International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

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Genomics, transcriptomics, bioinformatics symposiumStatistical problems of clusters of transcription factor binding sites in plant genomes

Statistical problems of clusters of transcription factor binding sites in plant genomes

No Comment on Statistical problems of clusters of transcription factor binding sites in plant genomes

Artur Dergilev1
1Institute of Cytology and Genetics SB RAS, arturd1993@yandex.ru

AbstractВ В В В 

This work presents the results of using computer scripts to analyze ChIP-seq data, calculate clusters, and visualize them in the form of heat maps. In the work, ChIP-seq peaks were used to study the stem cell niche of three plants, among which the well-known Talus (Arabidopsis Thailana), Physcomitrella patens, Chlamydomonas reinhardti. What about the tendency of co-localization of transcription factors in plant genomes? What are the features of this co-localization?

Systems computational biology: analysis, mathematical modeling and information technologies symposiumIntegration of transcriptomics data into a genome-scale metabolic model of the methanotrophic bacterium Methylotuvimicrobium alcaliphilum 20ZR

Integration of transcriptomics data into a genome-scale metabolic model of the methanotrophic bacterium Methylotuvimicrobium alcaliphilum 20ZR

No Comment on Integration of transcriptomics data into a genome-scale metabolic model of the methanotrophic bacterium Methylotuvimicrobium alcaliphilum 20ZR

Mikhail Kulyashov1, Ivan S. Evshin2, Nikita V. Ivanisenko3, Semyon K. Kolmykov4, Tamara M. Khlebodarova5, Ilya R. Akberdin6
1BIOSOFT.RU, LLC ; Novosibirsk State University; FRC Institute of Cytology and Genetics SB RAS, m.kulyashov@mail.ru
2BIOSOFT.RU, LLC; Institute of Computational Technologies SB RAS, ivan@developmentontheedge.com
3FRC Institute of Cytology and Genetics SB RAS, n.ivanisenko@gmail.com
4BIOSOFT.RU, LLC; Institute of Computational Technologies SB RAS; FRC Institute of Cytology and Genetics SB RAS, semyonk@developmentontheedge.com
5FRC Institute of Cytology and Genetics SB RAS, tamara@bionet.nsc.ru
6BIOSOFT.RU, LLC; FRC Institute of Cytology and Genetics SB RAS; Novosibirsk State University, akberdinir@gmail.com

Aerobic methane-oxidizing bacteria or methanotrophs have the unique ability to grow on methane as their sole source of carbon and energy. The main metabolic steps of the methane utilization by microorganisms have been identified and well-studied to date. However, a detailed understanding of molecular genetic mechanisms that provide an adaptive response at the level of transcription regulation to various growth conditions, high and low pH, temperature, and salinity is still elusive. To solve the issue we have conducted a detailed theoretical study of the molecular mechanisms of gene expression regulation in the bacterium Methylotuvimicrobium alcaliphilum 20ZR (hereinafter 20ZR) based on the integration of original omics data into genome-scale metabolic model of the 20ZR.

Genomics, transcriptomics, bioinformatics symposiumLTR-retrotransposon transcripts are ubiqutiously expressed, polyadenylated and underwent splicing in sunflower (Helianthus annuus L.)

LTR-retrotransposon transcripts are ubiqutiously expressed, polyadenylated and underwent splicing in sunflower (Helianthus annuus L.)

No Comment on LTR-retrotransposon transcripts are ubiqutiously expressed, polyadenylated and underwent splicing in sunflower (Helianthus annuus L.)

Pavel Merkulov, Murad Omarov, Ilya Kirov1
1All-Russian Research Institute of Agricultural Biotechnology RAS, paulmerkulov97@gmail.com

LTR-retrotransposons are mobile genetic elements widespread in plant genomes. Dispite the fact of significant part of genome engaged by retrotransposons (up to 80 percent), their activity is suppressed by multiple posttranscriptional and epigenetic mechanisms in normal conditions. Retrotransposon escape from silencing and subsequent expression are, in turn, purely described for plants.