Bradley R. Cairns, PhD

Chair, Department of Oncological Sciences

Research Interests

  • Cancer Biology
  • Chromatin
  • Transcription Factors
  • DNA Methylation
  • Zebrafish

Labs

Lab Website

Languages

  • English

Academic Information

  • Departments: Oncological Sciences - Professor
  • Cancer Center Programs: Nuclear Control of Cell Growth & Differentiation

Academic Office Information

  • 801-585-1822
  • Huntsman Cancer Institute
    Department of Oncological Sciences
    2000 Circle of Hope, Room: Rm 3725
    Salt Lake City, UT 84112

Academic Bio

Biography: Dr. Cairns received his B.S. (Honors) in Chemistry from Lewis and Clark College in Portland, Oregon in 1987. He conducted his graduate work at Stanford with Nobel Laureate Roger Kornberg PhD on both signal transduction and chromatin remodeling. He received his PhD in Cell Biology from Stanford in 1996, and also conducted an early phase of postdoctoral training (funding from the American Cancer Society). Dr. Cairns received formal postdoctoral training with Fred Winston PhD in the Department of Genetics at Harvard Medical School (funding from the Leukemia Society of America), where he continued to study chromatin remodeling complexes. In 1998, he joined the faculty of the Department of Oncological Sciences and the Huntsman Cancer Institute. In 2000, he was appointed as an Investigator with the Howard Hughes Medical Institute. He is currently Professor and Chair of the Department of Oncological Sciences, and is the Jon and Karen Huntsman Presidential Professor of Cancer Research and Senior Director of Basic Science at the Huntsman Cancer Institute – both within the University of Utah, School of Medicine. He is Co-Leader of the Nuclear Control of Cell Growth and Differentiation Program. He was elected to the American Academy of Arts and Sciences in 2017.

Research: The Cairns lab strives to understand chromatin-transcription relationships – with an emphasis on development and cancer – and effectively utilizes biochemistry, genetics, and genomics in multiple model systems. The areas/questions the lab addresses include 1) Chromatin remodeling: How are nucleosomes moved and ejected by chromatin-remodeling complexes, and how is this progress misregulated in cancer? 2) Germline and embryo gene packaging: Are genes important for embryo development (and oncogenesis) packaged in special chromatin structures while in the germline and what is their fate and impact in the early embryo? 3) How is Totipotency – the ability to become any cell type – established in early cleavage-stage embryos, and are the involved factors misregulated in cancer? 4) How does the genome ‘sculpt’ chromatin structure to achieve proper gene regulation prior to the onset of transcription in embryos?

Teaching: Dr. Cairns teaches in the Gene Expression core course, and has taught many specialty chromatin course. He organizes a weekly transcription journal club and has mentored 23 PhD students.

Administration and Service: Senior Director of Basic Science, Huntsman Cancer Institute. Chairman, Department of Oncological Sciences. Co-Leader, Nuclear Control of Cell Growth and Differentiation Program, Huntsman Cancer Institute. Chair, High-Throughput Genomics Core. Chair, Bioinformatics Core. Chair, Research Informatics Core. Service: Dr. Cairns is on the editorial board of Molecular Cell and Developmental Cell, reviews grants as a standing member or ad hoc member of multiple NIH sections, and has co-organized multiple scientific meetings for Keystone, ASBMB, FASEB, and EMBL.

Research Statement

Cancer is a disease involoving improper cell growth, death and differentiation. My research focuses on determining - at the mechanistic level - how a cell normally regulates processes important to cancer such as chromatin structure, transcription, and developmental decisions.

Research: The Cairns lab strives to understand chromatin-transcription relationships – with an emphasis on development and cancer – and effectively utilizes biochemistry, genetics, and genomics in multiple model systems. The areas/questions the lab addresses include 1) Chromatin remodeling: How are nucleosomes moved and ejected by chromatin-remodeling complexes, and how is this progress misregulated in cancer? 2) Germline and embryo gene packaging: Are genes important for embryo development (and oncogenesis) packaged in special chromatin structures while in the germline and what is their fate and impact in the early embryo? 3) How is Totipotency – the ability to become any cell type – established in early cleavage-stage embryos, and are the factors involved misregulated in cancer? 4) How does the genome ‘sculpt’ chromatin structure to achieve proper gene regulation prior to the onset of transcription in embryos.

Education History

Type School Degree
Postdoctoral Fellowship Harvard Medical School - Fred Winston, PhD
Genetics
Postdoctoral Fellow
Postdoctoral Fellowship Stanford University - Roger Kornberg, PhD
Structural Biology
Postdoctoral Fellow
Doctoral Training Stanford University - Roger Kornberg, PhD
Cell Biology
Ph.D.
Undergraduate Lewis and Clark College
Chemistry (honors)
B.S.

Selected Publications

Journal Article

  1. Khoddami V, Yerra A, Mosbruger TL, Fleming AM, Burrows CJ, Cairns BR (2019 Apr 2). Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution. Proc Natl Acad Sci U S A, 116(14), 6784-6789.
  2. Guo J, Cairns BR (2019 Jan 4). Isolation and Enrichment of Spermatogonial Stem Cells From Human Testis Tissues. Curr Protoc Stem Cell Biol, e77.
  3. Guo J, Grow EJ, Mlcochova H, Maher GJ, Lindskog C, Nie X, Guo Y, Takei Y, Yun J, Cai L, Kim R, Carrell DT, Goriely A, Hotaling JM, Cairns BR (2018 Oct 12). The adult human testis transcriptional cell atlas.LID - 10.1038/s41422-018-0099-2 [doi]. (Epub ahead of print) Cell Res.
  4. Gupta S, Albertson DJ, Parnell TJ, Butterfield A, Weston A, Pappas LM, Dalley B, OShea JM, Lowrance WT, Cairns BR, Schiffman JD, Sharma S (2018 Oct 9). Histone deacetylase inhibition has targeted clinical benefit in ARID1A mutated advanced urothelial carcinoma.LID - molcanther.0957.2017 [pii]LID - 10.1158/1535-7163.MCT-17-0957 [doi]. (Epub ahead of print) Mol Cancer Ther.
  5. Murphy PJ, Wu SF, James CR, Wike CL, Cairns BR (2018 Feb 22). Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming. Cell, 172(5), 993-1006.e13.
  6. Jenkins TG, James ER, Alonso DF, Hoidal JR, Murphy PJ, Hotaling JM, Cairns BR, Carrell DT, Aston KI (2017 Nov). Cigarette smoking significantly alters sperm DNA methylation patterns. Andrology, 5(6), 1089-1099.
  7. Guo J, Grow EJ, Yi C, Mlcochova H, Maher GJ, Lindskog C, Murphy PJ, Wike CL, Carrell DT, Goriely A, Hotaling JM, Cairns BR (2017 Oct 5). Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development. Cell Stem Cell, 21(4), 533-546.e6.
  8. Hendrickson PG, Dorais JA, Grow EJ, Whiddon JL, Lim JW, Wike CL, Weaver BD, Pflueger C, Emery BR, Wilcox AL, Nix DA, Peterson CM, Tapscott SJ, Carrell DT, Cairns BR (2017 Jun). Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nat Genet, 49(6), 925-934.
  9. Jones KB, Barrott JJ, Xie M, Haldar M, Jin H, Zhu JF, Monument MJ, Mosbruger TL, Langer EM, Randall RL, Wilson RK, Cairns BR, Ding L, Capecchi MR (2016 Sep 22). The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis. Oncogene, 35(38), 5021-32.
  10. Ramakrishnan S, Pokhrel S, Palani S, Pflueger C, Parnell TJ, Cairns BR, Bhaskara S, Chandrasekharan MB (2016 Jun 21). Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription. Nat Commun, 7, 11949.
  11. Clapier CR, Kasten MM, Parnell TJ, Viswanathan R, Szerlong H, Sirinakis G, Zhang Y, Cairns BR (2016 May 5). Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection. Mol Cell, 62(3), 453-461.
  12. Hendrickson PG, Cairns BR (2016 Apr). Tet proteins enhance the developmental hourglass. Nat Genet, 48(4), 345-7.
  13. Murphy PJ, Cairns BR (2016). Genome-wide DNA methylation profiling in zebrafish. Methods Cell Biol, 135, 345-59.
  14. Aston KI, Uren PJ, Jenkins TG, Horsager A, Cairns BR, Smith AD, Carrell DT (2015 Dec). Aberrant sperm DNA methylation predicts male fertility status and embryo quality. Fertil Steril, 104(6), 1388-97.e1-5.
  15. Huang F, Ramakrishnan S, Pokhrel S, Pflueger C, Parnell TJ, Kasten MM, Currie SL, Bhachech N, Horikoshi M, Graves BJ, Cairns BR, Bhaskara S, Chandrasekharan MB (2015 Nov 27). Interaction of the Jhd2 Histone H3 Lys-4 Demethylase with Chromatin Is Controlled by Histone H2A Surfaces and Restricted by H2B Ubiquitination. J Biol Chem, 290(48), 28760-77.
  16. Hammoud SS, Low DH, Yi C, Lee CL, Oatley JM, Payne CJ, Carrell DT, Guccione E, Cairns BR (2015 Nov 1). Transcription and imprinting dynamics in developing postnatal male germline stem cells. Genes Dev, 29(21), 2312-24.
  17. Varshney D, Vavrova-Anderson J, Oler AJ, Cairns BR, White RJ (2015 Nov-Dec). Selective repression of SINE transcription by RNA polymerase III. Mob Genet Elements, 5(6), 86-91.
  18. Parnell TJ, Schlichter A, Wilson BG, Cairns BR (2015 Mar 30). The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism. eLife, 4, e06073.
  19. Parnell T J, Schlicter A, Wilson B G, Cairns B R (). The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism. eLife, 4, e06073.
  20. Varshney D, Vavrova-Anderson J, Oler AJ, Cowling VH, Cairns BR, White RJ (2015 Mar 23). SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nat Commun, 6, 6569.
  21. Johnson DP, Spitz GS, Tharkar S, Quayle SN, Shearstone JR, Jones S, McDowell ME, Wellman H, Tyler JK, Cairns BR, Chandrasekharan MB, Bhaskara S (2015 Mar 10). HDAC1,2 inhibition impairs EZH2- and BBAP-mediated DNA repair to overcome chemoresistance in EZH2 gain-of-function mutant diffuse large B-cell lymphoma. Oncotarget, 6(7), 4863-87.
  22. Khoddami V, Yerra A, Cairns BR (2015). Experimental Approaches for Target Profiling of RNA Cytosine Methyltransferases. Methods Enzymol, 560, 273-96.
  23. Hammoud SS, Low DH, Yi C, Carrell DT, Guccione E, Cairns BR (2014 Aug 7). Chromatin and transcription transitions of mammalian adult germline stem cells and spermatogenesis. Cell Stem Cell, 15(2), 239-53.
  24. Jenkins TG, Aston KI, Pflueger C, Cairns BR, Carrell DT (2014 Jul). Age-associated sperm DNA methylation alterations: possible implications in offspring disease susceptibility. PLoS Genet, 10(7), e1004458.
  25. Khoddami V, Cairns BR (2014 Feb). Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP. Nat Protoc, 9(2), 337-61.
  26. Alla RK, Cairns BR (2014). RNA polymerase III transcriptomes in human embryonic stem cells and induced pluripotent stem cells, and relationships with pluripotency transcription factors. PLoS ONE, 9(1), e85648.
  27. Nelson AC, Cauceglia JW, Merkley SD, Youngson NA, Oler AJ, Nelson RJ, Cairns BR, Whitelaw E, Potts WK (2013 Dec 3). Reintroducing domesticated wild mice to sociality induces adaptive transgenerational effects on MUP expression. Proc Natl Acad Sci U S A, 110(49), 19848-53.
  28. Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE (2013 Nov 21). Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data. BMC Bioinformatics, 14, 337.
  29. Jenkins TG, Aston KI, Cairns BR, Carrell DT (2013 Oct). Paternal aging and associated intraindividual alterations of global sperm 5-methylcytosine and 5-hydroxymethylcytosine levels. Fertil Steril, 100(4), 945-51.
  30. Bhaskara S, Jacques V, Rusche JR, Olson EN, Cairns BR, Chandrasekharan MB (2013 Aug 15). Histone deacetylases 1 and 2 maintain S-phase chromatin and DNA replication fork progression. Epigenetics Chromatin, 6(1), 27.
  31. Potok ME, Nix DA, Parnell TJ, Cairns BR (2013 May 9). Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell, 153(4), 759-72.
  32. Khoddami V, Cairns BR (2013 May). Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nat Biotechnol, 31(5), 458-64.
  33. Schubert HL, Wittmeyer J, Kasten MM, Hinata K, Rawling DC, Heroux A, Cairns BR, Hill CP (2013 Feb 26). Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler. Proc Natl Acad Sci U S A, 110(9), 3345-50.
  34. Ehrensberger KM, Mason C, Corkins ME, Anderson C, Dutrow N, Cairns BR, Dalley B, Milash B, Bird AJ (2013 Jan 11). Zinc-dependent regulation of the Adh1 antisense transcript in fission yeast. J Biol Chem, 288(2), 759-69.
  35. Hammoud SS, Cairns BR, Carrell DT (2013). Analysis of gene-specific and genome-wide sperm DNA methylation. Methods Mol Biol, 927, 451-8.
  36. Clapier CR, Cairns BR (2012 Dec 13). Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature, 492(7428), 280-4.
  37. Oler AJ, Traina-Dorge S, Derbes RS, Canella D, Cairns BR, Roy-Engel AM (2012 Jun 20). Alu expression in human cell lines and their retrotranspositional potential. Mob DNA, 3(1), 11.
  38. Luo W, Milash B, Dalley B, Smith R, Zhou H, Dutrow N, Cairns BR, Lessnick SL (2012 Jun). Antibody detection of translocations in Ewing sarcoma. EMBO Mol Med, 4(6), 453-61.
  39. Swierczek SI, Piterkova L, Jelinek J, Agarwal N, Hammoud S, Wilson A, Hickman K, Parker CJ, Cairns BR, Prchal JT (2012 Mar 29). Methylation of AR locus does not always reflect X chromosome inactivation state. Blood, 119(13), e100-9.
  40. Oler AJ, Cairns BR (2012 Mar 21). PP4 dephosphorylates Maf1 to couple multiple stress conditions to RNA polymerase III repression. EMBO J, 31(6), 1440-52.
  41. Malik SS, Rich E, Viswanathan R, Cairns BR, Fischer CJ (2011 Sep 20). Allosteric interactions of DNA and nucleotides with S. cerevisiae RSC. Biochemistry, 50(37), 7881-90.
  42. Hammoud SS, Nix DA, Hammoud AO, Gibson M, Cairns BR, Carrell DT (2011 Sep). Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men. Hum Reprod, 26(9), 2558-69.
  43. Sirinakis G, Clapier CR, Gao Y, Viswanathan R, Cairns BR, Zhang Y (2011 May 6). The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. EMBO J, 30(12), 2364-72.
  44. Wu SF, Zhang H, Cairns BR (2011 Apr). Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome Res, 21(4), 578-89.
  45. Wu SF, Zhang H, Hammoud SS, Potok M, Nix DA, Jones DA, Cairns BR (2011). DNA methylation profiling in zebrafish. Methods Cell Biol, 104, 327-39.
  46. Hammoud SS, Purwar J, Pflueger C, Cairns BR, Carrell DT (2010 Oct). Alterations in sperm DNA methylation patterns at imprinted loci in two classes of infertility. Fertil Steril, 94(5), 1728-33.
  47. Rai K, Sarkar S, Broadbent TJ, Voas M, Grossmann KF, Nadauld LD, Dehghanizadeh S, Hagos FT, Li Y, Toth RK, Chidester S, Bahr TM, Johnson WE, Sklow B, Burt R, Cairns BR, Jones DA (2010 Sep 17). DNA demethylase activity maintains intestinal cells in an undifferentiated state following loss of APC. Cell, 142(6), 930-42.
  48. Coudreuse D, van Bakel H, Dewez M, Soutourina J, Parnell T, Vandenhaute J, Cairns B, Werner M, Hermand D (2010 Jun 22). A gene-specific requirement of RNA polymerase II CTD phosphorylation for sexual differentiation in S. pombe. Curr Biol, 20(12), 1053-64.
  49. Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, Cairns BR (2010 May). Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol, 17(5), 620-8.
  50. Rai K, Jafri IF, Chidester S, James SR, Karpf AR, Cairns BR, Jones DA (2010 Feb 5). Dnmt3 and G9a cooperate for tissue-specific development in zebrafish. J Biol Chem, 285(6), 4110-21.
  51. Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE (2010 Jan 1). The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics, 26(1), 38-45.
  52. Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns BR (2009 Jul 23). Distinctive chromatin in human sperm packages genes for embryo development. Nature, 460(7254), 473-8.
  53. Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR (2008 Dec 26). DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell, 135(7), 1201-12.
  54. Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, Cairns BR (2008 Aug). Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet, 40(8), 977-86.
  55. Szerlong H, Hinata K, Viswanathan R, Erdjument-Bromage H, Tempst P, Cairns BR (2008 May). The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat Struct Mol Biol, 15(5), 469-76.
  56. Parnell TJ, Huff JT, Cairns BR (2008 Jan 9). RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes. EMBO J, 27(1), 100-10.
  57. Fischer CJ, Saha A, Cairns BR (2007 Oct 30). Kinetic model for the ATP-dependent translocation of Saccharomyces cerevisiae RSC along double-stranded DNA. Biochemistry, 46(43), 12416-26.
  58. VanDemark AP, Kasten MM, Ferris E, Heroux A, Hill CP, Cairns BR (2007 Sep 7). Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Mol Cell, 27(5), 817-28.
  59. Gordon M, Holt DG, Panigrahi A, Wilhelm BT, Erdjument-Bromage H, Tempst P, Bahler J, Cairns BR (2007 Jun). Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries. Mol Cell Biol, 27(11), 4058-69.
  60. Leschziner AE, Saha A, Wittmeyer J, Zhang Y, Bustamante C, Cairns BR, Nogales E (2007 Mar 20). Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc Natl Acad Sci U S A, 104(12), 4913-8.
  61. Rai K, Chidester S, Zavala CV, Manos EJ, James SR, Karpf AR, Jones DA, Cairns BR (2007 Feb 1). Dnmt2 functions in the cytoplasm to promote liver, brain, and retina development in zebrafish. Genes Dev, 21(3), 261-6.
  62. Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C (2006 Nov 17). DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell, 24(4), 559-68.
  63. Rai K, Nadauld LD, Chidester S, Manos EJ, James SR, Karpf AR, Cairns BR, Jones DA (2006 Oct). Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development. Mol Cell Biol, 26(19), 7077-85.
  64. Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T, Carney D, Pena P, Lan F, Kaadige MR, Lacoste N, Cayrou C, Davrazou F, Saha A, Cairns BR, Ayer DE, Kutateladze TG, Shi Y, Cote J, Chua KF, Gozani O (2006 Jul 6). ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature, 442(7098), 96-9.
  65. Soutourina J, Bordas-Le Floch V, Gendrel G, Flores A, Ducrot C, Dumay-Odelot H, Soularue P, Navarro F, Cairns BR, Lefebvre O, Werner M (2006 Jul). Rsc4 connects the chromatin remodeler RSC to RNA polymerases. Mol Cell Biol, 26(13), 4920-33.
  66. Roberts DN, Wilson B, Huff JT, Stewart AJ, Cairns BR (2006 Jun 9). Dephosphorylation and genome-wide association of Maf1 with Pol III-transcribed genes during repression. Mol Cell, 22(5), 633-44.
  67. Da G, Lenkart J, Zhao K, Shiekhattar R, Cairns BR, Marmorstein R (2006 Feb 14). Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc Natl Acad Sci U S A, 103(7), 2057-62.
  68. Wilson B, Erdjument-Bromage H, Tempst P, Cairns BR (2006 Feb). The RSC chromatin remodeling complex bears an essential fungal-specific protein module with broad functional roles. Genetics, 172(2), 795-809.
  69. Zhang H, Roberts DN, Cairns BR (2005 Oct 21). Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell, 123(2), 219-31.
  70. Saha A, Wittmeyer J, Cairns BR (2005 Sep). Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat Struct Mol Biol, 12(9), 747-55.
  71. Chai B, Huang J, Cairns BR, Laurent BC (2005 Jul 15). Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair. Genes Dev, 19(14), 1656-61.
  72. Schlichter A, Cairns BR (2005 Mar 23). Histone trimethylation by Set1 is coordinated by the RRM, autoinhibitory, and catalytic domains. EMBO J, 24(6), 1222-31.
  73. Zhang H, Richardson DO, Roberts DN, Utley R, Erdjument-Bromage H, Tempst P, Cote J, Cairns BR (2004 Nov). The Yaf9 component of the SWR1 and NuA4 complexes is required for proper gene expression, histone H4 acetylation, and Htz1 replacement near telomeres. Mol Cell Biol, 24(21), 9424-36.
  74. Kasten M, Szerlong H, Erdjument-Bromage H, Tempst P, Werner M, Cairns BR (2004 Mar 24). Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14. EMBO J, 23(6), 1348-59.
  75. Wittmeyer J, Saha A, Cairns B (2004). DNA translocation and nucleosome remodeling assays by the RSC chromatin remodeling complex. Methods Enzymol, 377, 322-43.
  76. Roberts DN, Stewart AJ, Huff JT, Cairns BR (2003 Dec 9). The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc Natl Acad Sci U S A, 100(25), 14695-700.
  77. Kristjuhan A, Wittschieben BO, Walker J, Roberts D, Cairns BR, Svejstrup JQ (2003 Jun 24). Spreading of Sir3 protein in cells with severe histone H3 hypoacetylation. Proc Natl Acad Sci U S A, 100(13), 7551-6.
  78. Szerlong H, Saha A, Cairns BR (2003 Jun 16). The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J, 22(12), 3175-87.
  79. Romeo MJ, Angus-Hill ML, Sobering AK, Kamada Y, Cairns BR, Levin DE (2002 Dec). HTL1 encodes a novel factor that interacts with the RSC chromatin remodeling complex in Saccharomyces cerevisiae. Mol Cell Biol, 22(23), 8165-74.
  80. Kristjuhan A, Walker J, Suka N, Grunstein M, Roberts D, Cairns BR, Svejstrup JQ (2002 Oct). Transcriptional inhibition of genes with severe histone h3 hypoacetylation in the coding region. Mol Cell, 10(4), 925-33.
  81. Saha A, Wittmeyer J, Cairns BR (2002 Aug 15). Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev, 16(16), 2120-34.
  82. Damelin M, Simon I, Moy TI, Wilson B, Komili S, Tempst P, Roth FP, Young RA, Cairns BR, Silver PA (2002 Mar). The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol Cell, 9(3), 563-73.
  83. Sengupta SM, VanKanegan M, Persinger J, Logie C, Cairns BR, Peterson CL, Bartholomew B (2001 Apr 20). The interactions of yeast SWI/SNF and RSC with the nucleosome before and after chromatin remodeling. J Biol Chem, 276(16), 12636-44.
  84. Angus-Hill ML, Schlichter A, Roberts D, Erdjument-Bromage H, Tempst P, Cairns BR (2001 Apr). A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control. Mol Cell, 7(4), 741-51.
  85. Sengupta SM, VanKanegan M, Persinger J, Logie C, Cairns BR, Peterson CL, Bartholomew B (2001). The interactions of yeast SWI/SNF and RSC with the nucleosome before and after chromatin remodeling. (Epub ahead of print) J Biol Chem.
  86. Cairns BR, Schlichter A, Erdjument-Bromage H, Tempst P, Kornberg RD, Winston F (1999 Nov). Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol Cell, 4(5), 715-23.
  87. Neely KE, Hassan AH, Wallberg AE, Steger DJ, Cairns BR, Wright AP, Workman JL (1999 Oct). Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol Cell, 4(4), 649-55.
  88. Whitehouse I, Flaus A, Cairns BR, White MF, Workman JL, Owen-Hughes T (1999 Aug 19). Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature, 400(6746), 784-7.
  89. Cairns BR, Erdjument-Bromage H, Tempst P, Winston F, Kornberg RD (1998 Nov). Two actin-related proteins are shared functional components of the chromatin-remodeling complexes RSC and SWI/SNF. Mol Cell, 2(5), 639-51.
  90. Lorch Y, Cairns BR, Zhang M, Kornberg RD (1998 Jul 10). Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell, 94(1), 29-34.
  91. Cao Y, Cairns BR, Kornberg RD, Laurent BC (1997 Jun). Sfh1p, a component of a novel chromatin-remodeling complex, is required for cell cycle progression. Mol Cell Biol, 17(6), 3323-34.
  92. Cairns BR, Lorch Y, Li Y, Zhang M, Lacomis L, Erdjument-Bromage H, Tempst P, Du J, Laurent B, Kornberg RD (1996 Dec 27). RSC, an essential, abundant chromatin-remodeling complex. Cell, 87(7), 1249-60.
  93. Miller ME, Cairns BR, Levinson RS, Yamamoto KR, Engel DA, Smith MM (1996 Oct). Adenovirus E1A specifically blocks SWI/SNF-dependent transcriptional activation. Mol Cell Biol, 16(10), 5737-43.
  94. Wang W, Xue Y, Zhou S, Kuo A, Cairns BR, Crabtree GR (1996 Sep 1). Diversity and specialization of mammalian SWI/SNF complexes. Genes Dev, 10(17), 2117-30.
  95. Cairns BR, Levinson RS, Yamamoto KR, Kornberg RD (1996 Sep 1). Essential role of Swp73p in the function of yeast Swi/Snf complex. Genes Dev, 10(17), 2131-44.
  96. Cairns BR, Henry NL, Kornberg RD (1996 Jul). TFG/TAF30/ANC1, a component of the yeast SWI/SNF complex that is similar to the leukemogenic proteins ENL and AF-9. Mol Cell Biol, 16(7), 3308-16.
  97. Bardwell L, Cook JG, Chang EC, Cairns BR, Thorner J (1996 Jul). Signaling in the yeast pheromone response pathway: specific and high-affinity interaction of the mitogen-activated protein (MAP) kinases Kss1 and Fus3 with the upstream MAP kinase kinase Ste7. Mol Cell Biol, 16(7), 3637-50.
  98. Treich I, Cairns BR, de los Santos T, Brewster E, Carlson M (1995 Aug). SNF11, a new component of the yeast SNF-SWI complex that interacts with a conserved region of SNF2. Mol Cell Biol, 15(8), 4240-8.
  99. Cairns BR, Kim YJ, Sayre MH, Laurent BC, Kornberg RD (1994 Mar 1). A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast. Proc Natl Acad Sci U S A, 91(5), 1950-4.
  100. Cairns BR, Ramer SW, Kornberg RD (1992 Jul). Order of action of components in the yeast pheromone response pathway revealed with a dominant allele of the STE11 kinase and the multiple phosphorylation of the STE7 kinase. Genes Dev, 6(7), 1305-18.
  101. Genske JE, Cairns BR, Stack SP, Landfear SM (1991 Jan). Structure and regulation of histone H2B mRNAs from Leishmania enriettii. Mol Cell Biol, 11(1), 240-9.
  102. Stein DA, Cairns BR, Landfear SM (1990 Mar 25). Developmentally regulated transporter in Leishmania is encoded by a family of clustered genes. Nucleic Acids Res, 18(6), 1549-57.
  103. Cairns BR, Collard MW, Landfear SM (1989 Oct). Developmentally regulated gene from Leishmania encodes a putative membrane transport protein. Proc Natl Acad Sci U S A, 86(20), 7682-6.

Review

  1. Clapier CR, Iwasa J, Cairns BR, Peterson CL (2017 Jul). Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. [Review]. Nat Rev Mol Cell Biol, 18(7), 407-422.
  2. Hammoud SS, Cairns BR, Jones DA (2013 Apr). Epigenetic regulation of colon cancer and intestinal stem cells. [Review]. Curr Opin Cell Biol, 25(2), 177-83.
  3. Kasten MM, Clapier CR, Cairns BR (). SnapShot: Chromatin remodeling: SWI/SNF. [Review]. Cell, 144(2), 310.e.l..
  4. Cairns BR (2009 Sep 10). The logic of chromatin architecture and remodelling at promoters. [Review]. Nature, 461(7261), 193-8.
  5. Clapier CR, Cairns BR (2009). The biology of chromatin remodeling complexes. [Review]. Annu Rev Biochem, 78, 273-304.
  6. Cairns BR (2007 Nov). Chromatin remodeling: insights and intrigue from single-molecule studies. [Review]. Nat Struct Mol Biol, 14(11), 989-96.
  7. Saha A, Wittmeyer J, Cairns BR (2006 Jun). Chromatin remodelling: the industrial revolution of DNA around histones. [Review]. Nat Rev Mol Cell Biol, 7(6), 437-47.
  8. Saha A, Wittmeyer J, Cairns BR (2006). Mechanisms for nucleosome movement by ATP-dependent chromatin remodeling complexes. [Review]. Results Probl Cell Differ, 41, 127-48.
  9. Cairns BR (2005 Apr). Chromatin remodeling complexes: strength in diversity, precision through specialization. [Review]. Curr Opin Genet Dev, 15(2), 185-90.
  10. Cairns BR (). Around the world of DNA damage in 180 days. [Review]. Cell, 119(6), 733-5.
  11. Cairns BR (2001 Nov). Emerging roles for chromatin remodeling in cancer biology. [Review]. Trends Cell Biol, 11(11), S15-21.
  12. Cairns BR (1998 Jan). Chromatin remodeling machines: similar motors, ulterior motives. [Review]. Trends Biochem Sci, 23(1), 20-5.

Book Chapter

  1. Wittmeyer J, Saha A, Cairns B (2004). DNA translocation and nucleosome remodeling assays by the RSC chromatin remodeling complex. In C. David Allis and Carl Wu (Eds.), Methods in Enzymology-Chromatin and Chromatin Remodeling Enzymes, Part C (377, pp. 322-43). USA: Elsevier Science.
  2. Cairns B, Kingston R (2000-01-01). The SWI/SNF and RSC Chromatin Remodeling Complexes. In Chromatin Structure and Gene Expression (pp. Chapter 5). Oxford University Press.

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