Choosing a suitable method for the identification of replication origins in microbial genomes

Abstract

As the replication of genomic DNA is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. Making sense of DNA replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. Thus, clearly comprehending the positions and sequences of replication origins which are fundamental to chromosome organization and duplication is the first priority of all. In view of such important roles of replication origins, tremendous work has been aimed at identifying and testing the specificity of replication origins. A number of computational tools based on various skew types have been developed to predict replication origins. Using various in silico approaches such as Ori-Finder, and databases such as DoriC, researchers have predicted the locations of replication origins sites for thousands of bacterial chromosomes and archaeal genomes. Based on the predicted results, we should choose an effective method for identifying and confirming the interactions at origins of replication. Here we describe the main existing experimental methods that aimed to determine the replication origin regions and list some of the many the practical applications of these methods.

Yeast autonomously replicating sequence (ARS): Identification, function, and modification

“…Another mutation method is flanking ARS‐seq, which keeps the core ACS unchanged and makes mutants flanking sequences form a mutant library, combining with sequence analysis. This method effectively selects the appropriate flanking sequences, and investigates the function of ACS flanking region [19, 73]. Through mutation, we can obtain high‐efficiency ARSs and simply verify its efficiency by measuring the conversion rate [30, 74].…”

Computational prediction of species-specific yeast DNA replication origin via iterative feature representation

“…Several in vitro and in vivo experimental techniques, such as chromatin immunoprecipitation (ChIP), ChIP-sequencing, DNase I footprinting technique, electrophoretic mobility shift assays, gel retardation assay, isothermal titration calorimetry, replication initiation point mapping and surface plasmon resonance have been developed to identify DNA ORIs [ 5 ]. Lee and Bell [ 6 ] reported that the origin recognition complex (ORC) that binds ORIs could be accurately detected [ 7 ].…”

iROS-gPseKNC: Predicting replication origin sites in DNA by incorporating dinucleotide position-specific propensity into general pseudo nucleotide composition

“…Although the processes of DNA replications are different for bacteria, archaea, and eukaryotes, they all share the same core components as elaborated in [1–2]. For in-depth understanding the genome duplication, it is important to find the “origin of replication region” (Ori), or “replication origin” (RO) (Figure 1).…”

“…Actually, it is quite natural to establish the replication forks at multiple locations [3] in order for timely duplicating their larger linear chromosomes. Therefore, to in-depth understand the process of cell reproduction, it is fundamentally important to acquire the RO information [1]. …”