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OriDB: a DNA replication origin database

Conrad A. Nieduszynski, Shin-ichiro Hiraga, Prashanth Ak, Craig J. Benham, Anne D. Donaldson
2006 Nucleic Acids Research  
OriDB provides a web-based catalogue of these confirmed and predicted S.cerevisiae DNA replication origin sites.  ...  Finally, a Chromosome Viewer utility allows users to interactively generate graphical representations of DNA replication data genome-wide. OriDB is available at www.oridb.org.  ...  This database will provide a valuable resource to those working in the field of DNA replication.  ... 
doi:10.1093/nar/gkl758 pmid:17065467 pmcid:PMC1781122 fatcat:avu7gnuaefh7nfoanr7n6vieam

OriDB, the DNA replication origin database updated and extended

C. C. Siow, S. R. Nieduszynska, C. A. Muller, C. A. Nieduszynski
2011 Nucleic Acids Research  
OriDB (http://www.oridb.org/) is a database containing collated genome-wide mapping studies of confirmed and predicted replication origin sites.  ...  the collation of replication origin sites in the fission yeast Schizosaccharomyces pombe.  ...  ACKNOWLEDGEMENTS OriDB has been built on a large body of work only a fraction of which we have been able to mention here.  ... 
doi:10.1093/nar/gkr1091 pmid:22121216 pmcid:PMC3245157 fatcat:nwvzqved6jah5kl6btmpl7fd7e

Recent advances in the genome-wide study of DNA replication origins in yeast

Chong Peng, Hao Luo, Xi Zhang, Feng Gao
2015 Frontiers in Microbiology  
OriDB 1 is the most widely used database of DNA replication origins, which is limited to budding yeast (S. cerevisiae) and fission yeast (S. pombe) by present.  ...  The data of microarray-based techniques including heavy : light study, copy number study, ORC-ChIP, and MCM-ChIP, as well as ssDNA in HU study were downloaded from the DNA replication origin database OriDB  ...  Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest  ... 
doi:10.3389/fmicb.2015.00117 pmid:25745419 pmcid:PMC4333867 fatcat:uwq5dkaywzd3dc4xq7gqbfeucm

Recent Advances on the Machine Learning Methods in Identifying DNA Replication Origins in Eukaryotic Genomics

Fu-Ying Dao, Hao Lv, Fang Wang, Hui Ding
2018 Frontiers in Genetics  
The initiate site of DNA replication is called origins of replication (ORI) which is regulated by a set of regulatory proteins and plays important roles in the basic biochemical process during cell growth  ...  of DNA replication.  ...  OriDB is the most extensively used database for identifying eukaryotic DNA replication, in which each potential replication origin site has one of three confidence levels: confirmed, likely and dubious  ... 
doi:10.3389/fgene.2018.00613 pmid:30619452 pmcid:PMC6295579 fatcat:ktgfjq3jnfdjjj6afjspieys6e

Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains [article]

Jie Peng, Ishita Joshi, Gina Alvino, Elizabeth Kwan, Wenyi Feng
2021 bioRxiv   pre-print
AbstractWe performed a comparative analysis of replication origin activation by genome-wide single-stranded DNA mapping in two common laboratory strains of Saccharomyces cerevisiae challenged by hydroxyurea  ...  We also show that sequence polymorphism in the consensus motifs of the replication origins plays a minor role in determining origin usage.  ...  Accession numbers Raw DNA sequences of the A364a genome and microarray raw data will be uploaded to the GEO database before publication. .  ... 
doi:10.1101/2021.02.16.431410 fatcat:jrf673evcndqri3qxn7dgwjg74

The Origin Recognition Complex Interacts with a Subset of Metabolic Genes Tightly Linked to Origins of Replication

Erika Shor, Christopher L. Warren, Joshua Tietjen, Zhonggang Hou, Ulrika Müller, Ilaria Alborelli, Florence H. Gohard, Adrian I. Yemm, Lev Borisov, James R. Broach, Michael Weinreich, Conrad A. Nieduszynski (+3 others)
2009 PLoS Genetics  
Taken together, these results suggest a surprising connection among ORC, replication origins, and cellular metabolism.  ...  The origin recognition complex (ORC) marks chromosomal sites as replication origins and is essential for replication initiation.  ...  The wealth of information gathered from both individual and genome-wide origin studies has been systematically summarized in the DNA Replication Origin Database, OriDB (www.oridb.org; [19] ).  ... 
doi:10.1371/journal.pgen.1000755 pmid:19997491 pmcid:PMC2778871 fatcat:vgqcnnzuzbbuhhd4k3rv35wtxy

Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains

Ishita Joshi, Jie Peng, Gina Alvino, Elizabeth Kwan, Wenyi Feng, Arthur J. Lustig
2022 PLoS ONE  
We performed a comparative analysis of replication origin activation by genome-wide single-stranded DNA mapping in two yeast strains challenged by hydroxyurea, an inhibitor of the ribonucleotide reductase  ...  We gained understanding of the impact on origin activation by three factors: S-phase checkpoint control, DNA sequence polymorphisms, and relative positioning of origin and transcription unit.  ...  a likely origin (ARS( 14 No ARS, including dubious ARSs in the OriDB, was found in this region.  ... 
doi:10.1371/journal.pone.0263569 pmid:35157703 pmcid:PMC8843211 fatcat:vyaevww4lzbdlpd4qsxoxx5msu

Comprehensive Analysis of Replication Origins in Saccharomyces cerevisiae Genomes

Dan Wang, Feng Gao
2019 Frontiers in Microbiology  
DNA replication initiates from multiple replication origins (ORIs) in eukaryotes.  ...  Discovery and characterization of replication origins are essential for a better understanding of the molecular mechanism of DNA replication.  ...  ARSs from OriDB and DeOri databases, which makes it possible for us to conduct a large-scale comparison of replication origin sequences among various yeast strains from a population genomics perspective  ... 
doi:10.3389/fmicb.2019.02122 pmid:31572328 pmcid:PMC6753640 fatcat:guvrjuijrzfujanfarapuy2kb4

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads [article]

Carolin A Mueller, Michael A Boemo, Paolo Spingardi, Benedikt Kessler, Skirmantas Kriaucionis, Jared T Simpson, Conrad A Nieduszynski
2018 biorxiv/medrxiv   pre-print
We used sequencing reads of 20-160 kb, to generate the first whole genome single-molecule map of DNA replication dynamics and discover a new class of low frequency stochastic origins in budding yeast.  ...  Using this method, we detect BrdU incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse labelling period.  ...  OriDB, the DNA 352 replication origin database updated and extended. Nucleic Acids Res 40, , C.A. et al. The dynamics of genome replication using deep sequencing.  ... 
doi:10.1101/442814 fatcat:sy236slnujfyha5hpgnlpxssiq

Page 1847 of Genetics Vol. 180, Issue 4 [page]

2008 Genetics  
DOoNALDSON, 2007 OriDB: a DNA replication origin database. Nucleic Acids Res. 35: D40-D46. PATEL, P. K., B. ARCANGIOLI, S. P. BAKER, A. BENSIMON and N.  ...  RHIND, 2006 DNA replication origins fire stochastically in fission yeast. Mol. Biol. Cell 17: 308-316. RAGHURAMAN, M. K., E. A. WiInzELER, D. COLLINGWoop, S. HUNT, L.  ... 

Prediction of replication origins by calculating DNA structural properties

Wei Chen, Pengmian Feng, Hao Lin
2012 FEBS Letters  
Edited by Gianni Cesareni Keywords: Origin of replication Bendability Cleavage intensity Support vector machine a b s t r a c t In this study, we introduced two DNA structural characteristics, namely,  ...  bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the Saccharomyces cerevisiae genome.  ...  Materials and methods Dataset As September of 2009, the OriDB database [13] (confirmed, likely, or dubious) which expresses the level of confidence that the site genuinely corresponds to an origin  ... 
doi:10.1016/j.febslet.2012.02.034 pmid:22449982 fatcat:vxxjkr2ez5az7ar3hrze5bvgie

Asymmetry Indices for Analysis and Prediction of Replication Origins in Eukaryotic Genomes

Marie-Claude Marsolier-Kergoat, Conrad A. Nieduszynski
2012 PLoS ONE  
DNA replication was recently shown to induce the formation of compositional skews in the genomes of the yeasts Saccharomyces cerevisiae and Kluyveromyces lactis.  ...  Asymmetry indices related to GC and TA skews were defined, and a global asymmetry index I GC,TA was described.  ...  Asymmetry Indices for Replication Analysis PLOS ONE | www.plosone.org  ... 
doi:10.1371/journal.pone.0045050 pmid:23028755 pmcid:PMC3459929 fatcat:7vkl6rgtsjdwxagx57rj7wqale

Nuclear Mitochondrial DNA Activates Replication in Saccharomyces cerevisiae

Laurent Chatre, Miria Ricchetti, David Kirkpatrick
2011 PLoS ONE  
The nuclear genome of eukaryotes is colonized by DNA fragments of mitochondrial origin, called NUMTs. These insertions have been associated with a variety of germ-line diseases in humans.  ...  Here we provide functional evidence that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae.  ...  Payen for suggestions on replication profiles, and C. Alabert for technical advice on 2D-gels. Author Contributions  ... 
doi:10.1371/journal.pone.0017235 pmid:21408151 pmcid:PMC3050842 fatcat:kswujfaglbawnmiaxvfm3jvbmq

The Fkh1 Forkhead associated domain promotes ORC binding to a subset of DNA replication origins in budding yeast

Timothy Hoggard, Allison J Hollatz, Rachel E Cherney, Melissa R Seman, Catherine A Fox
2021 Nucleic Acids Research  
The pioneer event in eukaryotic DNA replication is binding of chromosomal DNA by the origin recognitioncomplex (ORC).  ...  Here, we uncover a role for the Fkh1 (Forkhead homolog) protein and its forkhead associated (FHA) domain in promoting ORC-origin binding and origin activity at a subset of origins in Saccharomyces cerevisiae  ...  ACKNOWLEDGEMENTS We are grateful for the help from Christen Geyer and the multiple undergraduate researchers who participated in the Team Origin Undergraduate Research Project (Supplementary Figure S8  ... 
doi:10.1093/nar/gkab450 pmid:34095951 pmcid:PMC8501964 fatcat:av76tehk55c2vpbhb3ta5hsldi

A Link between ORC-Origin Binding Mechanisms and Origin Activation Time Revealed in Budding Yeast

Timothy Hoggard, Erika Shor, Carolin A. Müller, Conrad A. Nieduszynski, Catherine A. Fox, Hiten D. Madhani
2013 PLoS Genetics  
Eukaryotic DNA replication origins are selected in G1-phase when the origin recognition complex (ORC) binds chromosomal positions and triggers molecular events culminating in the initiation of DNA replication  ...  Each chromosome uses multiple origins for its duplication, and each origin fires at a characteristic time during S-phase, creating a cell-type specific genome replication pattern relevant to differentiation  ...  to this origin regulation, the mean replication time (Trep values) acquired from a copy-number based analysis of DNA replication, was assessed for several groups of relevant origins [64] (Figure 6A  ... 
doi:10.1371/journal.pgen.1003798 pmid:24068963 pmcid:PMC3772097 fatcat:vfexwco7uncbhhqde63etuzgom
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