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

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...

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Main Authors:	Singh, Vinod Kumar, Krishnamachari, Annangarachari
Format:	Online
Language:	English
Published:	Elsevier 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971157/

id	pubmed-4971157
recordtype	oai_dc
spelling	pubmed-49711572016-08-09 Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome Singh, Vinod Kumar Krishnamachari, Annangarachari Regular Article 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. Elsevier 2016-07-19 /pmc/articles/PMC4971157/ /pubmed/27508123 http://dx.doi.org/10.1016/j.gdata.2016.07.005 Text en © 2016 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Singh, Vinod Kumar Krishnamachari, Annangarachari
spellingShingle	Singh, Vinod Kumar Krishnamachari, Annangarachari Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome
author_facet	Singh, Vinod Kumar Krishnamachari, Annangarachari
author_sort	Singh, Vinod Kumar
title	Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome
title_short	Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome
title_full	Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome
title_fullStr	Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome
title_full_unstemmed	Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome
title_sort	context based computational analysis and characterization of ars consensus sequences (acs) of saccharomyces cerevisiae genome
description	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.
publisher	Elsevier
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971157/
_version_	1613620151300653056

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

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