In Silico Estimation of the Abundance and Phylogenetic Significance of the Composite Oct4-Sox2 Binding Motifs within a Wide Range of Species

Arman Kulyyassov and Ruslan Kalendar
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Arman Kulyyassov: Republican State Enterprise “National Center for Biotechnology”, 13/5 Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan
Ruslan Kalendar: Department of Agricultural Sciences, University of Helsinki, FI-00014 Helsinki, Finland

Data, 2020, vol. 5, issue 4, 1-9

Abstract: High-throughput sequencing technologies have greatly accelerated the progress of genomics, transcriptomics, and metagenomics. Currently, a large amount of genomic data from various organisms is being generated, the volume of which is increasing every year. Therefore, the development of methods that allow the rapid search and analysis of DNA sequences is urgent. Here, we present a novel motif-based high-throughput sequence scoring method that generates genome information. We found and identified Utf1-like, Fgf4-like, and Hoxb1-like motifs, which are cis-regulatory elements for the pluripotency transcription factors Sox2 and Oct4 within the genomes of different eukaryotic organisms. The genome-wide analysis of these motifs was performed to understand the impact of their diversification on mammalian genome evolution. Utf1-like, Fgf4-like, and Hoxb1-like motif diversity was evaluated across genomes from multiple species.

Keywords: phylogeny; protein–protein interactions (PPI); in vivo DNA-dependent protein–protein interaction; pluripotency transcription factors Sox2 and Oct4; reprogramming (search for similar items in EconPapers)
JEL-codes: C8 C80 C81 C82 C83 (search for similar items in EconPapers)
Date: 2020
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