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Publications indexed to the term Nucleosomes

FacultyTitle
1A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA. (Doebley AL, Ko M, Liao H, Cruikshank AE, Santos K, Kikawa C, Hiatt JB, Patton RD, De Sarkar N, Collier KA, Hoge ACH, Chen K, Zimmer A, Weber ZT, Adil M, Reichel JB, Polak P, Adalsteinsson VA, Nelson PS, MacPherson D, Parsons HA, Stover DG, Ha G) Nat Commun 2022 Dec 03;13(1):7475       18 Citations
1Nucleosome Core Particle Reconstitution with Recombinant Histones and Widom 601 DNA. (Hammonds EF, Morrison EA) Methods Mol Biol 2023;2599:177-190       1 Citation
1Preparation of Recombinant Histones and Widom 601 DNA for Reconstitution of Nucleosome Core Particles. (Paintsil EA, Morrison EA) Methods Mol Biol 2023;2599:163-175       3 Citations
1Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes. (De Sarkar N, Patton RD, Doebley AL, Hanratty B, Adil M, Kreitzman AJ, Sarthy JF, Ko M, Brahma S, Meers MP, Janssens DH, Ang LS, Coleman IM, Bose A, Dumpit RF, Lucas JM, Nunez TA, Nguyen HM, McClure HM, Pritchard CC, Schweizer MT, Morrissey C, Choudhury AD, Baca SC, Berchuck JE, Freedman ML, Ahmad K, Haffner MC, Montgomery RB, Corey E, Henikoff S, Nelson PS, Ha G) Cancer Discov 2023 Mar 01;13(3):632-653       9 Citations
1Dynamic nucleosome landscape elicits a noncanonical GATA2 pioneer model. (Li T, Liu Q, Chen Z, Fang K, Huang F, Fu X, Wang Q, Jin VX) Nat Commun 2022 Jun 07;13(1):3145       2 Citations
2Histone H3 and H4 tails play an important role in nucleosome phase separation. (Hammonds EF, Harwig MC, Paintsil EA, Tillison EA, Hill RB, Morrison EA) Biophys Chem 2022 Apr;283:106767       3 Citations
1NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality. (Fang K, Li T, Huang Y, Jin VX) Genome Biol 2021 Aug 26;22(1):250       3 Citations
6Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1-like (DOT1L) and partnering complexes involved in leukemogenesis. (Stodola TJ, Chi YI, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R) Proteins 2022 Jan;90(1):282-298       2 Citations
1Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility. (Morrison EA, Baweja L, Poirier MG, Wereszczynski J, Musselman CA) Nucleic Acids Res 2021 May 07;49(8):4750-4767       26 Citations
1GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder. (Shieh C, Jones N, Vanle B, Au M, Huang AY, Silva APG, Lee H, Douine ED, Otero MG, Choi A, Grand K, Taff IP, Delgado MR, Hajianpour MJ, Seeley A, Rohena L, Vernon H, Gripp KW, Vergano SA, Mahida S, Naidu S, Sousa AB, Wain KE, Challman TD, Beek G, Basel D, Ranells J, Smith R, Yusupov R, Freckmann ML, Ohden L, Davis-Keppen L, Chitayat D, Dowling JJ, Finkel R, Dauber A, Spillmann R, Pena LDM, Undiagnosed Diseases Network, Metcalfe K, Splitt M, Lachlan K, McKee SA, Hurst J, Fitzpatrick DR, Morton JEV, Cox H, Venkateswaran S, Young JI, Marsh ED, Nelson SF, Martinez JA, Graham JM Jr, Kini U, Mackay JP, Pierson TM) Genet Med 2020 May;22(5):878-888       21 Citations
1A CHAF1B-Dependent Molecular Switch in Hematopoiesis and Leukemia Pathogenesis. (Volk A, Liang K, Suraneni P, Li X, Zhao J, Bulic M, Marshall S, Pulakanti K, Malinge S, Taub J, Ge Y, Rao S, Bartom E, Shilatifard A, Crispino JD) Cancer Cell 2018 Nov 12;34(5):707-723.e7       51 Citations
2Cyclin-dependent kinase 1 (CDK1) and CDK2 have opposing roles in regulating interactions of splicing factor 3B1 with chromatin. (Murthy T, Bluemn T, Gupta AK, Reimer M Jr, Rao S, Pillai MM, Minella AC) J Biol Chem 2018 Jun 29;293(26):10220-10234       11 Citations
1The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome. (Morrison EA, Bowerman S, Sylvers KL, Wereszczynski J, Musselman CA) Elife 2018 Apr 12;7       88 Citations
2Metabolically Derived Lysine Acylations and Neighboring Modifications Tune the Binding of the BET Bromodomains to Histone H4. (Olp MD, Zhu N, Smith BC) Biochemistry 2017 Oct 17;56(41):5485-5495       19 Citations
1DNA binding drives the association of BRG1/hBRM bromodomains with nucleosomes. (Morrison EA, Sanchez JC, Ronan JL, Farrell DP, Varzavand K, Johnson JK, Gu BX, Crabtree GR, Musselman CA) Nat Commun 2017 Jul 14;8:16080       51 Citations
1Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. (Ye Z, Chen Z, Sunkel B, Frietze S, Huang TH, Wang Q, Jin VX) Nucleic Acids Res 2016 Sep 19;44(16):7540-54       11 Citations
2The Triple-Code Model for Pancreatic Cancer: Cross Talk Among Genetics, Epigenetics, and Nuclear Structure. (Lomberk GA, Urrutia R) Surg Clin North Am 2015 Oct;95(5):935-52       18 Citations
1IUGR increases chromatin-remodeling factor Brg1 expression and binding to GR exon 1.7 promoter in newborn male rat hippocampus. (Ke X, McKnight RA, Gracey Maniar LE, Sun Y, Callaway CW, Majnik A, Lane RH, Cohen SS) Am J Physiol Regul Integr Comp Physiol 2015 Jul 15;309(2):R119-27       7 Citations
1Re-evaluation of the role of calcium homeostasis endoplasmic reticulum protein (CHERP) in cellular calcium signaling. (Lin-Moshier Y, Sebastian PJ, Higgins L, Sampson ND, Hewitt JE, Marchant JS) J Biol Chem 2013 Jan 04;288(1):355-67       74 Citations
1Stable chromatin binding prevents FoxA acetylation, preserving FoxA chromatin remodeling. (Kohler S, Cirillo LA) J Biol Chem 2010 Jan 01;285(1):464-72       26 Citations
1Acetylation curtails nucleosome binding, not stable nucleosome remodeling, by FoxO1. (Hatta M, Liu F, Cirillo LA) Biochem Biophys Res Commun 2009 Feb 20;379(4):1005-8       25 Citations
1HMGN1 modulates estrogen-mediated transcriptional activation through interactions with specific DNA-binding transcription factors. (Zhu N, Hansen U) Mol Cell Biol 2007 Dec;27(24):8859-73       21 Citations
1Chromatin opening and stable perturbation of core histone:DNA contacts by FoxO1. (Hatta M, Cirillo LA) J Biol Chem 2007 Dec 07;282(49):35583-93       103 Citations
1Integrase-specific enhancement and suppression of retroviral DNA integration by compacted chromatin structure in vitro. (Taganov KD, Cuesta I, Daniel R, Cirillo LA, Katz RA, Zaret KS, Skalka AM) J Virol 2004 Jun;78(11):5848-55       49 Citations
1Preparation of defined mononucleosomes, dinucleosomes, and nucleosome arrays in vitro and analysis of transcription factor binding. (Cirillo LA, Zaret KS) Methods Enzymol 2004;375:131-58       8 Citations
1The CBP bromodomain and nucleosome targeting are required for Zta-directed nucleosome acetylation and transcription activation. (Deng Z, Chen CJ, Chamberlin M, Lu F, Blobel GA, Speicher D, Cirillo LA, Zaret KS, Lieberman PM) Mol Cell Biol 2003 Apr;23(8):2633-44       43 Citations
1Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. (Cirillo LA, Lin FR, Cuesta I, Friedman D, Jarnik M, Zaret KS) Mol Cell 2002 Feb;9(2):279-89       924 Citations
1An early developmental transcription factor complex that is more stable on nucleosome core particles than on free DNA. (Cirillo LA, Zaret KS) Mol Cell 1999 Dec;4(6):961-9       192 Citations
1Binding of the winged-helix transcription factor HNF3 to a linker histone site on the nucleosome. (Cirillo LA, McPherson CE, Bossard P, Stevens K, Cherian S, Shim EY, Clark KL, Burley SK, Zaret KS) EMBO J 1998 Jan 02;17(1):244-54       315 Citations