WebMCOT web-service for prediction of co-occurred DNA motifs in ChIP-seq data

Poster (download) Aleksey Mukhin1, Victor Levitsky2, Dmitriy Y. Oschepkov3, Sergey A. Lashin41Institute Cytology and Genetics SB RAS Novosibirsk, Russia, mukhin@bionet.nsc.ru2Institute Cytology and Genetics SB RAS, levitsky@bionet.nsc.ru3Institute Cytology and Genetics SB RAS, diman@bionet.nsc.ru4Institute Cytology and Genetics SB RAS, lashin@bionet.nsc.ru Regulation of eukaryotic gene expression is controlled by specific regulatory proteins transcription factors. Binding sites of transcription factors are called motifs. Conventionally, genome-wide annotation of motifs performed with chromatin immunoprecipitation followed by massive sequencing (ChIP-seq) approach. The term composite element (CE) implied two closely located and frequently occurred in genomic DNA motifs. CEs contain two overlapping or spacing motifs. Earlier we proposed Motif Co-Occurrence Tool (MCOT) package that is capable of (a) predicting CEs with both overlapping and spacing of motifs in a single ChIP-seq dataset; (b) all predicted CEs were classified by conservation of both participant motifs. This work presents a web interface WebMCOT for MCOT package

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Functional annotation of the transcription factors from Methylotuvimicrobium alcaliphilum 20ZR

Semyon K. Kolmykov1, Nikita V. Ivanisenko2, Ivan S. Evshin3, Mikhail Kulyashov4, Tamara M. Khlebodarova5, Ilya R. Akberdin61Institute of Computational Technologies SB RAS, kolmykovsk@gmail.com2FRC Institute of Cytology and Genetics SB RAS, n.ivanisenko@gmail.com3Institute of Computational Technologies SB RAS, ivan@biosoft.ru4Institute of Computational Technologies SB RAS, m.kulyashov@mail.ru5FRC Institute of Cytology and Genetics SB RAS, tamara@bionet.nsc.ru6FRC Institute of Cytology and Genetics SB RAS, akberdinir@gmail.com Methane is a promising carbon source for biosynthesis of biotechnologically useful compounds using aerobic methanotrophic bacteria as biocatalysts. Despite more than a century-long history of discovering and studying of methanotrophic microorganisms, knowledge of the molecular mechanisms of gene expression regulation by transcription factors in these bacteria is very limited with only a few isolated cases being published. Therefore, the identification of potential transcription factors for methanotrophic organisms and their target genes is not only a foreground fundamental problem in the research field of methanotrophy, but it is also especially relevant for the active development of biotechnological application of methane-oxidizing microorganisms. In this study a comparative genomics approach together with the structural modeling techniques were applied to reveal the TFs in the 20ZR genome and predict their target regulatory genes.

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