Nucleotide correlation based measure for identifying origin of replication in genomic sequences

Shah, Kushal; Krishnamachari, Annangarachari

doi:10.1016/j.biosystems.2011.09.003

Cited by 18 publications

(28 citation statements)

References 32 publications

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“…This measure, unlike GC skew, takes into account dependencies at various positions that to some extent mimic the real biological sequence makeup. It has been successfully used in identification of origin sites in the apicoplast genome of P. falciparum [31]. It is important to note here that the prediction of the autocorrelation method matches well with the experimentally known replication origin in the apicoplast of P. falciparum whereas the prediction of the GC-skew method does not match with the experimental data [32].…”

Section: Introductionmentioning

confidence: 85%

Identification and characterization of ARS‐like sequences as putative origin(s) of replication in human malaria parasite Plasmodium falciparum

et al. 2017

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DNA replication is a fundamental process in genome maintenance, and initiates from several genomic sites (origins) in eukaryotes. In Saccharomyces cerevisiae, conserved sequences known as autonomously replicating sequences (ARSs) provide a landing pad for the origin recognition complex (ORC), leading to replication initiation. Although origins from higher eukaryotes share some common sequence features, the definitive genomic organization of these sites remains elusive. The human malaria parasite Plasmodium falciparum undergoes multiple rounds of DNA replication; therefore, control of initiation events is crucial to ensure proper replication. However, the sites of DNA replication initiation and the mechanism by which replication is initiated are poorly understood. Here, we have identified and characterized putative origins in P. falciparum by bioinformatics analyses and experimental approaches. An autocorrelation measure method was initially used to search for regions with marked fluctuation (dips) in the chromosome, which we hypothesized might contain potential origins. Indeed, S. cerevisiae ARS consensus sequences were found in dip regions. Several of these P. falciparum sequences were validated with chromatin immunoprecipitation-quantitative PCR, nascent strand abundance and a plasmid stability assay. Subsequently, the same sequences were used in yeast to confirm their potential as origins in vivo. Our results identify the presence of functional ARSs in P. falciparum and provide meaningful insights into replication origins in these deadly parasites. These data could be useful in designing transgenic vectors with improved stability for transfection in P. falciparum.

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Section: Introductionmentioning

confidence: 85%

Identification and characterization of ARS‐like sequences as putative origin(s) of replication in human malaria parasite Plasmodium falciparum

et al. 2017

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“… [2] . Correlation-based methods are also used for sequence alignment, detection of local similarities in DNA and ORI detection in prokaryotes [5] , [31] , [32] . Based on these studies, we introduced the Average sequence measure ( AS k ) for the sliding overlapping window of size w and at k th position of a given set of n centrally aligned sequences having equal length L was calculated as:

…”

Section: Methodsmentioning

confidence: 99%

“…Most bacterial genomes are circular and have single ORI site. Computational methods employed to detect these origin sites exploit the property of asymmetrically biased nucleotide composition, and this strategy is found to be successful in bacterial genomes [2] , [3] , [4] , [5] , [6] . Replication origin firing plays a significant role in cell cycle regulation.…”

Section: Introductionmentioning

confidence: 99%

Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome

Singh

Krishnamachari

2016

Genomics Data

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Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS) requires an essential consensus sequence (ACS) for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC) denoted as ORC-ACS and non-replicating ACS sequences (nrACS), that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme.

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“…This is an important contribution since unlike the other phylogenetic methods which are based on sequence alignment, a correlation based method is both much more simple and independent of the length of the DNA sequence. In another paper [7], jumps in correlation value along the DNA sequence were shown to be a better way to identify the origin of replication in various organisms. It was shown that a correlation based method is not only better than the conventional methods for identifying bacterial origins of replication, but it can also predict the origin of replication in certain higher organisms.…”

Section: Introductionmentioning

confidence: 99%

Plasmodium falciparum has rare correlation properties

Shah

2012

Nature Precedings

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A plot of the correlation function of a given DNA sequence has certain characteristic features common to almost all organisms. One common feature is that the correlation values at distances that are multiples of three is higher than correlation values at other distances. Because of this such a correlation plot can be divided into two or three curves with different scalings. P. falciparum has a rare correlation property which is probably unique. I have analyzed genomes of many bacteria, fungi and protozoa and found that P. falciparum is the only organism whose DNA sequence correlation plot can be divided into four curves with different scalings. This property is neither shared by other species of the Plasmodium genus nor by other AT rich genomes. This could be a hint that the DNA sequence of P. falciparum has undergone certain rare mutational events.

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Nucleotide correlation based measure for identifying origin of replication in genomic sequences

Cited by 18 publications

References 32 publications

Identification and characterization of ARS‐like sequences as putative origin(s) of replication in human malaria parasite Plasmodium falciparum

Identification and characterization of ARS‐like sequences as putative origin(s) of replication in human malaria parasite Plasmodium falciparum

Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome

Plasmodium falciparum has rare correlation properties

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