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.
Highlights
The processes of cell reprogramming to a pluripotent state at the molecular level starts with protein–protein convergence caused by binding to neighboring DNA sites [1,2]
Based on results from the proximity utilizing the biotinylation (PUB) method in a living cell, we previously discovered a high level of biotin labeling of transcription factors Sox2 and
It is interesting to note that other sequences in which there are combinatorial replacements of the Oct4 moiety in the Utf1 motif ATGCTAGT with another ATGCTAGA are present in the mouse genome
Summary
The processes of cell reprogramming to a pluripotent state at the molecular level starts with protein–protein convergence caused by binding to neighboring DNA sites [1,2]. The transcription factors of pluripotency Sox (SRY-box 2), Oct (Octamer-binding transcription factor 4), and Nanog are key in the transcriptional network that controls stem cell pluripotency and the induction of pluripotency in somatic cells [3,4,5]. All Sox proteins have the high-mobility group (HMG) box domain that may mediate non-sequence-specific and sequence-specific DNA binding [9]. HMG proteins are ubiquitous and abundant nuclear proteins that bind to nucleosomes and cause structural changes in chromatin. These non-histone proteins perform a significant role in DNA replication, recombination, transcription, and DNA repair processes. Sox participates in a stunningly diverse class of cells and tissue types, including pluripotent stem cells, lung tissue, nerve lines, ear, and eye [10,11]
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