first speculations of a functional relation of IIRs in Animalia were made in [7], where a correlation between the sizes of the two was observed [7]. More recent studies also found conserved structures comparing different regions, e.g., between introns and intergenic regions [8].…”

Section: Introductionmentioning

confidence: 99%

“…While the genomes of the Animalia species were analyzed in [8], the aim of this study was to search for conserved sequence structures within IIRs of Embryophyta, Protista and Fungi and to compare the results between the kingdoms (including Animalia). Standard sequence analysis tools, such as the NCBI Basic Local Alignment Search Tool (BLAST) [9], Genes 2021, 12, 1571 2 of 19 cannot be effectively used to search such structures within regions of sizes comparable to entire genomes [10].…”

Section: Introductionmentioning

confidence: 99%

“…While a standard k-mer analysis is sufficient to discover the conservation of sequence structures in general, it does not provide information about the sequence patterns responsible for this conservation. Therefore, we additionally analyzed the results by performing a decomposition of the correlation coefficient (see [8] for details) to quantify the contribution of individual DNA words to the respective correlation coefficients. The resulting word lists were then analyzed for peculiar patterns.…”

Section: Introductionmentioning

confidence: 99%

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

Sievers

Sauer

Hausmann

et al. 2021

Genes

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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.

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

Cited by 15 publications

References 38 publications

Whole-Genome k-mer Topic Modeling Associates Bacterial Families

Whole-Genome k-mer Topic Modeling Associates Bacterial Families

Immunological pathways of macrophage response to Brucella ovis infection

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

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