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Items: 1 to 50 of 112

1.

Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes.

Cakiroglu A, Clapier CR, Ehrensberger AH, Darbo E, Cairns BR, Luscombe NM, Svejstrup JQ.

Genome Res. 2019 Jun;29(6):988-998. doi: 10.1101/gr.243139.118. Epub 2019 May 16.

2.

Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution.

Khoddami V, Yerra A, Mosbruger TL, Fleming AM, Burrows CJ, Cairns BR.

Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6784-6789. doi: 10.1073/pnas.1817334116. Epub 2019 Mar 14. Erratum in: Proc Natl Acad Sci U S A. 2019 Apr 30;116(18):9136.

3.

Isolation and Enrichment of Spermatogonial Stem Cells From Human Testis Tissues.

Guo J, Cairns BR.

Curr Protoc Stem Cell Biol. 2019 Jun;49(1):e77. doi: 10.1002/cpsc.77. Epub 2019 Jan 4.

PMID:
30609304
4.

The adult human testis transcriptional cell atlas.

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.

Cell Res. 2018 Dec;28(12):1141-1157. doi: 10.1038/s41422-018-0099-2. Epub 2018 Oct 12.

5.

Histone Deacetylase Inhibition Has Targeted Clinical Benefit in ARID1A-Mutated Advanced Urothelial Carcinoma.

Gupta S, Albertson DJ, Parnell TJ, Butterfield A, Weston A, Pappas LM, Dalley B, O'Shea JM, Lowrance WT, Cairns BR, Schiffman JD, Sharma S.

Mol Cancer Ther. 2019 Jan;18(1):185-195. doi: 10.1158/1535-7163.MCT-17-0957. Epub 2018 Oct 9.

PMID:
30301863
6.

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming.

Murphy PJ, Wu SF, James CR, Wike CL, Cairns BR.

Cell. 2018 Feb 22;172(5):993-1006.e13. doi: 10.1016/j.cell.2018.01.022. Epub 2018 Feb 15.

7.

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.

Cell Stem Cell. 2017 Oct 5;21(4):533-546.e6. doi: 10.1016/j.stem.2017.09.003.

8.

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.

Andrology. 2017 Nov;5(6):1089-1099. doi: 10.1111/andr.12416. Epub 2017 Sep 26.

9.

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes.

Clapier CR, Iwasa J, Cairns BR, Peterson CL.

Nat Rev Mol Cell Biol. 2017 Jul;18(7):407-422. doi: 10.1038/nrm.2017.26. Epub 2017 May 17. Review.

PMID:
28512350
10.

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons.

Hendrickson PG, Doráis 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.

Nat Genet. 2017 Jun;49(6):925-934. doi: 10.1038/ng.3844. Epub 2017 May 1.

11.

Genome-wide DNA methylation profiling in zebrafish.

Murphy PJ, Cairns BR.

Methods Cell Biol. 2016;135:345-59. doi: 10.1016/bs.mcb.2016.05.002. Epub 2016 Jun 21.

PMID:
27443935
12.

Counteracting H3K4 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.

Nat Commun. 2016 Jun 21;7:11949. doi: 10.1038/ncomms11949.

13.

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.

Mol Cell. 2016 May 5;62(3):453-461. doi: 10.1016/j.molcel.2016.03.032.

14.

Tet proteins enhance the developmental hourglass.

Hendrickson PG, Cairns BR.

Nat Genet. 2016 Apr;48(4):345-7. doi: 10.1038/ng.3533.

PMID:
27023773
15.

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.

Oncogene. 2016 Sep 22;35(38):5021-32. doi: 10.1038/onc.2016.38. Epub 2016 Mar 7.

16.

Selective repression of SINE transcription by RNA polymerase III.

Varshney D, Vavrova-Anderson J, Oler AJ, Cairns BR, White RJ.

Mob Genet Elements. 2015 Sep 23;5(6):86-91. eCollection 2015 Nov-Dec.

17.

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.

Genes Dev. 2015 Nov 1;29(21):2312-24. doi: 10.1101/gad.261925.115.

18.

Interaction of the Jhd2 Histone H3 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.

J Biol Chem. 2015 Nov 27;290(48):28760-77. doi: 10.1074/jbc.M115.693085. Epub 2015 Oct 8.

19.

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.

Fertil Steril. 2015 Dec;104(6):1388-97.e1-5. doi: 10.1016/j.fertnstert.2015.08.019. Epub 2015 Sep 8.

PMID:
26361204
20.

Experimental Approaches for Target Profiling of RNA Cytosine Methyltransferases.

Khoddami V, Yerra A, Cairns BR.

Methods Enzymol. 2015;560:273-96. doi: 10.1016/bs.mie.2015.03.008. Epub 2015 May 28.

PMID:
26253975
21.

The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism.

Parnell TJ, Schlichter A, Wilson BG, Cairns BR.

Elife. 2015 Mar 30;4:e06073. doi: 10.7554/eLife.06073.

22.

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.

Nat Commun. 2015 Mar 23;6:6569. doi: 10.1038/ncomms7569.

23.

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.

Oncotarget. 2015 Mar 10;6(7):4863-87.

24.

Age-associated sperm DNA methylation alterations: possible implications in offspring disease susceptibility.

Jenkins TG, Aston KI, Pflueger C, Cairns BR, Carrell DT.

PLoS Genet. 2014 Jul 10;10(7):e1004458. doi: 10.1371/journal.pgen.1004458. eCollection 2014 Jul.

25.

Chromatin and transcription transitions of mammalian adult germline stem cells and spermatogenesis.

Hammoud SS, Low DH, Yi C, Carrell DT, Guccione E, Cairns BR.

Cell Stem Cell. 2014 Aug 7;15(2):239-53. doi: 10.1016/j.stem.2014.04.006. Epub 2014 May 15.

26.
27.

Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP.

Khoddami V, Cairns BR.

Nat Protoc. 2014 Feb;9(2):337-61. doi: 10.1038/nprot.2014.014. Epub 2014 Jan 16.

PMID:
24434802
28.

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.

Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE.

BMC Bioinformatics. 2013 Nov 21;14:337. doi: 10.1186/1471-2105-14-337.

29.

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.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19848-53. doi: 10.1073/pnas.1310427110. Epub 2013 Nov 18.

30.

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. doi: 10.1186/1756-8935-6-27.

31.

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. doi: 10.1016/j.fertnstert.2013.05.039. Epub 2013 Jun 27.

PMID:
23809503
32.

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. doi: 10.1016/j.cell.2013.04.030.

33.

Identification of direct targets and modified bases of RNA cytosine methyltransferases.

Khoddami V, Cairns BR.

Nat Biotechnol. 2013 May;31(5):458-64. doi: 10.1038/nbt.2566. Epub 2013 Apr 21.

34.

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. doi: 10.1016/j.ceb.2013.01.007. Epub 2013 Feb 8. Review.

35.

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 U S A. 2013 Feb 26;110(9):3345-50. doi: 10.1073/pnas.1215379110. Epub 2013 Feb 11.

36.

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.

J Biol Chem. 2013 Jan 11;288(2):759-69. doi: 10.1074/jbc.M112.406165. Epub 2012 Dec 5.

37.

Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes.

Clapier CR, Cairns BR.

Nature. 2012 Dec 13;492(7428):280-4. doi: 10.1038/nature11625. Epub 2012 Nov 11.

38.

Analysis of gene-specific and genome-wide sperm DNA methylation.

Hammoud SS, Cairns BR, Carrell DT.

Methods Mol Biol. 2013;927:451-8. Review.

PMID:
22992936
39.

Alu expression in human cell lines and their retrotranspositional potential.

Oler AJ, Traina-Dorge S, Derbes RS, Canella D, Cairns BR, Roy-Engel AM.

Mob DNA. 2012 Jun 20;3(1):11. doi: 10.1186/1759-8753-3-11.

40.

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. doi: 10.1002/emmm.201200225. Epub 2012 Mar 15.

41.

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. doi: 10.1038/emboj.2011.501. Epub 2012 Feb 14.

42.

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. doi: 10.1182/blood-2011-11-390351. Epub 2012 Jan 27. Erratum in: Blood. 2012 Nov 22;120(22):4447. Cairns, Bradley [corrected to Cairns, Bradley R].

43.

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. doi: 10.1016/B978-0-12-374814-0.00018-5.

PMID:
21924171
44.

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. doi: 10.1021/bi200837b. Epub 2011 Aug 26.

45.

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. doi: 10.1093/humrep/der192. Epub 2011 Jun 17.

46.

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. doi: 10.1038/emboj.2011.141.

47.

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. doi: 10.1101/gr.113167.110. Epub 2011 Mar 7.

48.

SnapShot: Chromatin remodeling: SWI/SNF.

Kasten MM, Clapier CR, Cairns BR.

Cell. 2011 Jan 21;144(2):310.e1. doi: 10.1016/j.cell.2011.01.007. No abstract available.

49.

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. doi: 10.1016/j.cell.2010.08.030.

50.

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. doi: 10.1038/nsmb.1801. Epub 2010 Apr 25.

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