Publications

Link to full Cairns BR bibliography via the NIH Pub Med Database

Remodeling

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes.
Clapier CR, Iwasa J, Cairns BR, Peterson CL (2017).
[Review]. Nat Rev Mol Cell Biol, 18(7), 407-422.

Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection.
Clapier CR, Kasten MM, Parnell TJ, Viswanathan R, Szerlong H, Sirinakis G, Zhang Y, Cairns BR (2016).
Mol Cell, 62(3), 453-61.

The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism.
Parnell TJ, Schlichter A, Wilson BG, Cairns BR (2015).
Elife, 4, e06073.

Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler.
Schubert HL, Wittmeyer J, Kasten MM, Hinata K, Rawling DC, Heroux A, Cairns BR, Hill CP (2013).
Proc Natl Acad Sci U S A, 110(9), 3345-50.

Histone deacetylases 1 and 2 maintain S-phase chromatin and DNA replication fork progression.
Bhaskara S, Jacques V, Rusche JR, Olson EN, Cairns BR, Chandrasekharan MB.
Epigenetics Chromatin 2013 Aug 15;6(1):27.

Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler.
Schubert HL, Wittmeyer J, Kasten MM, Hinata K, Rawling DC, Héroux A, Cairns BR, Hill CP.
Proc Natl Acad Sci USA 2013 Feb 26;110(9):3345-50.

Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes.
Clapier CR, Cairns BR.
Nature 2012 Dec 13;492(7428):280-4.

Allosteric interactions of DNA and nucleotides with S. cerevisiae RSC.
Malik SS, Rich E, Viswanathan R, Cairns BR, Fischer CJ.
Biochemistry 2011 Sep 20;50(37):7881-90.

The RSC chromatin remodelling ATPase translocates DNA with high force and small step size.
Sirinakis G, Clapier CR, Gao Y, Viswanathan R, Cairns BR, Zhang Y.
EMBO J 2011 May 6;30(12):2364-72.

SnapShot: Chromatin remodeling: SWI/SNF.
Kasten MM, Clapier CR, Cairns BR.
Cell 2011 Jan 21;144(2):310.e1.

The logic of chromatin architecture and remodelling at promoters.
Cairns BR.
Nature 2009 Sep 10;461(7261):193-8. Review.

The biology of chromatin remodeling complexes.
Clapier CR, Cairns BR.
Annu Rev Biochem 2009;78:273-304. Review.

The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases.
Szerlong H, Hinata K, Viswanathan R, Erdjument-Bromage H, Tempst P, Cairns BR.
Nat Struct Mol Biol 2008 May;15(5):469-76.

RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes.
Parnell TJ, Huff JT, Cairns BR.
EMBO J 2008 Jan 9;27(1):100-10.

Chromatin remodeling: insights and intrigue from single-molecule studies.
Cairns BR.
Nat Struct Mol Biol 2007 Nov;14(11):989-96. Review.

Kinetic model for the ATP-dependent translocation of Saccharomyces cerevisiae RSC along double-stranded DNA.
Fischer CJ, Saha A, Cairns BR.
Biochemistry 2007 Oct 30;46(43):12416-26.

Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation.
VanDemark AP, Kasten MM, Ferris E, Heroux A, Hill CP, Cairns BR.
Mol Cell 2007 Sep 7;27(5):817-28.

Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method.
Leschziner AE, Saha A, Wittmeyer J, Zhang Y, Bustamante C, Cairns BR, Nogales E.
Proc Natl Acad Sci USA 2007 Mar 20;104(12):4913-8.

DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC.
Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C.
Mol Cell 2006 Nov 17;24(4):559-68.

Chromatin remodelling: the industrial revolution of DNA around histones.
Saha A, Wittmeyer J, Cairns BR.
Nat Rev Mol Cell Biol 2006 Jun;7(6):437-47. Review.

Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes.
Da G, Lenkart J, Zhao K, Shiekhattar R, Cairns BR, Marmorstein R.
Proc Natl Acad Sci USA 2006 Feb 14;103(7):2057-62.

The RSC chromatin remodeling complex bears an essential fungal-specific protein module with broad functional roles.
Wilson B, Erdjument-Bromage H, Tempst P, Cairns BR.
Genetics 2006 Feb;172(2):795-809.

Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss.
Zhang H, Roberts DN, Cairns BR.
Cell 2005 Oct 21;123(2):219-31.

Chromatin remodeling through directional DNA translocation from an internal nucleosomal site.
Saha A, Wittmeyer J, Cairns BR.
Nat Struct Mol Biol 2005 Sep;12(9):747-55.

Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair.
Chai B, Huang J, Cairns BR, Laurent BC.
Genes Dev 2005 Jul 15;19(14):1656-61.

Histone trimethylation by Set1 is coordinated by the RRM, autoinhibitory, and catalytic domains.
Schlichter A, Cairns BR.
EMBO J 2005 Mar 23;24(6):1222-31.

The Yaf9 component of the SWR1 and NuA4 complexes is required for proper gene expression, histone H4 acetylation, and Htz1 replacement near telomeres.
Zhang H, Richardson DO, Roberts DN, Utley R, Erdjument-Bromage H, Tempst P, Côté J, Cairns BR.
Mol Cell Biol 2004 Nov;24(21):9424-36.

 

Development

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons.
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).
Nat Genet49(6), 925-934.

Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.
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).
Cell Stem Cell21(4), 533-546.e6.

Genome-wide DNA methylation profiling in zebrafish.
Murphy PJ, Cairns BR (2016).
Methods Cell Biol135, 345-59.

Tet proteins enhance the developmental hourglass.
Hendrickson PG, Cairns BR (2016).
Nat Genet48(4), 345-7.

Experimental Approaches for Target Profiling of RNA Cytosine Methyltransferases.
Khoddami V, Yerra A, Cairns BR (2015).
Methods Enzymol560, 273-96.

Transcription and imprinting dynamics in developing postnatal male germline stem cells.
Hammoud SS, Low DH, Yi C, Lee CL, Oatley JM, Payne CJ, Carrell DT, Guccione E, Cairns BR (2015).
Genes Dev29(21), 2312-24.

Aberrant sperm DNA methylation predicts male fertility status and embryo quality.
Aston KI, Uren PJ, Jenkins TG, Horsager A, Cairns BR, Smith AD, Carrell DT (2015).
Fertil Steril104(6), 1388-97.e1-5.

RNA polymerase III transcriptomes in human embryonic stem cells and induced pluripotent stem cells, and relationships with pluripotency transcription factors.
Alla RK, Cairns BR (2014).
PLoS One9(1), e85648.

Chromatin and transcription transitions of mammalian adult germline stem cells and spermatogenesis.
Hammoud SS, Low DH, Yi C, Carrell DT, Guccione E, Cairns BR (2014).
Cell Stem Cell15(2), 239-53.

Epigenetic regulation of colon cancer and intestinal stem cells.
Hammoud SS, Cairns BR, Jones DA (2013). 
[Review]. Curr Opin Cell Biol25(2), 177-83.

Zinc-dependent regulation of the Adh1 antisense transcript in fission yeast.
Ehrensberger KM, Mason C, Corkins ME, Anderson C, Dutrow N, Cairns BR, Dalley B, Milash B, Bird AJ (2013).
J Biol Chem288(2), 759-69.

Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern.
Potok ME, Nix DA, Parnell TJ, Cairns BR (2013).
Cell153(4), 759-72.

Paternal aging and associated intraindividual alterations of global sperm 5-methylcytosine and 5-hydroxymethylcytosine levels.
Jenkins TG, Aston KI, Cairns BR, Carrell DT (2013).
Fertil Steril100(4), 945-51.

Reintroducing domesticated wild mice to sociality induces adaptive transgenerational effects on MUP expression.
Nelson AC, Cauceglia JW, Merkley SD, Youngson NA, Oler AJ, Nelson RJ, Cairns BR, Whitelaw E, Potts WK (2013).
Proc Natl Acad Sci U S A110(49), 19848-53.

Epigenetic regulation of colon cancer and intestinal stem cells.
Hammoud SS, Cairns BR, Jones DA.
Curr Opin Cell Biol. 2013 Apr;25(2):177-83. Review.

Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern.
Potok ME, Nix DA, Parnell TJ, Cairns BR.
Cell. 2013 May 9;153(4):759-72. Cover of Cell

Paternal aging and associated intraindividual alterations of global sperm 5-methylcytosine and 5-hydroxymethylcytosine levels.
Jenkins TG, Aston KI, Cairns BR, Carrell DT.
Fertil Steril. 2013 Oct;100(4):945-51.

DNA methylation profiling in zebrafish.
Wu SF, Zhang H, Hammoud SS, Potok M, Nix DA, Jones DA, Cairns BR.
Methods Cell Biol. 2011;104:327-39.

Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm.
Wu SF, Zhang H, Cairns BR.
Genome Res. 2011 Apr;21(4):578-89.

Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men.
Hammoud SS, Nix DA, Hammoud AO, Gibson M, Cairns BR, Carrell DT.
Hum Reprod. 2011 Sep;26(9):2558-69.

Alterations in sperm DNA methylation patterns at imprinted loci in two classes of infertility.
Hammoud SS, Purwar J, Pflueger C, Cairns BR, Carrell DT.
Fertil Steril. 2010 Oct;94(5):1728-33.

Distinctive chromatin in human sperm packages genes for embryo development.
Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns BR.
Nature. 2009 Jul 23;460(7254):473-8.

Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries.
Gordon M, Holt DG, Panigrahi A, Wilhelm BT, Erdjument-Bromage H, Tempst P, Bähler J, Cairns BR.
Mol Cell Biol. 2007 Jun;27(11):4058-69.

Cancer

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming
Murphy PJ, Wu SF, James CR, Wike CL, Cairns BR (2018). Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming. Cell172(5), 993-1006.e13.

Cigarette smoking significantly alters sperm DNA methylation patterns.
Jenkins TG, James ER, Alonso DF, Hoidal JR, Murphy PJ, Hotaling JM, Cairns BR, Carrell DT, Aston KI (2017). 
Andrology5(6), 1089-1099.

Counteracting h2K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription.
Ramakrishnan S, Pokhrel S, Palani S, Pflueger C, Parnell TJ, Cairns BR, Bhaskara S, Chandrasekharan MB (2016).
Nat Commun7, 11949.

The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis.
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).
LID - 10.1038/onc.2016.38 [doi]. Oncogene.

HDAC1,2 inhibition impairs EZH2- and BBAP-mediated DNA repair to overcome chemoresistance in EZH2 gain-of-function mutant diffuse large B-cell lymphoma.
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).
Oncotarget6(7), 4863-87.

Interaction of the Jhd2 Histone h2 Lys-4 Demethylase with Chromatin Is Controlled by Histone H2A Surfaces and Restricted by H2B Ubiquitination.
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). J Biol Chem290(48), 28760-77.

Epigenetic regulation of colon cancer and intestinal stem cells.
Hammoud SS, Cairns BR, Jones DA (2013).
[Review]. Curr Opin Cell Biol25(2), 177-83.

Methylation of AR locus does not always reflect X chromosome inactivation state.
Swierczek SI, Piterkova L, Jelinek J, Agarwal N, Hammoud S, Wilson A, Hickman K, Parker CJ, Cairns BR, Prchal JT.
Blood. 2012 Mar 29;119(13):e100-9.

Antibody detection of translocations in Ewing sarcoma.
Luo W, Milash B, Dalley B, Smith R, Zhou H, Dutrow N, Cairns BR, Lessnick SL.
EMBO Mol Med. 2012 Jun;4(6):453-61.

Dnmt3 and G9a cooperate for tissue-specific development in zebrafish.
Rai K, Jafri IF, Chidester S, James SR, Karpf AR, Cairns BR, Jones DA.
J Biol Chem. 2010 Feb 5;285(6):4110-21.

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors.
Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, Cairns BR.
Nat Struct Mol Biol. 2010 May;17(5):620-8.

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors.
Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, Cairns BR.
Nat Struct Mol Biol. 2010 May;17(5):620-8.

DNA demethylase activity maintains intestinal cells in an undifferentiated state following loss of APC.
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.
Cell. 2010 Sep 17;142(6):930-42.

DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45.
Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR.
Cell. 2008 Dec 26;135(7):1201-12.

Dnmt2 functions in the cytoplasm to promote liver, brain, and retina development in zebrafish.
Rai K, Chidester S, Zavala CV, Manos EJ, James SR, Karpf AR, Jones DA, Cairns BR.
Genes Dev. 2007 Feb 1;21(3):261-6.

Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development.
Rai K, Nadauld LD, Chidester S, Manos EJ, James SR, Karpf AR, Cairns BR, Jones DA.
Mol Cell Biol. 2006 Oct;26(19):7077-85.

RNA Modifications

SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation.
Varshney D, Vavrova-Anderson J, Oler AJ, Cowling VH, Cairns BR, White RJ (2015).
Nat Commun6, 6569.

Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP.
Khoddami V, Cairns BR (2014).
Nat Protoc9(2), 337-61.

Identification of direct targets and modified bases of RNA cytosine methyltransferases.
Khoddami V, Cairns BR.
Nat Biotechnol. 2013 May;31(5):458-64.

PP4 dephosphorylates Maf1 to couple multiple stress conditions to RNA polymerase III repression.
Oler AJ, Cairns BR.
EMBO J. 2012 Mar 21;31(6):1440-52.

Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping.
Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, Cairns BR.
Nat Genet. 2008 Aug;40(8):977-86.

Dephosphorylation and genome-wide association of Maf1 with Pol III-transcribed genes during repression.
Roberts DN, Wilson B, Huff JT, Stewart AJ, Cairns BR.
Mol Cell. 2006 Jun 9;22(5):633-44.