Preprints
Aging leads to DNA methylation alterations associated with loss of lineage fidelity and breast cancer in mammary luminal epithelial cells
Parijat Senapati, Masaru Miyano, Rosalyn W. Sayaman, Mudaser Basam, Candi Trac, Amy Leung, Mark A. LaBarge, Dustin E. Schones
bioRxiv 2020.06.26.170043; doi: https://doi.org/10.1101/2020.06.26.170043
Mechanisms regulating interindividual epigenetic variability at transposable elements
Kevin R. Costello, Amy Leung, Candi Trac, Michael Lee, Mudasar Basam, J. Andrew Pospisilik, Dustin E. Schones
bioRxiv 2021.06.01.446659; doi: https://doi.org/10.1101/2021.06.01.446659
Regulatory diversity contributes to a divergent transcriptional response to dietary changes in mammals
Kevin R. Costello, Heon Shin, Candi Trac, Oleg Varlamov, Dustin E. Schones
bioRxiv 2020.11.01.364232; doi: https://doi.org/10.1101/2020.11.01.364232
Epigenetic changes with age primes mammary luminal epithelia for cancer initiation
Rosalyn W. Sayaman, Masaru Miyano, Parijat Senapati, Sundus Shalabi, Arrianna Zirbes, Michael E. Todhunter, Victoria Seewaldt, Susan L. Neuhausen, Martha R. Stampfer, Dustin E. Schones, Mark A. LaBarge
bioRxiv 2021.02.12.430777; doi: https://doi.org/10.1101/2021.02.12.430777
Dietary glutamine supplementation suppresses epigenetically-activated oncogenic pathways to inhibit melanoma tumour growth. Ishak Gabra MB, Yang Y, Li H,Senapati P, Hanse EA, Lowman XH, Tran TQ, Zhang L, Doan LT, Xu X, Schones DE, Fruman DA, Kong M. Nat Commun. 2020 Jul 3;11(1):3326
Hyperinsulinemia promotes aberrant histone acetylation in triple-negative breast cancer. Senapati P, Kato H, Lee M, Leung A, Thai C, Sanchez A, Gallagher EJ, LeRoith D, Seewaldt VL, Ann DK, Schones DE. Epigenetics Chromatin. 2019 Jul 17;12(1):44.
Arginine starvation kills tumor cells through aspartate exhaustion and mitochondrial dysfunction. Cheng CT, Qi Y, Wang YC, Chi KK, Chung Y, Ouyang C, Chen YR, Oh ME, Sheng X, Tang Y, Liu YR, Lin HH, Kuo CY, Schones D, Vidal CM, Chu JC, Wang HJ, Chen YH, Miller KM, Chu P, Yen Y, Jiang L, Kung HJ, Ann DK. Commun Biol. 2018 Oct 26;1:178.
LTRs activated by Epstein-Barr virus-induced transformation of B cells alter the transcriptome. Leung A, Trac C, Kato H, Costello KR, Chen Z, Natarajan R, Schones DE. Genome Res. 2018 Dec;28(12):1791-1798.
Diabetes Mellitus-Induced Long Noncoding RNA Dnm3os Regulates Macrophage Functions and Inflammation via Nuclear Mechanisms. Das S, Reddy MA, Senapati P, Stapleton K, Lanting L, Wang M, Amaram V, Ganguly R, Zhang L, Devaraj S, Schones DE, Natarajan R. Arterioscler Thromb Vasc Biol. 2018 Aug;38(8):1806-1820.
Estrogens and selective estrogen receptor modulators differentially antagonize Runx2 in ST2 mesenchymal progenitor cells. Amzaleg Y, Ji J, Kittivanichkul D, E Törnqvist A, Windahl S, Sabag E, Khalid AB, Sternberg H, West M, Katzenellenbogen JA, Krum SA, Chimge NO, Schones DE, Gabet Y, Ohlsson C, Frenkel B. J Steroid Biochem Mol Biol. 2018 Oct;183:10-17.
JMJD1B Demethylates H4R3me2s and H3K9me2 to Facilitate Gene Expression for Development of Hematopoietic Stem and Progenitor Cells. Li S, Ali S, Duan X, Liu S, Du J, Liu C, Dai H, Zhou M, Zhou L, Yang L, Chu P, Li L, Bhatia R, Schones DE, Wu X, Xu H, Hua Y, Guo Z, Yang Y, Zheng L, Shen B. Cell Rep. 2018 Apr 10;23(2):389-403.
Chromatin modifications in metabolic disease: Potential mediators of long-term disease risk. Costello KR, Schones DE. Wiley Interdiscip Rev Syst Biol Med. 2018 Jul;10(4):e1416
Regulation of angiotensin II actions by enhancers and super-enhancers in vascular smooth muscle cells. Das S, Senapati P, Chen Z, Reddy MA, Ganguly R, Lanting L, Mandi V, Bansal A, Leung A, Zhang S, Jia Y, Wu X, Schones DE, Natarajan R. Nat Commun. 2017 Nov 13;8(1):1467.
Vertical sleeve gastrectomy reverses diet-induced gene-regulatory changes impacting lipid metabolism. Du J, Tian J, Ding L, Trac C, Xia B, Sun S, Schones DE†, Huang W† († Joint Corresponding Authors). Sci Rep. 2017 Jul 13;7(1):5274.
Transgenerational programming of longevity through E(z)-mediated histone H3K27 trimethylation in Drosophila. Xia B, Gerstin E, Schones DE†, Huang W†, Steven de Belle J† († Joint Corresponding Authors). Aging (Albany NY). 2016 Nov 25;8(11):2988-3008.
Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation. Pan M, Reid MA, Lowman XH, Kulkarni RP, Tran TQ, Liu X, Yang Y, Hernandez-Davies JE, Rosales KK, Li H, Hugo W, Song C, Xu X, Schones DE, Ann DK, Gradinaru V, Lo RS, Locasale JW, Kong M. Nat Cell Biol. 2016 Oct;18(10):1090-101.
Chromatin variation associated with liver metabolism is mediated by transposable elements. Du J, Leung A, Trac C, Lee M, Parks BW, Lusis AJ, Natarajan R, Schones DE. Epigenetics Chromatin. 2016 Jul 8;9:28. * Highlighted in Nature Reviews Genetics, “Chromatin variation underLINEd“
Vertical sleeve gastrectomy activates GPBAR-1/TGR5 to sustain weight loss, improve fatty liver, and remit insulin resistance in mice. Ding L, Sousa KM, Jin L, Dong B, Kim BW, Ramirez R, Xiao Z, Gu Y, Yang Q, Wang J, Yu D, Pigazzi A, Schones D, Yang L, Moore D, Wang Z, Huang W. Hepatology. 2016 Sep;64(3):760-73.
Epigenomic profiling reveals an association between persistence of DNA methylation and metabolic memory in the DCCT/EDIC type 1 diabetes cohort. Chen Z, Miao F, Paterson AD, Lachin JM, Zhang L, Schones DE, Wu X, Wang J, Tompkins JD, Genuth S, Braffett BH, Riggs AD; DCCT/EDIC Research Group, Natarajan R. Proc Natl Acad Sci U S A. 2016 May 24;113(21):E3002-11.
Persistent Chromatin Modifications Induced by High Fat Diet. Leung A, Trac C, Du J, Natarajan R, Schones DE. J Biol Chem. 2016 May 13;291(20):10446-55. * Selected as “Paper of the Week” at J Biol Chem * Author Profile
RUNX1 prevents oestrogen-mediated AXIN1 suppression and β-catenin activation in ER-positive breast cancer. Chimge NO, Little GH, Baniwal SK, Adisetiyo H, Xie Y, Zhang T, O’Laughlin A, Liu ZY, Ulrich P, Martin A, Mhawech-Fauceglia P, Ellis MJ, Tripathy D, Groshen S, Liang C, Li Z, Schones DE, Frenkel B. Nat Commun. 2016 Feb 26;7:10751.
Chromatin Modifications Associated With Diabetes and Obesity. Schones DE, Leung A, Natarajan R. Arterioscler Thromb Vasc Biol. 2015 Jul;35(7):1557-61
Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells. Li Z, Dai H, Martos SN, Xu B, Gao Y, Li T, Zhu G, Schones DE, Wang Z. Genome Biol. 2015 Jun 2;16:115.
Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Jose CC, Xu B, Jagannathan L, Trac C, Mallela RK, Hattori T, Lai D, Koide S, Schones DE†, Cuddapah S† († Joint Corresponding Authors) Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14631-6.
G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors. Schones DE†, Chen X, Trac C, Setten R, Paddison PJ† († Joint Corresponding Authors). Epigenetics Chromatin. 2014 Sep 10;7:23.
Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. Leung A, Parks BW, Du J, Trac C, Setten R, Chen Y, Brown K, Lusis AJ, Natarajan R, Schones DE. J Biol Chem. 2014 Aug 22;289(34):23557-67.
Differential effects of RUNX2 on the androgen receptor in prostate cancer: synergistic stimulation of a gene set exemplified by SNAI2 and subsequent invasiveness. Little GH, Baniwal SK, Adisetiyo H, Groshen S, Chimge NO, Kim SY, Khalid O, Hawes D, Jones JO, Pinski J, Schones DE, Frenkel B. Cancer Res. 2014 May 15;74(10):2857-68.
The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter-proximal nucleosomes. Byeon B, Wang W, Barski A, Ranallo RT, Bao K, Schones DE, Zhao K, Wu C, Wu WH. J Biol Chem. 2013 Aug 9;288(32):23182-93.
Novel long noncoding RNAs are regulated by angiotensin II in vascular smooth muscle cells. Leung A, Trac C, Jin W, Lanting L, Akbany A, Sætrom P, Schones DE†, Natarajan R† († Joint Corresponding Authors). Circ Res. 2013 Jul 19;113(3):266-78.
High mobility group protein N5 (HMGN5) and lamina-associated polypeptide 2α (LAP2α) interact and reciprocally affect their genome-wide chromatin organization. Zhang S*, Schones DE*, Malicet C, Rochman M, Zhou M, Foisner R, Bustin M (* Equal contributing first authors). J Biol Chem. 2013 Jun 21;288(25):18104-9
A structural-based strategy for recognition of transcription factor binding sites. Xu B, Schones DE, Wang Y, Liang H, Li G. PLoS One. 2013;8(1):e52460.
Using epigenetic mechanisms to understand the impact of common disease causing alleles. Leung A, Schones DE, Natarajan R. Curr Opin Immunol. 2012 Oct;24(5):558-63.
The chromatin-binding protein HMGN1 regulates the expression of methyl CpG-binding protein 2 (MECP2) and affects the behavior of mice. Abuhatzira L, Shamir A, Schones DE, Schäffer AA, Bustin M. J Biol Chem. 2011 Dec 9;286(49):42051-62.
Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Hu G*, Schones DE*, Cui K, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo NP, Huang S, Zhao K (* Equal contributing first authors). Genome Res. 2011 Oct;21(10):1650-8.
Genome-wide approaches to studying yeast chromatin modifications. Schones DE, Cui K, Cuddapah S. Methods Mol Biol. 2011;759:61-71.
Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions. Cuddapah S*, Schones DE*, Cui K, Roh TY, Barski A, Wei G, Rochman M, Bustin M, Zhao K (* Equal contributing first authors). Mol Cell Biol. 2011 Feb;31(4):700-9.
Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis. Gan Q, Schones DE, Ho Eun S, Wei G, Cui K, Zhao K, Chen X. Genome Biol. 2010;11(4):R42.
Chromatin poises miRNA- and protein-coding genes for expression. Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K. Genome Res. 2009 Oct;19(10):1742-51.
Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K. Cell. 2009 Sep 4;138(5):1019-31. *Faculty of 1000 Selection
Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L. PLoS One. 2009 Aug 11;4(8):e6589.
Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells. Araki Y, Wang Z, Zang C, Wood WH 3rd, Schones D, Cui K, Roh TY, Lhotsky B, Wersto RP, Peng W, Becker KG, Zhao K, Weng NP. Immunity. 2009 Jun 19;30(6):912-25. *Faculty of 1000 Selection
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. Bioinformatics. 2009 Aug 1;25(15):1952-8.
Native chromatin preparation and Illumina/Solexa library construction. Cuddapah S, Barski A, Cui K, Schones DE, Wang Z, Wei G, Zhao K. Cold Spring Harb Protoc. 2009 Jun;2009(6):pdb.prot5237.
Determination of enriched histone modifications in non-genic portions of the human genome. Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. BMC Genomics. 2009 Mar 31;10:143.
Characterization of human epigenomes. Wang Z, Schones DE, Zhao K. Curr Opin Genet Dev. 2009 Apr;19(2):127-34.
Down-regulation of Gfi-1 expression by TGF-beta is important for differentiation of Th17 and CD103+ inducible regulatory T cells. Zhu J, Davidson TS, Wei G, Jankovic D, Cui K, Schones DE, Guo L, Zhao K, Shevach EM, Paul WE. J Exp Med. 2009 Feb 16;206(2):329-41.
Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, Schones DE, Peng W, Sun HW, Paul WE, O’Shea JJ, Zhao K. Immunity. 2009 Jan 16;30(1):155-67. *Faculty of 1000 Selection
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K. Cell Stem Cell. 2009 Jan 9;4(1):80-93.
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. Genome Res. 2009 Jan;19(1):24-32. *Faculty of 1000 Selection
Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression. Liao W, Schones DE, Oh J, Cui Y, Cui K, Roh TY, Zhao K, Leonard WJ. Nat Immunol. 2008 Nov;9(11):1288-96.
Combinatorial patterns of histone acetylations and methylations in the human genome. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Nat Genet. 2008 Jul;40(7):897-903. *Faculty of 1000 Selection
Dynamic regulation of nucleosome positioning in the human genome. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Cell. 2008 Mar 7;132(5):887-98. *Faculty of 1000 Selection
Genome-wide approaches to studying chromatin modifications. Schones DE, Zhao K. Nat Rev Genet. 2008 Mar;9(3):179-91.
Interferon regulatory factors are transcriptional regulators of adipogenesis. Eguchi J, Yan QW, Schones DE, Kamal M, Hsu CH, Zhang MQ, Crawford GE, Rosen ED. Cell Metab. 2008 Jan;7(1):86-94.
Neural potential of a stem cell population in the hair follicle. Mignone JL, Roig-Lopez JL, Fedtsova N, Schones DE, Manganas LN, Maletic-Savatic M, Keyes WM, Mills AA, Gleiberman A, Zhang MQ, Enikolopov G. Cell Cycle. 2007 Sep 1;6(17):2161-70.
High-resolution profiling of histone methylations in the human genome. Barski A*, Cuddapah S*, Cui K*, Roh TY*, Schones DE*, Wang Z*, Wei G*, Chepelev I, Zhao K (* Equal contributing first authors) Cell. 2007 May 18;129(4):823-37. *Faculty of 1000 Selection *Ranked No 3 of “hottest biology papers of 2009” by The Scientist
Statistical significance of cis-regulatory modules. Schones DE, Smith AD, Zhang MQ. BMC Bioinformatics. 2007 Jan 22;8:19.
Similarity of position frequency matrices for transcription factor binding sites. Schones DE, Sumazin P, Zhang MQ. Bioinformatics. 2005 Feb 1;21(3):307-13.
THE SCHONES LAB 