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Wu SF, Zhang H, Hammoud SS, Potok M, Nix DA, Jones DA, Cairns BR. DNA methylation profiling in zebrafish Methods Cell Biol. 2001;104:327-39 in process PMID: 21924171
Rai K, Sarkar S, Braodbent 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. Cell. 2010 Sep 17;142(6):930-42
Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, Cairns BR Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol. 2010 May;14(5):620-8 PMID: 20418882
Rai K, Jafri IF, Chidester S, James SR, Karpf AR, Cairns BR, Jones DA Dnmt3 and G9a cooperate for tissue-specific development in zebrafish. J Biol Chem. 2010 Feb 5;285(6):4110-21 PMID: 19946145
Hammoud SS, Purwar J, Pflueger C, Cairns BR, Carrell DT Alterations in sperm DNA methylation patterns at imprinted loci in two classes of infertility. Fertil Steril. 2010 Oct;94(5):1728-33 PMID: 19880108
Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, and Cairns BR. Human RNA Polymerase III transcriptomes and relationships to Pol II promoters, enhancer-binding factors and chromatin domains. Nat Struct Mol Biol 17, 620-628.
Malik SS, Rich E, Viswanathan R, Cairns BR, Fischer CJ (2011) Allosteric Interactions of DNA and Nucleotides with S. cerevisiae RSC. Biochemistry 50(37):7881-90. [Epub ahead of print]
Wu SF, Zhang H, and Cairns BR (2011) Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome Res. 2011 April; 21(4): 578–589.
Hammoud SS, NixDA, Hammoud AO, Gibson M, Cairns BR, and Carrell DT (2011) Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men. Human Reproduction, Vol.26, No.9 pp. 2558–2569.
Sirinakis G, Clapier GR, Gao1 Y, Viswanathan R, Cairns BR, and Zhang Y. (2011) The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. EMBO J. 30(12):2364-72.
Rai K, Sarkar S, Broadbent T, Voas M, Grossmann K, Nadauld L, Dehghanizadeh S, Hagos F, Li Y, Toth R, Chidester S, Bahr T, Johnson WE, Sklow B, Burt R, Cairns BR, and Jones DA (2010) DNA Demethylase Activity Maintains Intestinal Cells in an Undifferentiated State Following Loss of APC Cell 142(6): 930–942.
Rai K, Jafri I, Chidester S, James SR, Karpf AR, Cairns BR, and Jones DA. Dnmt3 and G9a Cooperate for Tissue-specific Development in Zebrafish J Biol Chem. 2010 Feb 5;285(6):4110-21 [Epub ahead of print]
Cairns BR. The logic of chromatin architecture and remodelling at promoters. Nature. 2009 Sep 10;461(7261):193-8.
Hammoud S, Nix D, Zhang H, Purwar J, Carrell D, Cairns BR (2009) Distinctive chromatin in human sperm packages genes for embryo development. Nature [Epub ahead of print]
Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE (2009) The GNUMAP algorithm: Unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics 26:38-45.
Clapier CR, Cairns BR (2009) The Biology of Chromatin Remodeling Complexes. Annu Rev Biochem 78:273-304 [Epub ahead of print]
Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR (2008) DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 13(7):1201-12 Data
Dutrow N, Nix D, Holt D, Milash B, Dalley B, Westbroek E, Parnell T, Cairns BR (2008) Dynamic Transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet 40(8):977-986
Szerlong H, Hinata K, Viswanathan R, Erdjument-Bromage H, Tempst P, Cairns BR (2008) The HSA domain binds actin-related proteins to regulate chromatin remodeling ATPases. Nat Struct Mol Biol 15(5):469-476
Parnell T, Huff JT, Cairns BR (2007) RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes. EMBO J 27(1):100-10 [Epub 2007]
Fischer C, Saha A, Cairns BR (2007) Kinetic Model for the ATP-dependent Translocation of S. cerevisiae RSC along double-stranded DNA. Biochemistry 46(43):12416-26
VanDemark AP, Kasten MM, Ferris E, Heroux A, Hill CP, Cairns BR (2007) Autoregulation of the Rsc4 Tandem Bromodomain by Gcn5 Acetylation. Mol Cell 27(5):817-28
Gordon M, Holt D, Panigrahi A, Wilhelm BT, Erdjument-Bromage H, Tempst P, Bähler J, Cairns BR (2007) Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries. Mol Cell Biol 27(11):4058-69
Leschziner AE, Saha A, Wittmeyer J, Zhang Y, Bustamante C, Cairns BR, Nogales E (2007) Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc Natl Acad Sci USA 104(12):4913-8
Rai K, Chidester S, Svala CV, Manos EJ, James SR, Karpf AR, Jones DA, Cairns BR (2007) Dnmt2 functions in the cytoplasm to promote liver, brain, and retina development in zebrafish. Genes Dev 21(3):261-266
Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C (2006) DNA Translocation and Loop Formation Mechanism of Chromatin Remodeling by SWI/SNF and RSC. Mol Cell 24:559-568
Rai K, Nadauld LD, Chidester S, Manos EJ, James SR, Karpf AR, Cairns BR, Jones DA (2006) Zebrafish dnmt1 and suv39h1 have overlapping and organ-specific functions in zebrafish development. Mol Cell Biol 26:7077-7085
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) ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature Jul 6;442(7098):96-9
Bordas-Le Floch V, Gendrel G, Soutorina J, Flores A, Dumay-Odelot H, Soularue P, Navarro F, Cairns BR, Lefebvre O, Werner M (2006) The Rsc4 C-terminus connects the chromatin remodeler RSC to RNA polymerases. Mol Cell Biol 26(13):4920-4933
Roberts D, Wilson B, Huff J, Stewart A, Cairns BR (2006) Dephosphorylation and genome-wide association of Maf1 with Pol III genes in transcriptional repression. Mol Cell, 22(5):633-644
Da G, Lenkart J, Zhao K, Shiekhattar R, Cairns BR, Marmorstein R (2006) Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc Natl Acad Sci 103(7):2057-2063
Wilson B, Erdjument Bromage H, Tempst P, Cairns BR (2006) The RSC chromatin remodeling complex bears an essential yeast-specific module with broad functional roles. Genetics 172 (2):795-809
Da G, Lenkart J, Zhao K, Shiekhattar R, Cairns BR, Marmorstein R (2006) Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc Natl Acad Sci 103(7):2057-2063
Supplemental method and images for above. Table 3. Table 4.
Schlichter A, Cairns BR (2005) Histone trimethylation by Set1 is coordinated by the RRM, autoinhibitory and catalytic domains. EMBO J 24:1222-1231.
Supplemental method and images for above: Table S1. Figure 1. Figure 2.
Chai B, Huang J, Cairns BR, Laurent BC (2005) Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-stranded break repair. Genes Dev 19(14):1656-61.
Supplemental images for above: Figure 1. Figure 2. Figure 3. Figure 4.
Saha A, Wittmeyer J, Cairns BR (2005) Chromatin remodeling through DNA translocation from an internal nucleosomal site. Nat Struct Mol Biol 12(9):747-55. Supplemental method and images for above: Method. Method (doc). Figure 1.
Wilson B, Erdjument Bromage H, Tempst P, Cairns BR (2005) The RSC chromatin remodeling complex bears an essential yeast-specific module with broad functional roles. Genetics (in press)
Zhang H, Roberts D, Cairns BR (2005) Genome-wide dynamics of Htz1, a conserved histone H2A variant that poises repressed genes for activation through histone loss. Cell.
Supplemental data and tables: Data. Table 3. Table 4.
Zhang H, Richardson DO, Roberts DN, Utley R, Erdjument-Bromage H, Tempst P, Cote J, Cairns BR (2004) 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 Nov;24(21):9424-36.
Supplemental methods, tables and images: Methods. Table 1. Microarray and ChIP Chip Data. Supplemental Images.
Kasten M, Szerlong H, Erdjument-Bromage H, Tempst P, Werner M, Cairns BR (2004) Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys 14. EMBO J (23)1348-1359
Supplemental methods and images for above: Method. Figure 1. Figure 2. Figure 3.
Roberts DN, Stewart AJ, Huff JT, Cairns BR (2003) The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships.
Proc Natl Acad Sci U S A Dec 9;100(25):14695-700
Supplemental tables for above: Table 1. Table 2. Table 3.
Supplemental methods and images (HTML) Roberts Supplemental
Szerlong H, Saha A, Cairns BR (2003) 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
Romeo MJ, Angus-Hill ML, Sobering AK, Kamada Y, Cairns BR, Levin DE (2002) HTL1 encodes a novel factor that interacts with the RSC chromatin remodeling complex in Saccharomyces cerevisiae. Mol Cell Biol 22(23):8165-74
Supplemental tables for above: Table 1. Table 2.
Kristjuhan A, Walker J, Suka N, Grunstein M, Roberts D, Cairns BR, Svejstrup JQ (2002) Transcriptional inhibition of genes with severe histone h3 hypoacetylation in the coding region. Mol Cell 10(4):925-33
Saha A, Wittmeyer J, Cairns BR (2002) Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev 16(16):2120-34
Damelin M, Simon I, Moy TI, Wilson B, Komili S, Tempst P, Roth FP, Young RA, Cairns BR, Silver PA (2002) 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
Cairns BR (2001) Emerging roles for chromatin remodeling in cancer biology. Trends Cell Biol 11(11):S15-21 [Review]
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. J Biol Chem 276(16):12636-44
Angus-Hill ML, Schlichter A, Roberts D, Erdjument-Bromage H, Tempst P, Cairns BR (2001) 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
Cairns BR, Schlichter A, Erdjument-Bromage H, Tempst P, Kornberg RD, Winston F (1999)
Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol Cell 4(5):715-23
Neely KE, Hassan AH, Wallberg AE, Steger DJ, Cairns BR, Wright AP, Workman JL (1999)
Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol Cell 4(4):649-55
Whitehouse I, Flaus A, Cairns BR, White MF, Workman JL, Owen-Hughes T (1999) Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature 400(6746):784-7
Cairns BR, Erdjument-Bromage H, Tempst P, Winston F, Kornberg RD (1998) Two actin-related proteins are shared functional components of the chromatin-remodeling complexes RSC and SWI/SNF. Mol Cell 2(5):639-51
Lorch Y, Cairns BR, Zhang M, Kornberg RD (1998) Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell 94(1):29-34
Cairns BR (1998) Chromatin remodeling machines: similar motors, ulterior motives. Trends Biochem Sci 23(1):20-5 [Review]
Cairns BR, Schlichter A, Tempst P, Kornberg RD, Winston F. (1999) Rsc1 and Rsc2 are in distinct forms of RSC and contain AT-hook, BAH, and bromodomains essential for the function of each complex. Mol Cell 2:715-723
Cao Y, Cairns BR, Kornberg RD, Laurent BC (1997) Sfh 1p, a component of a novel chromatin remodeling complex, is required for cell cycle progression. Mol Cell Biol 17:3323-3334
Cairns BR, Lorch Y, Li Y, Lacomis L, Erdjument-Bromage H, Tempst P, Du J, Laurent B, Kornberg RD (1996) RSC, an abundant, essential chromatin-remodeling complex. Cell 87:1249-1260
Miller ME, Cairns BR, Levinson RL, Yamamoto KR, Engel DA, Smith MM (1996) Adenovirus E1A Blocks SWI/SNF-dependent transcriptional activation. Mol Cell Biol 16:5737-5743
Cairns BR, Levinson RL, Yamamoto KR, Kornberg RD (1996) Essential role of Swp73p in the function of yeast SWI/SNF complex. Genes and Dev 10:2131-2144
Wang W, Yutong X, Zhou S, Kuo A, Cairns BR, Crabtree GR (1996) Diversity and specialization of mammalian SWI/SNF complexes. Genes and Dev 10:2117-2130
Bardwell L, Cook JG, Chang EC, Cairns BR, Thorner J (1996) Signaling in the yeast pheromone response pathway: specific and high-affinity interaction of the mitogen-activated protein (MAP) kinase Kss1 and Fus3 with the upstream MAP kinase STE7. Mol Cell Biol 16:3637-3650
Cairns BR, Henry LH, Kornberg RD (1996) TFG3/TAF30/ANCI, a component of the yeast SWI/SNF complex that is similar to the leukemogenic proteins ENL and AF-9. Mol Cell Biol 16:3308-3316
Treich I, Cairns BR, Santos T, Brewster E, Carlson M (1995) SNF11, a new component of the yeast SNF-SWI complex that interacts with a conserved region of SNF2. Mol Cell Biol 15:4240-4248
Cairns BR, Kim YJ, Sayre MH, Laurent BC, Kornberg RD (1994) A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5 and SNF6 gene products isolated from yeast. Proc Natl Acad Sci USA 91:1950-1954
Cairns BR, Ramer SW, Kornberg RD (1992) Order of action of components in the mating pathway revealed with a dominant allele of the STE11 kinase and the multiple phosphorylation of the STE7 kinase. Genes and Dev 6:1305-1318
Genske JE, Cairns BC, Stack SP, Landfear SM (1991) Structure and regulation of histone H2B mRNA’s from Leishmania entriettii. Mol Cell Biol 11:240-249
Stein DS, Cairns BR, Landfear SM (1990) A developmentally-regulated transporter in Leishmania is encoded by a family of clustered genes. Nucleic Acids Res 18:1549-1547
Cairns BR, Collard ML, Landfear SM (1989) A developmentally-regulated gene from Leishmania encodes a putative membrane transport protein. Proc Natl Acad Sci USA 86:7682-7686
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