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Items: 40


The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast.

Lynch KL, Alvino GM, Kwan EX, Brewer BJ, Raghuraman MK.

PLoS Genet. 2019 Oct 4;15(10):e1008430. doi: 10.1371/journal.pgen.1008430. eCollection 2019 Oct.


Phenotypic and Genotypic Consequences of CRISPR/Cas9 Editing of the Replication Origins in the rDNA of Saccharomyces cerevisiae.

Sanchez JC, Ollodart A, Large CRL, Clough C, Alvino GM, Tsuchiya M, Crane M, Kwan EX, Kaeberlein M, Dunham MJ, Raghuraman MK, Brewer BJ.

Genetics. 2019 Sep;213(1):229-249. doi: 10.1534/genetics.119.302351. Epub 2019 Jul 10.


Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast.

Sanchez JC, Kwan EX, Pohl TJ, Amemiya HM, Raghuraman MK, Brewer BJ.

PLoS Genet. 2017 Oct 16;13(10):e1007041. doi: 10.1371/journal.pgen.1007041. eCollection 2017 Oct.


rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants.

Kwan EX, Wang XS, Amemiya HM, Brewer BJ, Raghuraman MK.

G3 (Bethesda). 2016 Sep 8;6(9):2829-38. doi: 10.1534/g3.116.030296.


Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification.

Brewer BJ, Payen C, Di Rienzi SC, Higgins MM, Ong G, Dunham MJ, Raghuraman MK.

PLoS Genet. 2015 Dec 23;11(12):e1005699. doi: 10.1371/journal.pgen.1005699. eCollection 2015 Dec.


Analysis of ssDNA gaps and DSBs in genetically unstable yeast cultures.

Peng J, Raghuraman MK, Feng W.

Methods Mol Biol. 2014;1170:501-15. doi: 10.1007/978-1-4939-0888-2_27.


Analysis of replication timing using synchronized budding yeast cultures.

Peng J, Raghuraman MK, Feng W.

Methods Mol Biol. 2014;1170:477-99. doi: 10.1007/978-1-4939-0888-2_26.


GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

Liachko I, Youngblood RA, Tsui K, Bubb KL, Queitsch C, Raghuraman MK, Nislow C, Brewer BJ, Dunham MJ.

PLoS Genet. 2014 Mar 6;10(3):e1004169. doi: 10.1371/journal.pgen.1004169. eCollection 2014 Mar.


Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex.

Hiraga S, Alvino GM, Chang F, Lian HY, Sridhar A, Kubota T, Brewer BJ, Weinreich M, Raghuraman MK, Donaldson AD.

Genes Dev. 2014 Feb 15;28(4):372-83. doi: 10.1101/gad.231258.113.


The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

Payen C, Di Rienzi SC, Ong GT, Pogachar JL, Sanchez JC, Sunshine AB, Raghuraman MK, Brewer BJ, Dunham MJ.

G3 (Bethesda). 2014 Mar 20;4(3):399-409. doi: 10.1534/g3.113.009365.


A DNA sequence element that advances replication origin activation time in Saccharomyces cerevisiae.

Pohl TJ, Kolor K, Fangman WL, Brewer BJ, Raghuraman MK.

G3 (Bethesda). 2013 Nov 6;3(11):1955-63. doi: 10.1534/g3.113.008250.


A natural polymorphism in rDNA replication origins links origin activation with calorie restriction and lifespan.

Kwan EX, Foss EJ, Tsuchiyama S, Alvino GM, Kruglyak L, Kaeberlein M, Raghuraman MK, Brewer BJ, Kennedy BK, Bedalov A.

PLoS Genet. 2013;9(3):e1003329. doi: 10.1371/journal.pgen.1003329. Epub 2013 Mar 7.


Maintaining replication origins in the face of genomic change.

Di Rienzi SC, Lindstrom KC, Mann T, Noble WS, Raghuraman MK, Brewer BJ.

Genome Res. 2012 Oct;22(10):1940-52. doi: 10.1101/gr.138248.112. Epub 2012 Jun 4.


Functional centromeres determine the activation time of pericentric origins of DNA replication in Saccharomyces cerevisiae.

Pohl TJ, Brewer BJ, Raghuraman MK.

PLoS Genet. 2012;8(5):e1002677. doi: 10.1371/journal.pgen.1002677. Epub 2012 May 10.


Replication stress-induced chromosome breakage is correlated with replication fork progression and is preceded by single-stranded DNA formation.

Feng W, Di Rienzi SC, Raghuraman MK, Brewer BJ.

G3 (Bethesda). 2011 Oct;1(5):327-35. doi: 10.1534/g3.111.000554. Epub 2011 Oct 1.


The effect of Ku on telomere replication time is mediated by telomere length but is independent of histone tail acetylation.

Lian HY, Robertson ED, Hiraga S, Alvino GM, Collingwood D, McCune HJ, Sridhar A, Brewer BJ, Raghuraman MK, Donaldson AD.

Mol Biol Cell. 2011 May 15;22(10):1753-65. doi: 10.1091/mbc.E10-06-0549. Epub 2011 Mar 25.


Origin-dependent inverted-repeat amplification: a replication-based model for generating palindromic amplicons.

Brewer BJ, Payen C, Raghuraman MK, Dunham MJ.

PLoS Genet. 2011 Mar;7(3):e1002016. doi: 10.1371/journal.pgen.1002016. Epub 2011 Mar 17. No abstract available.


Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii.

Di Rienzi SC, Lindstrom KC, Lancaster R, Rolczynski L, Raghuraman MK, Brewer BJ.

Yeast. 2011 Feb;28(2):137-51. doi: 10.1002/yea.1826. Epub 2010 Nov 2.


Molecular analysis of the replication program in unicellular model organisms.

Raghuraman MK, Brewer BJ.

Chromosome Res. 2010 Jan;18(1):19-34. doi: 10.1007/s10577-009-9099-x.


Centromere replication timing determines different forms of genomic instability in Saccharomyces cerevisiae checkpoint mutants during replication stress.

Feng W, Bachant J, Collingwood D, Raghuraman MK, Brewer BJ.

Genetics. 2009 Dec;183(4):1249-60. doi: 10.1534/genetics.109.107508. Epub 2009 Oct 5.


Fragile genomic sites are associated with origins of replication.

Di Rienzi SC, Collingwood D, Raghuraman MK, Brewer BJ.

Genome Biol Evol. 2009 Sep 9;1:350-63. doi: 10.1093/gbe/evp034.


The temporal program of chromosome replication: genomewide replication in clb5{Delta} Saccharomyces cerevisiae.

McCune HJ, Danielson LS, Alvino GM, Collingwood D, Delrow JJ, Fangman WL, Brewer BJ, Raghuraman MK.

Genetics. 2008 Dec;180(4):1833-47. doi: 10.1534/genetics.108.094359. Epub 2008 Oct 1.


Structural changes in Mcm5 protein bypass Cdc7-Dbf4 function and reduce replication origin efficiency in Saccharomyces cerevisiae.

Hoang ML, Leon RP, Pessoa-Brandao L, Hunt S, Raghuraman MK, Fangman WL, Brewer BJ, Sclafani RA.

Mol Cell Biol. 2007 Nov;27(21):7594-602. Epub 2007 Aug 27.


Replication in hydroxyurea: it's a matter of time.

Alvino GM, Collingwood D, Murphy JM, Delrow J, Brewer BJ, Raghuraman MK.

Mol Cell Biol. 2007 Sep;27(18):6396-406. Epub 2007 Jul 16.


Mapping yeast origins of replication via single-stranded DNA detection.

Feng W, Raghuraman MK, Brewer BJ.

Methods. 2007 Feb;41(2):151-7.


Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication.

Feng W, Collingwood D, Boeck ME, Fox LA, Alvino GM, Fangman WL, Raghuraman MK, Brewer BJ.

Nat Cell Biol. 2006 Feb;8(2):148-55. Epub 2006 Jan 22.


The dynamics of chromosome replication in yeast.

Lucas IA, Raghuraman MK.

Curr Top Dev Biol. 2003;55:1-73. Review. No abstract available.


Assaying replication fork direction and migration rates.

van Brabant AJ, Raghuraman MK.

Methods Enzymol. 2002;351:539-68. Review. No abstract available.


Replication dynamics of the yeast genome.

Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ, Fangman WL.

Science. 2001 Oct 5;294(5540):115-21.


The positioning and dynamics of origins of replication in the budding yeast nucleus.

Heun P, Laroche T, Raghuraman MK, Gasser SM.

J Cell Biol. 2001 Jan 22;152(2):385-400.


CLB5-dependent activation of late replication origins in S. cerevisiae.

Donaldson AD, Raghuraman MK, Friedman KL, Cross FR, Brewer BJ, Fangman WL.

Mol Cell. 1998 Aug;2(2):173-82.


Cell cycle-dependent establishment of a late replication program.

Raghuraman MK, Brewer BJ, Fangman WL.

Science. 1997 May 2;276(5313):806-9.


Analysis of the temporal program of replication initiation in yeast chromosomes.

Friedman KL, Raghuraman MK, Fangman WL, Brewer BJ.

J Cell Sci Suppl. 1995;19:51-8.


Eukaryotic replication origins: control in space and time.

Diller JD, Raghuraman MK.

Trends Biochem Sci. 1994 Aug;19(8):320-5. Review.


Activation of a yeast replication origin near a double-stranded DNA break.

Raghuraman MK, Brewer BJ, Fangman WL.

Genes Dev. 1994 Mar 1;8(5):554-62.


The topography of chromosome replication in yeast.

Brewer BJ, Diller JD, Friedman KL, Kolor KM, Raghuraman MK, Fangman WL.

Cold Spring Harb Symp Quant Biol. 1993;58:425-34. No abstract available.


Monovalent cation-induced structure of telomeric DNA: the G-quartet model.

Williamson JR, Raghuraman MK, Cech TR.

Cell. 1989 Dec 1;59(5):871-80.


Assembly and self-association of oxytricha telomeric nucleoprotein complexes.

Raghuraman MK, Cech TR.

Cell. 1989 Nov 17;59(4):719-28.


Oxytricha telomeric nucleoprotein complexes reconstituted with synthetic DNA.

Raghuraman MK, Dunn CJ, Hicke BJ, Cech TR.

Nucleic Acids Res. 1989 Jun 12;17(11):4235-53.

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