OriDB: a DNA replication origin database

被引：132

作者：

Nieduszynski, Conrad A. ^{[1
]}

Hiraga, Shin-ichiro

Ak, Prashanth

Benham, Craig J.

Donaldson, Anne D.

机构：

[1] Univ Aberdeen, Inst Med Sci, Aberdeen AB25 2ZD, Scotland

[2] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

基金：

美国国家科学基金会;

关键词：

D O I：

10.1093/nar/gkl758

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Replication of eukaryotic chromosomes initiates at multiple sites called replication origins. Replication origins are best understood in the budding yeast Saccharomyces cerevisiae, where several complementary studies have mapped their locations genome-wide. We have collated these datasets, taking account of the resolution of each study, to generate a single list of distinct origin sites. OriDB provides a web-based catalogue of these confirmed and predicted S.cerevisiae DNA replication origin sites. Each proposed or confirmed origin site appears as a record in OriDB, with each record comprising seven pages. These pages provide, in text and graphical formats, the following information: genomic location and chromosome context of the origin site; time of origin replication; DNA sequence of proposed or experimentally confirmed origin elements; free energy required to open the DNA duplex (stress-induced DNA duplex destabilization or SIDD); and phylogenetic conservation of sequence elements. In addition, OriDB encourages community submission of additional information for each origin site through a User Notes facility. Origin sites are linked to several external resources, including the Saccharomyces Genome Database (SGD) and relevant publications at PubMed. 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.

引用

页码：D40 / D46

页数：7

共 41 条

[31] The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence [J].

Theis, JF ;

Newlon, CS .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (20) :10786-10791

[32] THE EASE OF DNA UNWINDING AS A DETERMINANT OF INITIATION AT YEAST REPLICATION ORIGINS [J].

UMEK, RM ;

KOWALSKI, D .

CELL, 1988, 52 (04) :559-567

[33] MUTATIONAL ANALYSIS OF THE CONSENSUS SEQUENCE OF A REPLICATION ORIGIN FROM YEAST CHROMOSOME-III [J].

VANHOUTEN, JV ;

NEWLON, CS .

MOLECULAR AND CELLULAR BIOLOGY, 1990, 10 (08) :3917-3925

[34] Histone acetylation regulates the time of replication origin firing [J].

Vogelauer, M ;

Rubbi, L ;

Lucas, I ;

Brewer, BJ ;

Grunstein, M .

MOLECULAR CELL, 2002, 10 (05) :1223-1233

[35] Database resources of the national center for biotechnology information [J].

Wheeler, David L. ;

Barrett, Tanya ;

Benson, Dennis A. ;

Bryant, Stephen H. ;

Canese, Kathi ;

Chetvernin, Vyacheslav ;

Church, Deanna M. ;

DiCuccio, Michael ;

Edgar, Ron ;

Federhen, Scott ;

Geer, Lewis Y. ;

Helmberg, Wolfgang ;

Kapustin, Yuri ;

Kenton, David L. ;

Khovayko, Oleg ;

Lipman, David J. ;

Madden, Thomas L. ;

Maglott, Donna R. ;

Ostell, James ;

Pruitt, Kim D. ;

Schuler, Gregory D. ;

Schriml, Lynn M. ;

Sequeira, Edwin ;

Sherry, Stephen T. ;

Sirotkin, Karl ;

Souvorov, Alexandre ;

Starchenko, Grigory ;

Suzek, Tugba O. ;

Tatusov, Roman ;

Tatusova, Tatiana A. ;

Wagner, Lukas ;

Yaschenko, Eugene .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D173-D180

[36] The B2 element of the Saccharomyces cerevisiae ARS1 origin of replication requires specific sequences to facilitate pre-RC formation [J].

Wilmes, GM ;

Bell, SP .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (01) :101-106

[37] Genome-wide distribution of ORC and MCM proteins in S-cerevisiae:: High-resolution mapping of replication origins [J].

Wyrick, JJ ;

Aparicio, JG ;

Chen, T ;

Barnett, JD ;

Jennings, EG ;

Young, RA ;

Bell, SP ;

Aparicio, OM .

SCIENCE, 2001, 294 (5550) :2357-2360

[38] Mapping of early firing origins on a replication profile of budding yeast [J].

Yabuki, N ;

Terashima, H ;

Kitada, K .

GENES TO CELLS, 2002, 7 (08) :781-789

[39] The efficiency and timing of initiation of replication of multiple replicons of Saccharomyces cerevisiae chromosome VI [J].

Yamashita, M ;

Hori, Y ;

Shinomiya, T ;

Obuse, C ;

Tsurimoto, T ;

Yoshikawa, H ;

Shirahige, K .

GENES TO CELLS, 1997, 2 (11) :655-665

[40] LOCALIZATION OF A DNA-REPLICATION ORIGIN AND TERMINATION ZONE ON CHROMOSOME-III OF SACCHAROMYCES-CEREVISIAE [J].

ZHU, JG ;

NEWLON, CS ;

HUBERMAN, JA .

MOLECULAR AND CELLULAR BIOLOGY, 1992, 12 (10) :4733-4741

← 1 2 3 4 5 →