Rine Lab

University of California, Berkeley
Department of Molecular & Cell Biology


Farris D, Saxton DS, Rine J. A novel allele of SIR2 reveals a heritable intermediate state of gene silencing. Genetics. 2021 May 17;218(1):iyab041. PMID: 33713126



Saxton DS, Rine J. Nucleosome Positioning Regulates the Establishment, Stability, and Inheritance of Heterochromatin in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2020 Nov 3;117(44):27493-27501. PMID: 33077593



Goodnight D, Rine J. S-phase-independent silencing establishment in Saccharomyces cerevisiae. Elife. 2020 Jul 20;9:e58910. PMID: 32687055



Sun S, Weile J, Verby M, Wu Y, Wang Y, Cote AG, Fotiadou I, Kitaygorodsky J, Vidal M, Rine J, Jesina P, Kozich V, Roth FP. A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase. Genome Med. 2020 Jan 3012(1):13. PMID: 32000841



Saxton DS, Rine J. Epigenetic memory independent of symmetric histone inheritance. Elife. 2019 Oct 15;8. pii: e51421. PMID: 31613222



Schlissel G, Rine J. The nucleosome core particle remembers its position through DNA replication and RNA transcription. Proc Natl Acad Sci U S A. 2019 Sep 11. PMID: 31511420



Brothers M, Rine J. Mutations in the PCNA DNA Polymerase Clamp of Saccharomyces cerevisiae Reveal Complexities of the Cell Cycle and Ploidy on Heterochromatin Assembly. Genetics. 2019 Aug 26. PMID: 31451562



Kasak L, et al. Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Hum Mutat. 2019 Sep;40(9):1530-1545. PMID 31301157



Marini NJ, Asrani K, Yang W, Rine J, Shaw GM. Accumulation of rare coding variants in genes implicated in risk of human cleft lip with or without cleft palate. Am J Med Genet A. 2019 May 7. PMID: 31063268.



Gonseth S, Shaw GM, Roy R, Segal MR, Asrani K, Rine J, Wiemels J, Marini NJ. Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions indisease risk. Epigenetics. 2019 Feb;14(2):198-213. PMID: 30870065.



Janke R, King GA, Kupiec M, Rine J. Pivotal roles of PCNA loading and unloading in heterochromatin function. Proc Natl Acad Sci U S A. 2018 Feb 27;115(9):E2030-E2039. PMID: 29440488.



Sieverman KJ, Rine J. Impact of Homologous Recombination on Silent Chromatin in Saccharomyces cerevisiae. Genetics. 2018 Mar;208(3):1099-1113. PMID: 29339409.



Asrani K, Shaw GM, Rine J, Marini NJ. DNA Methylome Profiling on the Infinium HumanMethylation450 Array from Limiting Quantities of Genomic DNA from a Single, Small Archived Bloodspot. Genet Test Mol Biomarkers. 2017 Aug;21(8):516-519. PMID: 28609193.



Janke R, Iavarone AT, Rine J. Oncometabolite D-2-Hydroxyglutarate enhances gene silencing through inhibition of specific H3K36 histone demethylases. Elife. 2017 Mar 27;6. pii: e22451. PMID: 28346139.



Schlissel G, Krzyzanowski MK, Caudron F, Barral Y, Rine J. Aggregation of the Whi3 protein, not loss of heterochromatin, causes sterility in old yeast cells. Science. 2017 Mar 17;355(6330):1184-1187. PMID: 28302853.



McCleary DF, Rine J. Nutritional Control of Chronological Aging and Heterochromatin in Saccharomyces cerevisiae. Genetics. 2017 Mar;205(3):1179-1193. PMID: 28064165.



Dodson AE, Rine J. Donor Preference Meets Heterochromatin: Moonlighting Activities of a Recombinational Enhancer in Saccharomyces cerevisiae. Genetics. 2016 Nov;204(3):1065-1074. PMID: 27655944.



Marini NJ, Yang W, Asrani K, Witte JS, Rine J, Lammer EJ, Shaw GM. Sequence variation in folate pathway genes and risks of human cleft lip with or withoutcleft palate. Am J Med Genet A. 2016 Nov;170(11):2777-2787. PMID: 27604992.



Thurtle-Schmidt DM, Dodson AE, Rine J. Histone Deacetylases with Antagonistic Roles in Saccharomyces cerevisiae Heterochromatin Formation. Genetics. 2016 Sep;204(1):177-90. PMID: 27489001.



McCleary DF, Steakley DL, Rine J. Sir protein-independent repair of dicentric chromosomes in Saccharomyces cerevisiae. Mol Biol Cell. 2016 Sep 15;27(18):2879-83. PMID: 27466318.



Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. GENOME ENGINEERING. The Genome Project-Write.Science. 2016 Jul 8;353(6295):126-7. PMID: 27256881.



Liu TY, Dodson AE, Terhorst J, Song YS, Rine J. Riches of phenotype computationally extracted from microbial colonies. Proc Natl Acad Sci U S A. 2016 May 17;113(20):E2822-31. PMID: 27140647.



Ellahi A, Rine J. Evolution and Functional Trajectory of Sir1 in Gene Silencing. Mol Cell Biol. 2016 Jan 25;36(7):1164-79. PMID: 26811328.



Rine J, Fagen AP. The State of Federal Research Funding in Genetics as Reflected by Members of the Genetics Society of America. Genetics. 2015 Aug;200(4):1015-9. PMID: 26178966.



Steakley DL, Rine J. On the Mechanism of Gene Silencing in Saccharomyces cerevisiae. G3 (Bethesda). 2015 Jun 16;5(8):1751-63. PMID: 26082137.



Ellahi A, Thurtle DM, Rine J. The Chromatin and Transcriptional Landscape of Native Saccharomyces cerevisiae Telomeres and Subtelomeric Domains. Genetics. 2015 Jun;200(2):505-21. PMID: 25823445.



Dodson AE, Rine J. Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae. Elife. 2015 Jan 12;4:e05007. PMID: 25581000.



Lombardi LM, Davis MD, Rine J. Maintenance of nucleosomal balance in cis by conserved AAA-ATPase Yta7. Genetics. 2015 Jan;199(1):105-16. PMID: 25406467.



Sadhu MJ, Moresco JJ, Zimmer AD, Yates JR 3rd, Rine J. Multiple inputs control sulfur-containing amino acid synthesis in Saccharomyces cerevisiae. Mol Biol Cell. 2014 May;25(10):1653-65. PMID: 24648496.



Rine J. A future of the model organism model. Mol Biol Cell. 2014 Mar;25(5):549-53. PMID: 24577733.



Thurtle DM, Rine J. The molecular topography of silenced chromatin in Saccharomyces cerevisiae. Genes Dev. 2014 Feb 1;28(3):245-58. PMID: 24493645.



Teytelman L, Thurtle DM, Rine J, van Oudenaarden A. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18602-7. PMID: 24173036.



Sadhu MJ, Guan Q, Li F, Sales-Lee J, Iavarone AT, Hammond MC, Cande WZ, Rine J. Nutritional control of epigenetic processes in yeast and human cells. Genetics. 2013 Nov;195(3):831-44. PMID: 23979574.



Dimster-Denk D, Tripp KW, Marini NJ, Marqusee S, Rine J. Mono and dual cofactor dependence of human cystathionine β-synthase enzyme variants in vivo andin vitro. G3 (Bethesda). 2013 Oct 3;3(10):1619-28. PMID: 23934999.



Teytelman L, Osborne Nishimura EA, Özaydin B, Eisen MB, Rine J. The enigmatic conservation of a Rap1 binding site in the Saccharomyces cerevisiae HMR-E silencer. G3 (Bethesda). 2012 Dec;2(12):1555-62. PMID: 23275878.



Zill OA, Scannell DR, Kuei J, Sadhu M, Rine J. Evolutionary analysis of heterochromatin protein compatibility by interspecies complementation in Saccharomyces. Genetics. 2012 Nov;192(3):1001-14. PMID: 22923378.



Zunder RM, Rine J. Direct interplay among histones, histone chaperones, and a chromatin boundary protein in the control of histone gene expression. Mol Cell Biol. 2012 Nov;32(21):4337-49. PMID: 22907759.



Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda). 2011 Jun;1(1):11-25. PMID: 22384314.



Mayfield JA, Davies MW, Dimster-Denk D, Pleskac N, McCarthy S, Boydston EA, Fink L, Lin XX, Narain AS, Meighan M, Rine J. Surrogate genetics and metabolic profiling for characterization of human disease alleles.Genetics. 2012 Apr;190(4):1309-23. PMID: 22267502.



Zunder RM, Antczak AJ, Berger JM, Rine J. Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing. Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):E144-53. PMID: 22198837.



Marini NJ, Hoffmann TJ, Lammer EJ, Hardin J, Lazaruk K, Stein JB, Gilbert DA, Wright C, Lipzen A, Pennacchio LA, Carmichael SL, Witte JS, Shaw GM, Rine J. Agenetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis. PLoS One. 2011;6(11):e28408. PMID: 22140583.



Anderson WA, et al. Competencies: a cure for pre-med curriculum. Science. 2011 Nov 11;334(6057):760-1. PMID: 22076362.



Lombardi LM, Ellahi A, Rine J. Direct regulation of nucleosome density by the conserved AAA-ATPase Yta7.Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):E1302-11. PMID: 22074782.



Osborne EA, Hiraoka Y, Rine J. Symmetry, asymmetry, and kinetics of silencing establishment in Saccharomyces cerevisiae revealed by single-cell optical assays. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1209-16. PMID: 21262833.



Zill OA, Scannell D, Teytelman L, Rine J. Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol. 2010 Nov 30;8(11):e1000550. PMID: 21151344.



Mayfield JA, Fontana MF, Rine J. Genetic control of immune cell types in fungal disease. Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22202-6. PMID: 21135228.



Halley JE, Kaplan T, Wang AY, Kobor MS, Rine J. Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory. PLoS Biol. 2010 Jun 22;8(6):e1000401. PMID: 20582323.



Marini NJ, Thomas PD, Rine J. The use of orthologous sequences to predict the impact of amino acid substitutions on protein function. PLoS Genet. 2010 May 27;6(5):e1000968. PMID: 20523748.



Rusche LN, Rine J. Switching the mechanism of mating type switching: a domesticated transposase supplants a domesticated homing endonuclease. Genes Dev. 2010 Jan 1;24(1):10-4. PMID: 20047997.



Wang AY, Schulze JM, Skordalakes E, Gin JW, Berger JM, Rine J, Kobor MS. Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation. Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21573-8. PMID: 19966225.



Ozaydin B, Rine J. Expanded roles of the origin recognition complex in the architecture and function of silenced chromatin in Saccharomyces cerevisiae. Mol Cell Biol. 2010 Feb;30(3):626-39. PMID: 19948882.



Teytelman L, Ozaydin B, Zill O, Lefrançois P, Snyder M, Rine J, Eisen MB. Impact of chromatin structures on DNA processing for genomic analyses. PLoS One. 2009 Aug 20;4(8):e6700. PMID: 19693276.



Osborne EA, Dudoit S, Rine J. The establishment of gene silencing at single-cell resolution. Nat Genet. 2009 Jul;41(7):800-6. PMID: 19543267.


Gallagher JE, Babiarz JE, Teytelman L, Wolfe KH, Rine J. Elaboration, diversification and regulation of the Sir1 family of silencing proteins in Saccharomyces. Genetics. 2009 Apr;181(4):1477-91. PMID: 19171939.



Teytelman L, Eisen MB, Rine J. Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts. PLoS Genet. 2008 Nov;4(11):e1000247. PMID: 18989454.



Chao LY, Rine J, Marletta MA. Spectroscopic and kinetic studies of Nor1, a cytochrome P450 nitric oxide reductase from the fungal pathogen Histoplasma capsulatum. Arch Biochem Biophys. 2008 Dec 15;480(2):132-7. PMID: 18804446.



American Association for Cancer Research Human Epigenome Task Force; European Union, Network of Excellence, Scientific Advisory Board. Moving AHEAD with an international human epigenome project.Nature. 2008 Aug 7;454(7205):711-5. PMID: 18685699.



Zill OA, Rine J. Interspecies variation reveals a conserved repressor of alpha-specific genes in Saccharomyces yeasts. Genes Dev. 2008 Jun 15;22(12):1704-16. PMID: 18559484.



Chao LY, Marletta MA, Rine J. Sre1, an iron-modulated GATA DNA-binding protein of iron-uptake genes in the fungal pathogen Histoplasma capsulatum. Biochemistry. 2008 Jul 8;47(27):7274-83. PMID: 18549241.



Marini NJ, Gin J, Ziegle J, Keho KH, Ginzinger D, Gilbert DA, Rine J. The prevalence of folate-remedial MTHFR enzyme variants in humans. Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):8055-60. PMID: 18523009.



Hwang LH, Mayfield JA, Rine J, Sil A. Histoplasma requires SID1, a member of an iron-regulated siderophore gene cluster, for host colonization. PLoS Pathog. 2008 Apr 11;4(4):e1000044. PMID: 18404210.



Suter B, Pogoutse O, Guo X, Krogan N, Lewis P, Greenblatt JF, Rine J, Emili A. Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p. BMC Biol. 2007 Sep 19;5:38. PMID: 17880717.



Mayfield JA, Rine J. The genetic basis of variation in susceptibility to infection with Histoplasma capsulatumin the mouse. Genes Immun. 2007 Sep;8(6):468-74. PMID: 17625601.



Ashby MN, Rine J, Mongodin EF, Nelson KE, Dimster-Denk D. Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl Environ Microbiol. 2007 Jul;73(14):4532-42. PMID: 17526780.



Jeong H, Herskowitz I, Kroetz DL, Rine J. Function-altering SNPs in the human multidrug transporter gene ABCB1 identified using a Saccharomyces-based assay. PLoS Genet. 2007 Mar 9;3(3):e39. PMID: 17352537.



Davies BS, Rine J. A role for sterol levels in oxygen sensing in Saccharomyces cerevisiae. Genetics. 2006 Sep;174(1):191-201. PMID: 16783004.



Babiarz JE, Halley JE, Rine J. Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae. Genes Dev. 2006 Mar 15;20(6):700-10. PMID: 16543222.



Neff MW, Rine J. A fetching model organism. Cell. 2006 Jan 27;124(2):229-31. Review. PMID: 16439192.



Kirchmaier AL, Rine J. Cell cycle requirements in assembling silent chromatin in Saccharomyces cerevisiae.Mol Cell Biol. 2006 Feb;26(3):852-62. PMID: 16428441.



Olaharski AJ, Rine J, Marshall BL, Babiarz J, Zhang L, Verdin E, Smith MT. The flavoring agent dihydrocoumarin reverses epigenetic silencing and inhibitssirtuin deacetylases. PLoS Genet. 2005 Dec;1(6):e77. PMID: 16362078.



Rine J. Cell biology. Twists in the tale of the aging yeast. Science. 2005 Nov 18;310(5751):1124-5. PMID: 16293743.



Roberts TM, Kobor MS, Bastin-Shanower SA, Ii M, Horte SA, Gin JW, Emili A, Rine J, Brill SJ, Brown GW. Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4. Mol Biol Cell. 2006 Jan;17(1):539-48. PMID: 16267268.



Pillus L, Rine J. SIR1 and the origin of epigenetic states in Saccharomyces cerevisiae. Cold Spring Harb Symp Quant Biol. 2004;69:259-65. Review. PMID: 16117657.



Davies BS, Wang HS, Rine J. Dual activators of the sterol biosynthetic pathway of Saccharomyces cerevisiae: similar activation/regulatory domains but different response mechanisms. Mol Cell Biol. 2005 Aug;25(16):7375-85. PMID: 16055745.



Lynch PJ, Fraser HB, Sevastopoulos E, Rine J, Rusche LN. Sum1p, the origin recognition complex, and the spreading of a promoter-specific repressor in Saccharomyces cerevisiae. Mol Cell Biol. 2005 Jul;25(14):5920-32. PMID: 15988008.



Suter B, Tong A, Chang M, Yu L, Brown GW, Boone C, Rine J. The origin recognition complex links replication, sister chromatid cohesion and transcriptional silencing in Saccharomyces cerevisiae. Genetics. 2004 Jun;167(2):579-91. PMID: 15238513.



Beh CT, Rine J. A role for yeast oxysterol-binding protein homologs in endocytosis and in the maintenance of intracellular sterol-lipid distribution. J Cell Sci. 2004 Jun 15;117(Pt 14):2983-96. PMID: 15173322.



Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ, Madhani HD, Rine J. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004 May;2(5):E131. PMID: 15045029.



Tong AH, et al. Global mapping of the yeast genetic interaction network. Science. 2004 Feb 6;303(5659):808-13. PMID: 14764870.



Rine J. Obituary: Ira Herskowitz. Curr Biol. 2003 Aug 5;13(15):R581-2. PMID: 12906802.



Hwang L, Hocking-Murray D, Bahrami AK, Andersson M, Rine J, Sil A. Identifying phase-specific genes in the fungal pathogen Histoplasma capsulatum using a genomic shotgun microarray. Mol Biol Cell. 2003 Jun;14(6):2314-26. PMID: 12808032.



Rusche LN, Kirchmaier AL, Rine J. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem. 2003;72:481-516. PMID: 12676793.



Aström SU, Cline TW, Rine J. The Drosophila melanogaster sir2+ gene is nonessential and has only minor effects on position-effect variegation. Genetics. 2003 Mar;163(3):931-7. PMID: 12663533.



Rusché LN, Kirchmaier AL, Rine J. Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol Biol Cell. 2002 Jul;13(7):2207-22. PMID: 12134062.



Garber PM, Rine J. Overlapping roles of the spindle assembly and DNA damage checkpoints in the cell-cycle response to altered chromosomes in Saccharomyces cerevisiae. Genetics. 2002 Jun;161(2):521-34. PMID: 12072451.



Vik A, Rine J. Upc2p and Ecm22p, dual regulators of sterol biosynthesis in Saccharomyces cerevisiae. Mol Cell Biol. 2001 Oct;21(19):6395-405. PMID: 11533229.



Rusché LN, Rine J. Conversion of a gene-specific repressor to a regional silencer. Genes Dev. 2001 Apr 15;15(8):955-67. PMID: 11316790.



Beh CT, Cool L, Phillips J, Rine J. Overlapping functions of the yeast oxysterol-binding protein homologues.Genetics. 2001 Mar;157(3):1117-40. Erratum in: Genetics 2001 Jul;158(3):1387. PMID: 11238399.



Metallinos D, Rine J. Exclusion of EDNRB and KIT as the basis for white spotting in Border Collies. Genome Biol. 2000;1(2):RESEARCH0004. PMID: 11178229.



Kirchmaier AL, Rine J. DNA replication-independent silencing in S. cerevisiae. Science. 2001 Jan 26;291(5504):646-50. PMID: 11158676.



Chang YW, Howard SC, Budovskaya YV, Rine J, Herman PK. The rye mutants identify a role for Ssn/Srb proteins of the RNA polymerase II holoenzyme duringstationary phase entry in Saccharomyces cerevisiae.Genetics. 2001 Jan;157(1):17-26. PMID: 11139488.



Vik A, Rine J. Membrane biology: membrane-regulated transcription. Curr Biol. 2000 Nov 30;10(23):R869-71. PMID: 11114535.



Aström SU, Kegel A, Sjöstrand JO, Rine J. Kluyveromyces lactis Sir2p regulates cation sensitivity and maintains a specialized chromatin structure atthe cryptic alpha-locus. Genetics. 2000 Sep;156(1):81-91. PMID: 10978277.



Trueblood CE, Boyartchuk VL, Picologlou EA, Rozema D, Poulter CD, Rine J. TheCaaX proteases, Afc1p and Rce1p, have overlapping but distinct substrate specificities. Mol Cell Biol. 2000 Jun;20(12):4381-92. PMID: 10825201.



Ehrenhofer-Murray AE, Kamakaka RT, Rine J. A role for the replication proteins PCNA, RF-C, polymerase epsilon and Cdc45 in transcriptional silencing inSaccharomyces cerevisiae. Genetics. 1999 Nov;153(3):1171-82. PMID: 10545450.



Xu EY, Kim S, Replogle K, Rine J, Rivier DH. Identification of SAS4 and SAS5,two genes that regulate silencing in Saccharomyces cerevisiae. Genetics. 1999 Sep;153(1):13-23. PMID: 10471696.



Rine J. On the mechanism of silencing in Escherichia coli. Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8309-11. PMID: 10411864.



Acland GM, Ray K, Mellersh CS, Langston AA, Rine J, Ostrander EA, Aguirre GD. A novel retinal degeneration locus identified by linkage and comparative mapping of canine early retinal degeneration.Genomics. 1999 Jul 15;59(2):134-42. PMID: 10409424.



Dimster-Denk D, Rine J, Phillips J, Scherer S, Cundiff P, DeBord K, Gilliland D, Hickman S, Jarvis A, Tong L, Ashby M. Comprehensive evaluation of isoprenoid biosynthesis regulation in Saccharomyces cerevisiaeutilizing the Genome Reporter Matrix. J Lipid Res. 1999 May;40(5):850-60. PMID: 10224154.



Donze D, Adams CR, Rine J, Kamakaka RT. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 1999 Mar 15;13(6):698-708. PMID: 10090726.



Aström SU, Okamura SM, Rine J. Yeast cell-type regulation of DNA repair. Nature. 1999 Jan 28;397(6717):310. PMID: 9950423.



Neff MW, Broman KW, Mellersh CS, Ray K, Acland GM, Aguirre GD, Ziegle JS, Ostrander EA, Rine J. A second-generation genetic linkage map of the domestic dog, Canis familiaris. Genetics. 1999 Feb;151(2):803-20. PMID: 9927471.



Rivier DH, Ekena JL, Rine J. HMR-I is an origin of replication and a silencer in Saccharomyces cerevisiae.Genetics. 1999 Feb;151(2):521-9. PMID: 9927448.



Gardner KA, Rine J, Fox CA. A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with the Orc1 protein in Saccharomyces cerevisiae. Genetics. 1999 Jan;151(1):31-44. PMID: 9872946.



Gardner R, Cronin S, Leader B, Rine J, Hampton R. Sequence determinants for regulated degradation of yeast 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell. 1998 Sep;9(9):2611-26. Erratum in: Mol Biol Cell 1999 Mar;10(3):precedi. Leder B [corrected to Leader B]. PMID: 9725915.



Boyartchuk VL, Rine J. Roles of prenyl protein proteases in maturation of Saccharomyces cerevisiae a-Factor. Genetics. 1998 Sep;150(1):95-101. PMID: 9725832.



Kamakaka RT, Rine J. Sir- and silencer-independent disruption of silencing in Saccharomyces by Sas10p.Genetics. 1998 Jun;149(2):903-14. PMID: 9611201.



Metallinos DL, Bowling AT, Rine J. A missense mutation in the endothelin-B receptor gene is associated with Lethal White Foal Syndrome: an equine version ofHirschsprung disease. Mamm Genome. 1998 Jun;9(6):426-31. PMID: 9585428.



Carver EA, Issel-Tarver L, Rine J, Olsen AS, Stubbs L. Location of mouse and human genes corresponding to conserved canine olfactory receptor gene subfamilies. Mamm Genome. 1998 May;9(5):349-54. PMID: 9545490.



Acland GM, Ray K, Mellersh CS, Gu W, Langston AA, Rine J, Ostrander EA, Aguirre GD. Linkage analysis and comparative mapping of canine progressive rod-cone degeneration (prcd) establishes potential locus homology with retinitis pigmentosa (RP17) in humans. Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):3048-53. PMID: 9501213.



Aström SU, Rine J. Theme and variation among silencing proteins in Saccharomyces cerevisiae and Kluyveromyces lactis. Genetics. 1998 Mar;148(3):1021-9. PMID: 9539421.



Dillin A, Rine J. Roles for ORC in M phase and S phase. Science. 1998 Mar 13;279(5357):1733-7. PMID: 9497294.



Dillin A, Rine J. Separable functions of ORC5 in replication initiation and silencing in Saccharomyces cerevisiae. Genetics. 1997 Nov;147(3):1053-62. PMID: 9383052.



Herman PK, Rine J. Yeast spore germination: a requirement for Ras protein activity during re-entry into the cell cycle. EMBO J. 1997 Oct 15;16(20):6171-81. PMID: 9321396.



Trueblood CE, Boyartchuk VL, Rine J. Substrate specificity determinants in the farnesyltransferase beta-subunit. Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10774-9. PMID: 9380709.



Whistler JL, Rine J. Ras2 and Ras1 protein phosphorylation in Saccharomyces cerevisiae. J Biol Chem. 1997 Jul 25;272(30):18790-800. PMID: 9228053.



Fox CA, Ehrenhofer-Murray AE, Loo S, Rine J. The origin recognition complex, SIR1, and the S phase requirement for silencing. Science. 1997 Jun 6;276(5318):1547-51. PMID: 9171055.



Yalovsky S, Trueblood CE, Callan KL, Narita JO, Jenkins SM, Rine J, Gruissem W. Plant farnesyltransferase can restore yeast Ras signaling and mating. Mol Cell Biol. 1997 Apr;17(4):1986-94. PMID: 9121446.



Ehrenhofer-Murray AE, Rivier DH, Rine J. The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics. 1997 Apr;145(4):923-34. PMID: 9093847.



Boyartchuk VL, Ashby MN, Rine J. Modulation of Ras and a-factor function by carboxyl-terminal proteolysis.Science. 1997 Mar 21;275(5307):1796-800. PMID: 9065405.



Moazed D, Kistler A, Axelrod A, Rine J, Johnson AD. Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3. Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2186-91. PMID: 9122169.



Issel-Tarver L, Rine J. The evolution of mammalian olfactory receptor genes. Genetics. 1997 Jan;145(1):185-95. PMID: 9017400.



Hampton RY, Gardner RG, Rine J. Role of 26S proteasome and HRD genes in the degradation of 3-hydroxy-3-methylglutaryl-CoA reductase, an integral endoplasmic reticulum membrane protein. Mol Biol Cell. 1996 Dec;7(12):2029-44. PMID: 8970163.



Issel-Tarver L, Rine J. Organization and expression of canine olfactory receptor genes. Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10897-902. PMID: 8855279.



Dimster-Denk D, Rine J. Transcriptional regulation of a sterol-biosynthetic enzyme by sterol levels in Saccharomyces cerevisiae. Mol Cell Biol. 1996 Aug;16(8):3981-9. PMID: 8754796.



Fox CA, Rine J. Influences of the cell cycle on silencing. Curr Opin Cell Biol. 1996 Jun;8(3):354-7. Review. PMID: 8743886.



Hampton R, Dimster-Denk D, Rine J. The biology of HMG-CoA reductase: the pros of contra-regulation.Trends Biochem Sci. 1996 Apr;21(4):140-5. Review. PMID: 8701471.



Hampton RY, Koning A, Wright R, Rine J. In vivo examination of membrane protein localization and degradation with green fluorescent protein. Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):828-33. PMID: 8570643.



Ehrenhofer-Murray AE, Gossen M, Pak DT, Botchan MR, Rine J. Separation of origin recognition complex functions by cross-species complementation. Science. 1995 Dec 8;270(5242):1671-4. PMID: 7502078.



Parrish ML, Sengstag C, Rine JD, Wright RL. Identification of the sequences in HMG-CoA reductase required for karmellae assembly. Mol Biol Cell. 1995 Nov;6(11):1535-47. PMID: 8589454.



Loo S, Laurenson P, Foss M, Dillin A, Rine J. Roles of ABF1NPL3, and YCL54 in silencing in Saccharomyces cerevisiae. Genetics. 1995 Nov;141(3):889-902. PMID: 8582634.



Dillin A, Rine J. On the origin of a silencer. Trends Biochem Sci. 1995 Jun;20(6):231-5. Review. PMID: 7631420.



Loo S, Fox CA, Rine J, Kobayashi R, Stillman B, Bell S. The origin recognition complex in silencing, cell cycle progression, and DNA replication. Mol Biol Cell. 1995 Jun;6(6):741-56. PMID: 7579692.



Fox CA, Loo S, Dillin A, Rine J. The origin recognition complex has essential functions in transcriptional silencing and chromosomal replication. Genes Dev. 1995 Apr 15;9(8):911-24. PMID: 7774809.



Kamb A, Wang C, Thomas A, DeHoff BS, Norris FH, Richardson K, Rine J, Skolnick MH, Rosteck PR Jr. Software trapping: a strategy for finding genes in large genomic regions. Comput Biomed Res. 1995 Apr;28(2):140-53. PMID: 7656550.



Ostrander EA, Mapa FA, Yee M, Rine J. One hundred and one new simple sequence repeat-based markers for the canine genome. Mamm Genome. 1995 Mar;6(3):192-5. PMID: 7749226.



Loo S, Rine J. Silencing and heritable domains of gene expression. Annu Rev Cell Dev Biol. 1995;11:519-48. Review. PMID: 8689568.



Dimster-Denk D, Schafer WR, Rine J. Control of RAS mRNA level by the mevalonate pathway. Mol Biol Cell. 1995 Jan;6(1):59-70. PMID: 7749195.



Ashby MN, Rine J. Ras and a-factor converting enzyme. Methods Enzymol. 1995;250:235-51. PMID: 7651155.



Hiser L, Basson ME, Rine J. ERG10 from Saccharomyces cerevisiae encodes acetoacetyl-CoA thiolase. J Biol Chem. 1994 Dec 16;269(50):31383-9. PMID: 7989303.



Loo S, Rine J. Silencers and domains of generalized repression. Science. 1994 Jun 17;264(5166):1768-71. PMID: 8209257.



Lowry SR, Wilson K, Blazej R, Chiu J, Rine J, Ostrander EA. Identification, characterization, and physical mapping of 14 polymorphic simple sequence repeat markers on human chromosome 21. Genomics. 1994 Jun;21(3):633-7. PMID: 7959742.



Dimster-Denk D, Thorsness MK, Rine J. Feedback regulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase in Saccharomyces cerevisiae. Mol Biol Cell. 1994 Jun;5(6):655-65. PMID: 7949422.



Rine J. Saccharomyces and company. Science. 1994 May 13;264(5161):1006-8. PMID: 17830102.



Hampton RY, Rine J. Regulated degradation of HMG-CoA reductase, an integral membrane protein of the endoplasmic reticulum, in yeast. J Cell Biol. 1994 Apr;125(2):299-312. PMID: 8163547.



Lishanski A, Ostrander EA, Rine J. Mutation detection by mismatch binding protein, MutS, in amplified DNA: application to the cystic fibrosis gene. Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2674-8. PMID: 7511817.



Foss M, McNally FJ, Laurenson P, Rine J. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. Science. 1993 Dec 17;262(5141):1838-44. PMID: 8266071.



Foss M, Rine J. Molecular definition of the PAS1-1 mutation which affects silencing in Saccharomyces cerevisiae. Genetics. 1993 Nov;135(3):931-5. PMID: 8293990.



Ostrander EA, Rine J, Sack GH Jr, Cork LC. What is the role of molecular genetics in modern veterinary practice? J Am Vet Med Assoc. 1993 Nov 1;203(9):1259-62. PMID: 7902832.



Ashby MN, Errada PR, Boyartchuk VL, Rine J. Isolation and DNA sequence of the STE14 gene encoding farnesyl cysteine: carboxyl methyltransferase. Yeast. 1993 Aug;9(8):907-13. PMID: 8212897.



Trueblood CE, Ohya Y, Rine J. Genetic evidence for in vivo cross-specificity of the CaaX-box protein prenyltransferases farnesyltransferase and geranylgeranyltransferase-I in Saccharomyces cerevisiae. Mol Cell Biol. 1993 Jul;13(7):4260-75. PMID: 8321228.



Ostrander EA, Sprague GF Jr, Rine J. Identification and characterization of dinucleotide repeat (CA)n markers for genetic mapping in dog. Genomics. 1993 Apr;16(1):207-13. PMID: 8486359.



Fox CA, Loo S, Rivier DH, Foss MA, Rine J. A transcriptional silencer as a specialized origin of replication that establishes functional domains of chromatin. Cold Spring Harb Symp Quant Biol. 1993;58:443-55. PMID: 7956058.



Laurenson P, Rine J. Silencers, silencing, and heritable transcriptional states. Microbiol Rev. 1992 Dec;56(4):543-60. Review. PMID: 1480108.



Ashby MN, King DS, Rine J. Endoproteolytic processing of a farnesylated peptide in vitro. Proc Natl Acad Sci U S A. 1992 May 15;89(10):4613-7. PMID: 1584798.



Rivier DH, Rine J. An origin of DNA replication and a transcription silencer require a common element.Science. 1992 May 1;256(5057):659-63. PMID: 1585179.



Ostrander EA, Jong PM, Rine J, Duyk G. Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3419-23. PMID: 1314388.



Rivier DH, Rine J. Silencing: the establishment and inheritance of stable, repressed transcription states. Curr Opin Genet Dev. 1992 Apr;2(2):286-92. Review. PMID: 1638123.



Schafer WR, Rine J. Protein prenylation: genes, enzymes, targets, and functions. Annu Rev Genet. 1992;26:209-37. Review. PMID: 1482112.



McNally FJ, Rine J. A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae.Mol Cell Biol. 1991 Nov;11(11):5648-59. PMID: 1922068.



Laurenson P, Rine J. SUM1-1: a suppressor of silencing defects in Saccharomyces cerevisiae. Genetics. 1991 Nov;129(3):685-96. PMID: 1752414.



Axelrod A, Rine J. A role for CDC7 in repression of transcription at the silent mating-type locus HMR in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Feb;11(2):1080-91. PMID: 1990268.



Rine J. Gene overexpression in studies of Saccharomyces cerevisiae. Methods Enzymol. 1991;194:239-51. PMID: 2005790.



Kim R, Rine J, Kim SH. Prenylation of mammalian Ras protein in Xenopus oocytes. Mol Cell Biol. 1990 Nov;10(11):5945-9. PMID: 2233726.



Wright R, Keller G, Gould SJ, Subramani S, Rine J. Cell-type control of membrane biogenesis induced by HMG-CoA reductase. New Biol. 1990 Oct;2(10):915-21. PMID: 2078559.



Schafer WR, Trueblood CE, Yang CC, Mayer MP, Rosenberg S, Poulter CD, Kim SH, Rine J. Enzymatic coupling of cholesterol intermediates to a mating pheromone precursor and to the ras protein. Science. 1990 Sep 7;249(4973):1133-9. PMID: 2204115.



Finegold AA, Schafer WR, Rine J, Whiteway M, Tamanoi F. Common modifications of trimeric G proteins and ras protein: involvement of polyisoprenylation. Science. 1990 Jul 13;249(4965):165-9. PMID: 1695391.



Rine J, Kim SH. A role for isoprenoid lipids in the localization and function of an oncoprotein. New Biol. 1990 Mar;2(3):219-26. Review. PMID: 2149074.



Sengstag C, Stirling C, Schekman R, Rine J. Genetic and biochemical evaluation of eucaryotic membrane protein topology: multiple transmembrane domains of Saccharomyces cerevisiae 3-hydroxy-3-methylglutaryl coenzyme A reductase. Mol Cell Biol. 1990 Feb;10(2):672-80. PMID: 2405252.



Thorsness M, Schafer W, D'Ari L, Rine J. Positive and negative transcriptional control by heme of genes encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase in Saccharomyces cerevisiae. Mol Cell Biol. 1989 Dec;9(12):5702-12. PMID: 2685574.



Pillus L, Rine J. Epigenetic inheritance of transcriptional states in S. cerevisiae. Cell. 1989 Nov 17;59(4):637-47. PMID: 2684414.



Schafer WR, Kim R, Sterne R, Thorner J, Kim SH, Rine J. Genetic and pharmacological suppression of oncogenic mutations in ras genes of yeast and humans. Science. 1989 Jul 28;245(4916):379-85. PMID: 2569235.



Schnell R, D'Ari L, Foss M, Goodman D, Rine J. Genetic and molecular characterization of suppressors of SIR4 mutations in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):29-46. PMID: 2471670.



Rine J, Kenyon C. A Well-Studied Worm: The Nematode Caenorhabditis elegans. Science. 1989 Apr 14;244(4901):235. PMID: 17835358.



Wright R, Rine J. Transmission electron microscopy and immunocytochemical studies of yeast: analysis of HMG-CoA reductase overproduction by electron microscopy. Methods Cell Biol. 1989;31:473-512. PMID: 2674630.



Basson ME, Thorsness M, Finer-Moore J, Stroud RM, Rine J. Structural and functional conservation between yeast and human 3-hydroxy-3-methylglutaryl coenzyme A reductases, the rate-limiting enzyme of sterol biosynthesis. Mol Cell Biol. 1988 Sep;8(9):3797-808. PMID: 3065625.



Wright R, Basson M, D'Ari L, Rine J. Increased amounts of HMG-CoA reductase induce "karmellae": a proliferation of stacked membrane pairs surrounding the yeast nucleus. J Cell Biol. 1988 Jul;107(1):101-14. PMID: 3292536.



Kimmerly W, Buchman A, Kornberg R, Rine J. Roles of two DNA-binding factors in replication, segregation and transcriptional repression mediated by a yeastsilencer. EMBO J. 1988 Jul;7(7):2241-53. PMID: 3046937.



Rio DC, Barnes G, Laski FA, Rine J, Rubin GM. Evidence for Drosophila P element transposase activity in mammalian cells and yeast. J Mol Biol. 1988 Mar 20;200(2):411-5. PMID: 2836597.



Buchman AR, Kimmerly WJ, Rine J, Kornberg RD. Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Jan;8(1):210-25. PMID: 3275867.



Kimmerly WJ, Rine J. Replication and segregation of plasmids containing cis-acting regulatory sites of silent mating-type genes in Saccharomyces cerevisiae are controlled by the SIR genes. Mol Cell Biol. 1987 Dec;7(12):4225-37. PMID: 3325822.



Basson ME, Moore RL, O'Rear J, Rine J. Identifying mutations in duplicated functions in Saccharomyces cerevisiae: recessive mutations in HMG-CoA reductase genes. Genetics. 1987 Dec;117(4):645-55. PMID: 2828155.



Rine J, Herskowitz I. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics. 1987 May;116(1):9-22. PMID: 3297920.



Basson ME, Thorsness M, Rine J. Saccharomyces cerevisiae contains two functional genes encoding 3-hydroxy-3-methylglutaryl-coenzyme A reductase. Proc Natl Acad Sci U S A. 1986 Aug;83(15):5563-7. PMID: 3526336.



O'Rear J, Rine J. Precocious meiotic centromere separation of a novel yeast chromosome. Genetics. 1986 Jul;113(3):517-29. Erratum in: Genetics 1987 Mar;115(3):579. PMID: 3525321.



Schnell R, Rine J. A position effect on the expression of a tRNA gene mediated by the SIR genes in Saccharomyces cerevisiae. Mol Cell Biol. 1986 Feb;6(2):494-501. PMID: 3023851.



Barnes G, Rine J. Regulated expression of endonuclease EcoRI in Saccharomyces cerevisiae: nuclear entry and biological consequences. Proc Natl Acad Sci U S A. 1985 Mar;82(5):1354-8. PMID: 2983340.



Barnes G, Hansen WJ, Holcomb CL, Rine J. Asparagine-linked glycosylation in Saccharomyces cerevisiae: genetic analysis of an early step. Mol Cell Biol. 1984 Nov;4(11):2381-8. PMID: 6096695.



Rine J, Hansen W, Hardeman E, Davis RW. Targeted selection of recombinant clones through gene dosage effects. Proc Natl Acad Sci U S A. 1983 Nov;80(22):6750-4. PMID: 6316322.



Sprague GF Jr, Rine J, Herskowitz I. Control of yeast cell type by the mating type locus. II. Genetic interactions between MAT alpha and unlinked alpha-specific STE genes. J Mol Biol. 1981 Dec 5;153(2):323-35. PMID: 7040682.



Rine J, Sprague GF Jr, Herskowitz I. rme1 Mutation of Saccharomyces cerevisiae: map position and bypass of mating type locus control of sporulation. Mol Cell Biol. 1981 Oct;1(10):958-60. PMID: 7050660.



Sprague GF Jr, Rine J, Herskowitz I. Homology and non-homology at the yeast mating type locus. Nature. 1981 Jan 22;289(5795):250-2. PMID: 6256657.



Rine J, Jensen R, Hagen D, Blair L, Herskowitz I. Pattern of switching and fate of the replaced cassette in yeast mating-type interconversion. Cold Spring Harb Symp Quant Biol. 1981;45 Pt 2:951-60. PMID: 6266770.



Rine J, Herskowitz I. The trans action of HMRa in mating type interconversion. Mol Gen Genet. 1980;180(1):99-105. PMID: 7003314.



Rine J, Strathern JN, Hicks JB, Herskowitz I. A suppressor of mating-type locus mutations in Saccharomyces cerevisiae: evidence for and identification of cryptic mating-type loci. Genetics. 1979 Dec;93(4):877-901. PMID: 397913.



Jacklet JW, Rine J. Facilitation at neuromuscular junctions: contribution to habituation and dishabituation of the Aplysia gill withdrawal reflex. Proc Natl Acad Sci U S A. 1977 Mar;74(3):1267-71. PMID: 265569.