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Epigenetic memory independent of symmetric histone inheritance.

Saxton DS, Rine J.

Elife. 2019 Oct 15;8. pii: e51421. doi: 10.7554/eLife.51421.


The nucleosome core particle remembers its position through DNA replication and RNA transcription.

Schlissel G, Rine J.

Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20605-20611. doi: 10.1073/pnas.1911943116. Epub 2019 Sep 11.


Mutations in the PCNA DNA Polymerase Clamp of Saccharomyces cerevisiae Reveal Complexities of the Cell Cycle and Ploidy on Heterochromatin Assembly.

Brothers M, Rine J.

Genetics. 2019 Oct;213(2):449-463. doi: 10.1534/genetics.119.302452. Epub 2019 Aug 26.


Assessing Patient Participation Burden Based on Protocol Design Characteristics.

Getz K, Sethuraman V, Rine J, Peña Y, Ramanathan S, Stergiopoulos S.

Ther Innov Regul Sci. 2019 Aug 19:2168479019867284. doi: 10.1177/2168479019867284. [Epub ahead of print]


Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants.

Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Radivojac P, Rousseau F, Pal LR, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I.

Hum Mutat. 2019 Sep;40(9):1530-1545. doi: 10.1002/humu.23868. Epub 2019 Sep 3.


Accumulation of rare coding variants in genes implicated in risk of human cleft lip with or without cleft palate.

Marini NJ, Asrani K, Yang W, Rine J, Shaw GM.

Am J Med Genet A. 2019 Jul;179(7):1260-1269. doi: 10.1002/ajmg.a.61183. Epub 2019 May 7.


Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk.

Gonseth S, Shaw GM, Roy R, Segal MR, Asrani K, Rine J, Wiemels J, Marini NJ.

Epigenetics. 2019 Feb;14(2):198-213. doi: 10.1080/15592294.2019.1581591. Epub 2019 Mar 14.


An Expanded Treatment Protocol of Panobinostat Plus Bortezomib and Dexamethasone in Patients With Previously Treated Myeloma.

Hansen VL, Coleman M, Elkins S, Letzer JP, Levy MY, Seneviratne L, Rine J, White M, Kuriakose ET.

Clin Lymphoma Myeloma Leuk. 2018 Jun;18(6):400-407.e1. doi: 10.1016/j.clml.2018.03.002. Epub 2018 Mar 14.


Pivotal roles of PCNA loading and unloading in heterochromatin function.

Janke R, King GA, Kupiec M, Rine J.

Proc Natl Acad Sci U S A. 2018 Feb 27;115(9):E2030-E2039. doi: 10.1073/pnas.1721573115. Epub 2018 Feb 13.


Impact of Homologous Recombination on Silent Chromatin in Saccharomyces cerevisiae.

Sieverman KJ, Rine J.

Genetics. 2018 Mar;208(3):1099-1113. doi: 10.1534/genetics.118.300704. Epub 2018 Jan 16.


DNA Methylome Profiling on the Infinium HumanMethylation450 Array from Limiting Quantities of Genomic DNA from a Single, Small Archived Bloodspot.

Asrani K, Shaw GM, Rine J, Marini NJ.

Genet Test Mol Biomarkers. 2017 Aug;21(8):516-519. doi: 10.1089/gtmb.2017.0019. Epub 2017 Jun 13.


Oncometabolite D-2-Hydroxyglutarate enhances gene silencing through inhibition of specific H3K36 histone demethylases.

Janke R, Iavarone AT, Rine J.

Elife. 2017 Mar 27;6. pii: e22451. doi: 10.7554/eLife.22451.


Aggregation of the Whi3 protein, not loss of heterochromatin, causes sterility in old yeast cells.

Schlissel G, Krzyzanowski MK, Caudron F, Barral Y, Rine J.

Science. 2017 Mar 17;355(6330):1184-1187. doi: 10.1126/science.aaj2103. Epub 2017 Mar 16.


Nutritional Control of Chronological Aging and Heterochromatin in Saccharomyces cerevisiae.

McCleary DF, Rine J.

Genetics. 2017 Mar;205(3):1179-1193. doi: 10.1534/genetics.116.196485. Epub 2017 Jan 6.


Donor Preference Meets Heterochromatin: Moonlighting Activities of a Recombinational Enhancer in Saccharomyces cerevisiae.

Dodson AE, Rine J.

Genetics. 2016 Nov;204(3):1065-1074. doi: 10.1534/genetics.116.194696. Epub 2016 Sep 21.


Sequence variation in folate pathway genes and risks of human cleft lip with or without cleft palate.

Marini NJ, Yang W, Asrani K, Witte JS, Rine J, Lammer EJ, Shaw GM.

Am J Med Genet A. 2016 Nov;170(11):2777-2787. doi: 10.1002/ajmg.a.37874. Epub 2016 Sep 8.


Histone Deacetylases with Antagonistic Roles in Saccharomyces cerevisiae Heterochromatin Formation.

Thurtle-Schmidt DM, Dodson AE, Rine J.

Genetics. 2016 Sep;204(1):177-90. doi: 10.1534/genetics.116.190835. Epub 2016 Aug 3.


Sir protein-independent repair of dicentric chromosomes in Saccharomyces cerevisiae.

McCleary DF, Steakley DL, Rine J.

Mol Biol Cell. 2016 Sep 15;27(18):2879-83. doi: 10.1091/mbc.E16-02-0102. Epub 2016 Jul 27.


MEKC-UV as an effective tool for the separation and identification of explosives, high explosives, and their degradation products in environmental samples.

Copper C, Brensinger K, Rollman C, Clark A, Perez M, Genzman A, Rine J, Moini M.

Electrophoresis. 2016 Oct;37(19):2554-2557. doi: 10.1002/elps.201600198. Epub 2016 Jul 19.


GENOME ENGINEERING. The Genome Project-Write.

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.

Science. 2016 Jul 8;353(6295):126-7. doi: 10.1126/science.aaf6850. Epub 2016 Jun 2. No abstract available.


Riches of phenotype computationally extracted from microbial colonies.

Liu TY, Dodson AE, Terhorst J, Song YS, Rine J.

Proc Natl Acad Sci U S A. 2016 May 17;113(20):E2822-31. doi: 10.1073/pnas.1523295113. Epub 2016 May 2.


Evolution and Functional Trajectory of Sir1 in Gene Silencing.

Ellahi A, Rine J.

Mol Cell Biol. 2016 Jan 25;36(7):1164-79. doi: 10.1128/MCB.01013-15.


Novel CE-MS technique for detection of high explosives using perfluorooctanoic acid as a MEKC and mass spectrometric complexation reagent.

Brensinger K, Rollman C, Copper C, Genzman A, Rine J, Lurie I, Moini M.

Forensic Sci Int. 2016 Jan;258:74-9. doi: 10.1016/j.forsciint.2015.11.007. Epub 2015 Nov 23.


Metabolism and epigenetics.

Janke R, Dodson AE, Rine J.

Annu Rev Cell Dev Biol. 2015;31:473-496. doi: 10.1146/annurev-cellbio-100814-125544. Epub 2015 Sep 10. Review.


The State of Federal Research Funding in Genetics as Reflected by Members of the Genetics Society of America.

Rine J, Fagen AP.

Genetics. 2015 Aug;200(4):1015-9. doi: 10.1534/genetics.115.179523. Epub 2015 Jul 15.


On the Mechanism of Gene Silencing in Saccharomyces cerevisiae.

Steakley DL, Rine J.

G3 (Bethesda). 2015 Jun 16;5(8):1751-63. doi: 10.1534/g3.115.018515.


The Chromatin and Transcriptional Landscape of Native Saccharomyces cerevisiae Telomeres and Subtelomeric Domains.

Ellahi A, Thurtle DM, Rine J.

Genetics. 2015 Jun;200(2):505-21. doi: 10.1534/genetics.115.175711. Epub 2015 Mar 30.


Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae.

Dodson AE, Rine J.

Elife. 2015 Jan 12;4:e05007. doi: 10.7554/eLife.05007.


Maintenance of nucleosomal balance in cis by conserved AAA-ATPase Yta7.

Lombardi LM, Davis MD, Rine J.

Genetics. 2015 Jan;199(1):105-16. doi: 10.1534/genetics.114.168039. Epub 2014 Nov 17.


Multiple inputs control sulfur-containing amino acid synthesis in Saccharomyces cerevisiae.

Sadhu MJ, Moresco JJ, Zimmer AD, Yates JR 3rd, Rine J.

Mol Biol Cell. 2014 May;25(10):1653-65. doi: 10.1091/mbc.E13-12-0755. Epub 2014 Mar 19.


A future of the model organism model.

Rine J.

Mol Biol Cell. 2014 Mar;25(5):549-53. doi: 10.1091/mbc.E12-10-0768.


The molecular topography of silenced chromatin in Saccharomyces cerevisiae.

Thurtle DM, Rine J.

Genes Dev. 2014 Feb 1;28(3):245-58. doi: 10.1101/gad.230532.113.


Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins.

Teytelman L, Thurtle DM, Rine J, van Oudenaarden A.

Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18602-7. doi: 10.1073/pnas.1316064110. Epub 2013 Oct 30.


Nutritional control of epigenetic processes in yeast and human cells.

Sadhu MJ, Guan Q, Li F, Sales-Lee J, Iavarone AT, Hammond MC, Cande WZ, Rine J.

Genetics. 2013 Nov;195(3):831-44. doi: 10.1534/genetics.113.153981. Epub 2013 Aug 26.


Mono and dual cofactor dependence of human cystathionine β-synthase enzyme variants in vivo and in vitro.

Dimster-Denk D, Tripp KW, Marini NJ, Marqusee S, Rine J.

G3 (Bethesda). 2013 Oct 3;3(10):1619-28. doi: 10.1534/g3.113.006916.


Phase II trial of panobinostat, an oral pan-deacetylase inhibitor in patients with primary myelofibrosis, post-essential thrombocythaemia, and post-polycythaemia vera myelofibrosis.

DeAngelo DJ, Mesa RA, Fiskus W, Tefferi A, Paley C, Wadleigh M, Ritchie EK, Snyder DS, Begna K, Ganguly S, Ondovik MS, Rine J, Bhalla KN.

Br J Haematol. 2013 Aug;162(3):326-35. doi: 10.1111/bjh.12384. Epub 2013 May 23.


The enigmatic conservation of a Rap1 binding site in the Saccharomyces cerevisiae HMR-E silencer.

Teytelman L, Osborne Nishimura EA, Özaydin B, Eisen MB, Rine J.

G3 (Bethesda). 2012 Dec;2(12):1555-62. doi: 10.1534/g3.112.004077. Epub 2012 Dec 1.


Evolutionary analysis of heterochromatin protein compatibility by interspecies complementation in Saccharomyces.

Zill OA, Scannell DR, Kuei J, Sadhu M, Rine J.

Genetics. 2012 Nov;192(3):1001-14. doi: 10.1534/genetics.112.141549. Epub 2012 Aug 24.


Direct interplay among histones, histone chaperones, and a chromatin boundary protein in the control of histone gene expression.

Zunder RM, Rine J.

Mol Cell Biol. 2012 Nov;32(21):4337-49. doi: 10.1128/MCB.00871-12. Epub 2012 Aug 20.


The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus.

Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT.

G3 (Bethesda). 2011 Jun;1(1):11-25. doi: 10.1534/g3.111.000273. Epub 2011 Jun 1.


Surrogate genetics and metabolic profiling for characterization of human disease alleles.

Mayfield JA, Davies MW, Dimster-Denk D, Pleskac N, McCarthy S, Boydston EA, Fink L, Lin XX, Narain AS, Meighan M, Rine J.

Genetics. 2012 Apr;190(4):1309-23. doi: 10.1534/genetics.111.137471. Epub 2012 Jan 20. Erratum in: Genetics. 2012 Oct;192(2):759-60.


Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing.

Zunder RM, Antczak AJ, Berger JM, Rine J.

Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):E144-53. doi: 10.1073/pnas.1119095109. Epub 2011 Dec 23.


A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis.

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.

PLoS One. 2011;6(11):e28408. doi: 10.1371/journal.pone.0028408. Epub 2011 Nov 30.


Competencies: a cure for pre-med curriculum.

Anderson WA, Amasino RM, Ares M Jr, Banerjee U, Bartel B, Corces VG, Drennan CL, Elgin SC, Epstein IR, Fanning E, Guillette LJ Jr, Handelsman J, Hatfull GF, Hoy RR, Kelley D, Leinwand LA, Losick R, Lu Y, Lynn DG, Neuhauser C, O'Dowd DK, Olivera T, Pevzner P, Richards-Kortum RR, Rine J, Sah RL, Strobel SA, Walker GC, Walt DR, Warner IM, Wessler S, Willard HF, Zare RN.

Science. 2011 Nov 11;334(6057):760-1. doi: 10.1126/science.334.6057.760-b. No abstract available.


Direct regulation of nucleosome density by the conserved AAA-ATPase Yta7.

Lombardi LM, Ellahi A, Rine J.

Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):E1302-11. doi: 10.1073/pnas.1116819108. Epub 2011 Nov 9.


Symmetry, asymmetry, and kinetics of silencing establishment in Saccharomyces cerevisiae revealed by single-cell optical assays.

Osborne EA, Hiraoka Y, Rine J.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1209-16. doi: 10.1073/pnas.1018742108. Epub 2011 Jan 24.


Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly.

Zill OA, Scannell D, Teytelman L, Rine J.

PLoS Biol. 2010 Nov 30;8(11):e1000550. doi: 10.1371/journal.pbio.1000550.


Genetic control of immune cell types in fungal disease.

Mayfield JA, Fontana MF, Rine J.

Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22202-6. doi: 10.1073/pnas.1012925108. Epub 2010 Dec 6.


Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory.

Halley JE, Kaplan T, Wang AY, Kobor MS, Rine J.

PLoS Biol. 2010 Jun 22;8(6):e1000401. doi: 10.1371/journal.pbio.1000401.


The use of orthologous sequences to predict the impact of amino acid substitutions on protein function.

Marini NJ, Thomas PD, Rine J.

PLoS Genet. 2010 May 27;6(5):e1000968. doi: 10.1371/journal.pgen.1000968.

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