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ISCB-LA SoIBio BioNetMX 2020 | Oct 28 – 29, 2020 | Virtual Symposium | Symposium Programme

ISCB-LA SoIBio BioNetMX Symposium 2020 Virtual Viewing Hall

Bioinformatic strategies and methods to unravel RNA Genomics - 37: Insights to unravel the differential expression of small RNAs derived from ncRNAs in dengue virus infected HMEC-1 cells

Keywords: Differential expression small RNAseq ncRNAs Mapping Problem Dengue
  • Aimer Gutiérrez-Díaz, Grupo Rnomica Teórica y Computacional, Departamento de Biología, Universidad Nacional de Colombia, Colombia
  • Diego Álvarez-Díaz, Molecular and Translational Medicine Group, Universidad de Antioquia, Medellín, Colombia, Colombia
  • Steve Hoffmann, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Germany
  • Juan Carlos Gallego-Gómez, Molecular and Translational Medicine Group, Universidad de Antioquia, Medellín, Colombia, Colombia
  • Clara Isabel Bermudez-Santana, Grupo Rnomica Teórica y Computacional, Departamento de Biología, Universidad Nacional de Colombia, Colombia

Short Abstract: In the last years it has become apparent that small RNA-mediated gene regulation may be even more complex than previously believed. For example, studies have found small fragments derived from ncRNAs (sfd-RNAs) varying between 20 and 30nt with silencing or interference activity derived from tRNAs and snoRNAs. Despite their structural and functional resemblance to miRNAs, current tools developed to test the differential expression of miRNAs may not be readily applied to sfd-RNAs. Two of the major causes of this problem is a lack of accurate annotation of small RNAs (ncRNAs) and the effect of the multi-mapping reads (MMR) placement problem in differential expression analysis. To solve these issues, we generated an integrated copy-number corrected ncRNA annotation and a reproducibility-qualifier methodology that allows the detection of differential expression of sfd-RNAs including canonical miRNAs. We present sixteen different computational strategies composed of combinations of four aligners and four normalization methods to detect differential expressed small RNAs derived from ncRNAs in dengue virus infected human dermal microvascular endothelial cells (HMEC-1). Expression blocks associated with sfd-RNAs have been ranked based on the sixteen different strategies. Notably, our approach let us to detect differential expressed small RNAs that has not been previously annotated in the human genome. Those strategies simultaneously detect differential expression of miRNAs and sfd-RNAs in DENV-2 infected HMEC-1 cells, systematically addressing the MMR placement problem. A set of diferential expressed sfd-RNAs during DENV-2 infection was detected for subsequent experimental validation.

Bioinformatic strategies and methods to unravel RNA Genomics - 40: Interactomics reveal the molecular regulatory network of the beneficial immune effect of yoga and exercise

Keywords: Yoga Exercise Integrative genomics Protein protein interaction
  • Manoj Khokhar, All India Institute of Medical Sciences Jodhpur, India
  • Dr. Purvi Purohit, All India institute of Medical Sciences Jodhpur, India

Short Abstract: Background: Yoga is a multifaceted spiritual tool that helps in maintaining health, peace of mind and positive thoughts. The crucial dimensions of yoga are asana (physical posture), pranayama (regulated breathing) and meditation. In the context of asana, yoga is similar to physical exercise. Introduction: This study aims to construct a molecular network to find molecules that play essential roles in both physical exercise and yoga. Method: Several keywords, including “yoga”, “exercise”, “Blood”, “Liver”, “Homo sapiens” and “20200820 to 20200830” were searched in GEO datasets. For gene ontology (GO), and KEGG pathway analysis. Protein-protein interaction (PPI) network and cluster analysis detect the potential regulatory seed genes in yoga and exercise, protecting the body from diseases and disorders. Result: We downloaded two gene expression profiles (GSE44777 and GSE6053) from the GEO database and analyzed with GEO2R. There were 666 and 361 DEGs in GSE44777 and GSE6053 respectively. A total of 32 genes co-exist in the DEGs of the two data sets. KEGG pathway analysis showed that 32 DEGs have enriched in immune system regulation and process and novel biological process (ROS, RNS production in phagocytes). We found ECT2, ILR1+, CASP9 were the most important mRNAs in the network analyzed by Cytoscape APP centiscape by MCODE Cluster formation. We constructed a miRNA-mRNA regulatory network seven targetings microRNA control the expression of CASP9. Conclusion: This integrative genomics study identified both well-characterized immune system regulatory process and novel biological process (ROS, RNS production in phagocytes) in DEGs of yoga and exercise, thus showing potential for protection against diseases and maintenance of homeostasis.

Bioinformatic strategies and methods to unravel RNA Genomics - 41: network-interactions: Assessment of TF-gene predicted interactions in gene regulatory networks

Keywords: Gene Regulatory Networks pattern-matching motif Transcription Factor Regulatory Sequence Analysis Tools (RSAT)
  • Mónica Padilla-Gálvez, International Laboratory of Human's Genome Research (LIIGH), Mexico
  • Andrea Streit, King's College London, United Kingdom
  • Alejandra Medina-Rivera, International Laboratory of Human's Genome Research (LIIGH), Mexico

Short Abstract: Gene Regulatory Networks (GRNs) are responsible for fundamental aspects in biological systems such as environment response and physiological processes, being key in development and disease progression [1,2]. Several efforts have been done to infer them, with approaches based in coexpression, orthology, sequence motifs, etc [3]. However, there is not one perfect method and in the means of further improving the inferred GRNs, a motif-based correction underlying putative interactions can be applied as a second step. Here, we present network-interactions, a user-friendly GRN reconstruction pipeline based on pattern-matching integrated in the Regulatory Sequence Analysis Tools (RSAT) [4] platform that can help refine GRNs obtained by other tools. It takes as input a list of transcriptional factors (TFs) of interest, a file of regulatory genomic regions, the genome version of the organism of interest, and an optional previously obtained network. network-interactions runs matrix-scan using, on its default mode, JASPAR’s 2020 vertebrates nonredundant motif collection to search for TF-gene target interactions; and thereby computes several networks: a complete network for all TF-gene interactions, another for only TF-TF interactions, one with indirect interactions, and when provided an input GRN, the complements and the intersection between it and the complete network, where the intersection would contain the common results from both tools including putative TF binding information. The presented tool extends RSAT’s suite and offers a straightforward and flexible method, which facilitates the expansion and refinement of GRNs. [1] Levine, M., & Davidson, E. H. (2005). Gene regulatory networks for development. Proceedings of the National Academy of Sciences, 102(14), 4936-4942. [2] Fazilaty, H., Rago, L., Youssef, K. K., Ocaña, O. H., Garcia-Asencio, F., Arcas, A., ... & Nieto, M. A. (2019). A gene regulatory network to control EMT programs in development and disease. Nature communications, 10(1), 1-16. [3] Mercatelli, D., Scalambra, L., Triboli, L., Ray, F., & Giorgi, F. M. (2020). Gene regulatory network inference resources: A practical overview. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 1863(6), 194430. [4] Nguyen, N. T. T., Contreras-Moreira, B., Castro-Mondragon, J. A., Santana-Garcia, W., Ossio, R., Robles-Espinoza, C. D., ... & van Helden, J. (2018). RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic acids research, 46(W1), W209-W214.

Bioinformatic strategies and methods to unravel RNA Genomics - 49: Head transcriptome analysis of nonreceptor olfactory genes in the round-headed pine beetle Dendroctonus adjunctus Blandford (Coleoptera: Curculionidae)

Keywords: bark beetles semiochemicals olfactory proteins host colonization
  • Brenda Torres-Huerta, Colegio de Postgraduados, Mexico
  • Obdulia L. Segura-León, Colegio de Postgraduados, Mexico
  • Marco A. Aragón-Magadán, Colegio de Postgraduados, Mexico
  • Héctor Hérnandez-González, Colegio de Postgraduados, Mexico
  • Brenda Torres-Huerta, Colegio de Postgraduados, Mexico
  • Obdulia L. Segura-León, Colegio de Postgraduados, Mexico
  • Marco A. Aragón-Magadán, Colegio de Postgraduados, Mexico
  • Héctor Hérnandez-González, Colegio de Postgraduados, Mexico

Short Abstract: The round-headed pine beetle Dendroctonus adjunctus is one of the five most critical primary pests in forest ecosystems in Mexico, their dispersion and colonization behaviors are linked to a communication system mediated by semiochemicals. Antennae are the primary sensory organs of insects, olfactory processing includes different perireceptor events where a set of nonreceptor olfactory proteins are involved, and whose study has sharply increased in the last decade; their size, stability, resistance to high temperature, and proteolytic digestion make them candidates for the development of different biotechnological tools and applications in agriculture. This study provides the first head transcriptome analysis of D. adjunctus collected in infested trees during their higher incidence period and the identification of olfactory genes involved in the perception of odors. De novo assembly yielded 44,420 unigenes, and GO annotations were similar to those of antennal transcriptomes, which reflect metabolic processes related to smell and signal transduction. A total of 36 new transcripts of nonreceptor olfactory genes were identified, of which 27 encode OBPs, 7 encode CSPs, and 2 encode SNMP candidates. The inclusion of a comparative analysis of sequence motifs of OBPs, CSPs, and SNMPs provides clear information on the distinct characteristics of each family and their subclasses. The integration of motif patterns into phylogenetic analysis allowing not only an improved understanding of the evolutionary process but also the conservation of motif patterns between nonreceptor protein families of different Scolytinae and Coleoptera species may suggest distinct regions with functional or structural importance. Our study provides information on genes encoding nonreceptor proteins in D. adjunctus and broadens the knowledge of olfactory genes in bark beetle species, and will help to understand colonization and aggregation behaviors for the development of tools that complement management strategies.

Bioinformatic strategies and methods to unravel RNA Genomics - 60: Analysis of Myc-type BHLH transcription factors role in the reproductive development-hormone signaling network reveals regulation involving viroid-siRNAs, and miPs in tomato host

Keywords: network analysis RNA mediated regulation non-coding RNA plant reproductive development microprotein predictions siRNAs predictions plant-pathogen interactions
  • Katia Aviña-Padilla, CINVESTAV-Unidad Irapuato, Mexico
  • Peter Abrahamian, USDA-ARS, United States
  • Nancy Kreger, USDA-ARS, United States
  • Emilio Herrera-Oropeza, Kings College London, United Kingdom
  • Rose Hammond, USDA-ARS, United States
  • Maribel Hernández-Rosales, CINVESTAV-Unidad Irapuato, Mexico

Short Abstract: Viroids are minimal pathogens of angiosperms, consisting of non-coding RNA (239-401nt) that cause severe diseases in agronomic interest crops. In tomato, the infection symptoms by Pospiviroid species include dwarfism, reduction in vigor, abortion of flowers, and reduced size and number in fruits. The transition from vegetative growth to reproductive development requires gene network coordination, where transcription factors (TFs) act as essential organ morphogenesis components. Symptoms associated with viroid infection are linked to reproductive development in hosts, related to hormone signaling pathways, affecting the expression levels of involved TFs, including the possibility that vd-siRNAs or host factors may be involved in genetic regulation. We proposed a network of gene associations between hormonal pathways to infer a mechanism of interaction during viroid infection. Signaling pathways of hormones are primarily implicit within this network. The objective was to break down the nodes of the proposed network to analyze the transcription factors and critical targets related to the host symptoms. Our analysis highlighted that the tomato SolBigPetal1:SIBHLH036 gene ortholog of Arabidopsis thaliana BIGPETAL-1 (petal size-morphology) contains 20 of 21 nts of exon sequence corresponding to the region within the P domain of the viroid genome, and it is highly induced in tomato during infection. Another striking finding was that two PIF-TFs (SlBHLH06, SlBHLH052) are potentially linked with microproteins (miPs) regulation in brassinosteroid pathways. Besides, we identified key interactor genes in jasmonic acid (Omega 3 fatty acid desaturase/Fad7), gibberellins (Gibberellin B hydroxylase/ 3OH-1), and auxins (indoleacetic acid 3/ IAA3) hormone pathways, being negatively regulated via predicted Pospiviroid derived siRNAs. Overall, our study confirms the participation of vd-siRNAs as modulators of target genes in hormone pathways and represents the first approach to study the role of BHLH-miPs and their interactors in the genetic regulation of reproductive developmental processes during viroid infection.

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