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

Arman Kulyyassov; Ruslan Kalendar

doi:10.3390/data5040111

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

Arman Kulyyassov
, Ruslan Kalendar

Ministry of Education and Science of the Republic of Kazakhstan
National Center of Biotechnology
Institut Gustave Roussy
CNRS
Nazarbayev University

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

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.

Original language	English
Article number	111
Pages (from-to)	1-9
Number of pages	9
Journal	Data
Volume	5
Issue number	4
DOIs	https://doi.org/10.3390/data5040111
Publication status	Published - Dec 2020

Funding

This work was supported by a grant from the Ministry of education and science of the Republic of Kazakhstan (AP05132131). Open access funding was provided by University of Helsinki including Helsinki University Central Hospital. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We warmly thank Alexander Bolshoy (Palack? University Olomouc, Czech Republic) for critical reading of the manuscript.

Funders	Funder number
University of Helsinki including Helsinki University Central Hospital
Alexander Bolshoy
University Olomouc
Ministry of Education and Science of the Republic of Kazakhstan	AP05132131

Keywords

In vivo DNA-dependent protein–protein interaction
Phylogeny
Pluripotency transcription factors Sox2 and Oct4
Protein–protein interactions (PPI)
Reprogramming

ASJC Scopus subject areas

Computer Science Applications
Information Systems
Information Systems and Management

Access to Document

10.3390/data5040111Licence: CC BY-ND

Cite this

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

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. ",

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AU - Kalendar, Ruslan

PY - 2020/12

Y1 - 2020/12

N2 - 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.

AB - 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.

KW - In vivo DNA-dependent protein–protein interaction

KW - Phylogeny

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KW - Protein–protein interactions (PPI)

KW - Reprogramming

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

Abstract

Funding

Keywords

ASJC Scopus subject areas

Access to Document

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