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Myeloid-derived suppressor cell function and epigenetic expression evolves over time after surgical sepsis.

Hollen MK, Stortz JA, Darden D, Dirain ML, Nacionales DC, Hawkins RB, Cox MC, Lopez MC, Rincon JC, Ungaro R, Wang Z, Wu Q, Brumback B, Gauthier ML, Kladde M, Leeuwenburgh C, Segal M, Bihorac A, Brakenridge S, Moore FA, Baker HV, Mohr AM, Moldawer LL, Efron PA.

Crit Care. 2019 Nov 13;23(1):355. doi: 10.1186/s13054-019-2628-x.


Publisher Correction: Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma.

Lorentsen KJ, Cho JJ, Luo X, Zuniga AN, Urban JF Jr, Zhou L, Gharaibeh R, Jobin C, Kladde MP, Avram D.

Nat Commun. 2018 Jul 19;9(1):2901. doi: 10.1038/s41467-018-05360-9.


Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma.

Lorentsen KJ, Cho JJ, Luo X, Zuniga AN, Urban JF Jr, Zhou L, Gharaibeh R, Jobin C, Kladde MP, Avram D.

Nat Commun. 2018 Apr 26;9(1):1679. doi: 10.1038/s41467-018-04111-0. Erratum in: Nat Commun. 2018 Jul 19;9(1):2901.


High Fractional Occupancy of a Tandem Maf Recognition Element and Its Role in Long-Range β-Globin Gene Regulation.

Stees JR, Hossain MA, Sunose T, Kudo Y, Pardo CE, Nabilsi NH, Darst RP, Poudyal R, Igarashi K, Huang S, Kladde MP, Bungert J.

Mol Cell Biol. 2015 Oct 26;36(2):238-50. doi: 10.1128/MCB.00723-15. Print 2016 Jan 15.


Integrated DNA methylation and chromatin structural analysis at single-molecule resolution.

Pardo CE, Nabilsi NH, Darst RP, Kladde MP.

Methods Mol Biol. 2015;1288:123-41. doi: 10.1007/978-1-4939-2474-5_9.


Human lymphoid translocation fragile zones are hypomethylated and have accessible chromatin.

Lu Z, Lieber MR, Tsai AG, Pardo CE, Müschen M, Kladde MP, Hsieh CL.

Mol Cell Biol. 2015 Apr;35(7):1209-22. doi: 10.1128/MCB.01085-14. Epub 2015 Jan 26.


TRIM29 suppresses TWIST1 and invasive breast cancer behavior.

Ai L, Kim WJ, Alpay M, Tang M, Pardo CE, Hatakeyama S, May WS, Kladde MP, Heldermon CD, Siegel EM, Brown KD.

Cancer Res. 2014 Sep 1;74(17):4875-87. doi: 10.1158/0008-5472.CAN-13-3579. Epub 2014 Jun 20.


Local depletion of DNA methylation identifies a repressive p53 regulatory region in the NEK2 promoter.

Nabilsi NH, Ryder DJ, Peraza-Penton AC, Poudyal R, Loose DS, Kladde MP.

J Biol Chem. 2013 Dec 13;288(50):35940-51. doi: 10.1074/jbc.M113.523837. Epub 2013 Oct 25.


Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma.

Nabilsi NH, Deleyrolle LP, Darst RP, Riva A, Reynolds BA, Kladde MP.

Genome Res. 2014 Feb;24(2):329-39. doi: 10.1101/gr.161737.113. Epub 2013 Oct 8.


Microbiota impact on the epigenetic regulation of colorectal cancer.

Yang T, Owen JL, Lightfoot YL, Kladde MP, Mohamadzadeh M.

Trends Mol Med. 2013 Dec;19(12):714-25. doi: 10.1016/j.molmed.2013.08.005. Epub 2013 Sep 16. Review.


The ZEB1 pathway links glioblastoma initiation, invasion and chemoresistance.

Siebzehnrubl FA, Silver DJ, Tugertimur B, Deleyrolle LP, Siebzehnrubl D, Sarkisian MR, Devers KG, Yachnis AT, Kupper MD, Neal D, Nabilsi NH, Kladde MP, Suslov O, Brabletz S, Brabletz T, Reynolds BA, Steindler DA.

EMBO Mol Med. 2013 Aug;5(8):1196-212. doi: 10.1002/emmm.201302827. Epub 2013 Jul 1.


Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus.

Darst RP, Haecker I, Pardo CE, Renne R, Kladde MP.

Nucleic Acids Res. 2013 Mar 1;41(5):2993-3009. doi: 10.1093/nar/gkt033. Epub 2013 Jan 29.


DNA methyltransferase accessibility protocol for individual templates by deep sequencing.

Darst RP, Nabilsi NH, Pardo CE, Riva A, Kladde MP.

Methods Enzymol. 2012;513:185-204. doi: 10.1016/B978-0-12-391938-0.00008-2.


Fibroblast growth factor receptor 2 homodimerization rapidly reduces transcription of the pluripotency gene Nanog without dissociation of activating transcription factors.

Santostefano KE, Hamazaki T, Pardo CE, Kladde MP, Terada N.

J Biol Chem. 2012 Aug 31;287(36):30507-17. doi: 10.1074/jbc.M112.388181. Epub 2012 Jul 11.


Simultaneous single-molecule detection of endogenous C-5 DNA methylation and chromatin accessibility using MAPit.

Darst RP, Pardo CE, Pondugula S, Gangaraju VK, Nabilsi NH, Bartholomew B, Kladde MP.

Methods Mol Biol. 2012;833:125-41. doi: 10.1007/978-1-61779-477-3_9.


Restraint of angiogenesis by zinc finger transcription factor CTCF-dependent chromatin insulation.

Tang M, Chen B, Lin T, Li Z, Pardo C, Pampo C, Chen J, Lien CL, Wu L, Ai L, Wang H, Yao K, Oh SP, Seto E, Smith LE, Siemann DW, Kladde MP, Cepko CL, Lu J.

Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15231-6. doi: 10.1073/pnas.1104662108. Epub 2011 Sep 6.


WIF1 is a frequent target for epigenetic silencing in squamous cell carcinoma of the cervix.

Delmas AL, Riggs BM, Pardo CE, Dyer LM, Darst RP, Izumchenko EG, Monroe M, Hakam A, Kladde MP, Siegel EM, Brown KD.

Carcinogenesis. 2011 Nov;32(11):1625-33. doi: 10.1093/carcin/bgr193. Epub 2011 Aug 26.


Simultaneous single-molecule mapping of protein-DNA interactions and DNA methylation by MAPit.

Pardo CE, Darst RP, Nabilsi NH, Delmas AL, Kladde MP.

Curr Protoc Mol Biol. 2011 Jul;Chapter 21:Unit 21.22. doi: 10.1002/0471142727.mb2122s95.


MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects.

Pardo CE, Carr IM, Hoffman CJ, Darst RP, Markham AF, Bonthron DT, Kladde MP.

Nucleic Acids Res. 2011 Jan;39(1):e5. doi: 10.1093/nar/gkq716. Epub 2010 Oct 19.


Bisulfite sequencing of DNA.

Darst RP, Pardo CE, Ai L, Brown KD, Kladde MP.

Curr Protoc Mol Biol. 2010 Jul;Chapter 7:Unit 7.9.1-17. doi: 10.1002/0471142727.mb0709s91.


SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes.

Dechassa ML, Sabri A, Pondugula S, Kassabov SR, Chatterjee N, Kladde MP, Bartholomew B.

Mol Cell. 2010 May 28;38(4):590-602. doi: 10.1016/j.molcel.2010.02.040.


Coupling phosphate homeostasis to cell cycle-specific transcription: mitotic activation of Saccharomyces cerevisiae PHO5 by Mcm1 and Forkhead proteins.

Pondugula S, Neef DW, Voth WP, Darst RP, Dhasarathy A, Reynolds MM, Takahata S, Stillman DJ, Kladde MP.

Mol Cell Biol. 2009 Sep;29(18):4891-905. doi: 10.1128/MCB.00222-09. Epub 2009 Jul 13.


DNA methyltransferase probing of chromatin structure within populations and on single molecules.

Pardo C, Hoose SA, Pondugula S, Kladde MP.

Methods Mol Biol. 2009;523:41-65. doi: 10.1007/978-1-59745-190-1_4.


Single-molecule analysis of chromatin: changing the view of genomes one molecule at a time.

Pondugula S, Kladde MP.

J Cell Biochem. 2008 Oct 1;105(2):330-7. doi: 10.1002/jcb.21849. Review.


Single-molecule and population probing of chromatin structure using DNA methyltransferases.

Kilgore JA, Hoose SA, Gustafson TL, Porter W, Kladde MP.

Methods. 2007 Mar;41(3):320-32.


DNA methyltransferase probing of DNA-protein interactions.

Hoose SA, Kladde MP.

Methods Mol Biol. 2006;338:225-44.


Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters.

Jessen WJ, Hoose SA, Kilgore JA, Kladde MP.

Nat Struct Mol Biol. 2006 Mar;13(3):256-63. Epub 2006 Feb 19.


Promoter occupancy is a major determinant of chromatin remodeling enzyme requirements.

Dhasarathy A, Kladde MP.

Mol Cell Biol. 2005 Apr;25(7):2698-707. Erratum in: Mol Cell Biol. 2006 Jan;26(1):388.


Conserved properties of HP1(Hsalpha).

Norwood LE, Grade SK, Cryderman DE, Hines KA, Furiasse N, Toro R, Li Y, Dhasarathy A, Kladde MP, Hendrix MJ, Kirschmann DA, Wallrath LL.

Gene. 2004 Jul 7;336(1):37-46.


Mapping chromatin structure in vivo using DNA methyltransferases.

Jessen WJ, Dhasarathy A, Hoose SA, Carvin CD, Risinger AL, Kladde MP.

Methods. 2004 May;33(1):68-80.


Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins.

Carvin CD, Parr RD, Kladde MP.

Nucleic Acids Res. 2003 Nov 15;31(22):6493-501.


Targeted cytosine methylation for in vivo detection of protein-DNA interactions.

Carvin CD, Dhasarathy A, Friesenhahn LB, Jessen WJ, Kladde MP.

Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7743-8. Epub 2003 Jun 13.


Transcriptional activation of deoxyribonucleic acid polymerase alpha gene expression in MCF-7 cells by 17 beta-estradiol.

Samudio I, Vyhlidal C, Wang F, Stoner M, Chen I, Kladde M, Barhoumi R, Burghardt R, Safe S.

Endocrinology. 2001 Mar;142(3):1000-8.


DNA methyltransferases as probes for chromatin structure in yeast.

Kladde MP, Xu M, Simpson RT.

Methods Mol Biol. 1999;119:395-416. Review. No abstract available.


Mechanisms of transcriptional activation of bcl-2 gene expression by 17beta-estradiol in breast cancer cells.

Dong L, Wang W, Wang F, Stoner M, Reed JC, Harigai M, Samudio I, Kladde MP, Vyhlidal C, Safe S.

J Biol Chem. 1999 Nov 5;274(45):32099-107.


Transcriptional activation of c-fos protooncogene by 17beta-estradiol: mechanism of aryl hydrocarbon receptor-mediated inhibition.

Duan R, Porter W, Samudio I, Vyhlidal C, Kladde M, Safe S.

Mol Endocrinol. 1999 Sep;13(9):1511-21.


DNA methyltransferases as probes of chromatin structure in vivo.

Kladde MP, Xu M, Simpson RT.

Methods Enzymol. 1999;304:431-47. No abstract available.


Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC.

Xu M, Kladde MP, Van Etten JL, Simpson RT.

Nucleic Acids Res. 1998 Sep 1;26(17):3961-6.


Rapid detection of functional expression of C-5-DNA methyltransferases in yeast.

Kladde MP, Simpson RT.

Nucleic Acids Res. 1998 Mar 1;26(5):1354-5.


Effects of Sin- versions of histone H4 on yeast chromatin structure and function.

Wechser MA, Kladde MP, Alfieri JA, Peterson CL.

EMBO J. 1997 Apr 15;16(8):2086-95.


Chromatin structure mapping in vivo using methyltransferases.

Kladde MP, Simpson RT.

Methods Enzymol. 1996;274:214-33. No abstract available.


The non-B-DNA structure of d(CA/TG)n differs from that of Z-DNA.

Kladde MP, Kohwi Y, Kohwi-Shigematsu T, Gorski J.

Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1898-902.


Positioned nucleosomes inhibit Dam methylation in vivo.

Kladde MP, Simpson RT.

Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1361-5.

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