Suresh Cuddapah

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Suresh Cuddapah

Assistant Professor;
Departments of Environmental Medicine and Biochemistry and Molecular Pharmacology

Contact Info

57 Old Forge Road
Floor 2 Room 258
Sterling Forest
Tuxedo, NY 10987

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Research Summary

The eukaryotic genome is organized into higher order chromatin structures. The structure of chromatin and DNA accessibility is regulated, in part, by epigenetic features such as DNA methylation and histone modifications. The goal of our research is to understand the epigenetic regulation of chromatin structure and gene expression programs during differentiation and disease manifestation. We are particularly interested in understanding the causes for aberrant silencing of tumor suppressor genes, which contribute to malignancies. Understanding how and why certain genes are turned off will help unravel the disease mechanism. Aberration in the chromatin structure is one of the causes for mis-regulation of gene expression. Currently, we are investigating the role of transcription factors and epigenetic features of the genome that are involved in maintaining normal chromatin architecture and the anomalies that lead to aberrant gene silencing. In addition, we are also interested in understanding the alterations in epigenetic regulation due to pathogenesis, which in turn may favor disease progression.

Research Interests

Epigenetic regulation of chromatin structure and gene expression

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All data from NYU Health Sciences Library Faculty Bibliography — -


Epigenetic dysregulation by nickel through repressive chromatin domain disruption
Jose, Cynthia C; Xu, Beisi; Jagannathan, Lakshmanan; Trac, Candi; Mallela, Ramya K; Hattori, Takamitsu; Lai, Darson; Koide, Shohei; Schones, Dustin E; Cuddapah, Suresh
2014 Sep;:531-531, Proceedings of the National Academy of Sciences of the United States of America (PNAS)
— id: 1259292, year: 2014, vol: , page: 531, stat: Journal Article,

Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes
Lhoumaud, Priscillia; Hennion, Magali; Gamot, Adrien; Cuddapah, Suresh; Queille, Sophie; Liang, Jun; Micas, Gael; Morillon, Pauline; Urbach, Serge; Bouchez, Olivier; Severac, Dany; Emberly, Eldon; Zhao, Keji; Cuvier, Olivier
2014 Jun;:10042-10071, EMBO journal
— id: 1033612, year: 2014, vol: , page: 10042, stat: Journal Article,

Chromatin immunoprecipitation indirect peaks highlight long-range interactions of insulator proteins and Pol II pausing
Liang, Jun; Lacroix, Laurent; Gamot, Adrien; Cuddapah, Suresh; Queille, Sophie; Lhoumaud, Priscillia; Lepetit, Pierre; Martin, Pascal G P; Vogelmann, Jutta; Court, Franck; Hennion, Magali; Micas, Gael; Urbach, Serge; Bouchez, Olivier; Nollmann, Marcelo; Zhao, Keji; Emberly, Eldon; Cuvier, Olivier
2014 Feb;53(4):672-681, Molecular cell
— id: 978582, year: 2014, vol: 53, page: 672, stat: Journal Article,

A novel human polycomb binding site acts as a functional polycomb response element in Drosophila
Cuddapah, Suresh; Roh, Tae-Young; Cui, Kairong; Jose, Cynthia C; Fuller, Margaret T; Zhao, Keji; Chen, Xin
2012 ;7(5):e36365-e36365 e36365, PLoS one
— id: 166805, year: 2012, vol: 7, page: e36365, stat: Journal Article,

Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
Freudenberg, Johannes M; Ghosh, Swati; Lackford, Brad L; Yellaboina, Sailu; Zheng, Xiaofeng; Li, Ruifang; Cuddapah, Suresh; Wade, Paul A; Hu, Guang; Jothi, Raja
2012 Apr;40(8):3364-3377, Nucleic acids research
— id: 165603, year: 2012, vol: 40, page: 3364, stat: Journal Article,

Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions
Cuddapah, Suresh; Schones, Dustin E; Cui, Kairong; Roh, Tae-Young; Barski, Artem; Wei, Gang; Rochman, Mark; Bustin, Michael; Zhao, Keji
2011 Feb;31(4):700-709, Molecular & cellular biology
— id: 232472, year: 2011, vol: 31, page: 700, stat: Journal Article,

Genome-wide approaches to studying yeast chromatin modifications
Schones, Dustin E; Cui, Kairong; Cuddapah, Suresh
2011 ;759:61-71, Methods in molecular biology
— id: 232462, year: 2011, vol: 759, page: 61, stat: Journal Article,

Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes
Barski, Artem; Chepelev, Iouri; Liko, Dritan; Cuddapah, Suresh; Fleming, Alastair B; Birch, Joanna; Cui, Kairong; White, Robert J; Zhao, Keji
2010 May;17(5):629-634, Nature structural & molecular biology
— id: 112084, year: 2010, vol: 17, page: 629, stat: Journal Article,

Epigenomics of T cell activation, differentiation, and memory
Cuddapah, Suresh; Barski, Artem; Zhao, Keji
2010 Jun;22(3):341-347, Current opinion in immunology
— id: 112085, year: 2010, vol: 22, page: 341, stat: Journal Article,

Chromatin poises miRNA- and protein-coding genes for expression
Barski, Artem; Jothi, Raja; Cuddapah, Suresh; Cui, Kairong; Roh, Tae-Young; Schones, Dustin E; Zhao, Keji
2009 Oct;19(10):1742-1751, Genome research
— id: 112087, year: 2009, vol: 19, page: 1742, stat: Journal Article,

Native chromatin preparation and Illumina/Solexa library construction
Cuddapah, Suresh; Barski, Artem; Cui, Kairong; Schones, Dustin E; Wang, Zhibin; Wei, Gang; Zhao, Keji
2009 Jun;2009(6):pdb.prot5237-pdb.prot5237, Cold Spring Harbor protocols
— id: 112086, year: 2009, vol: 2009, page: pdb.prot5237, stat: Journal Article,

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
Cuddapah, Suresh; Jothi, Raja; Schones, Dustin E; Roh, Tae-Young; Cui, Kairong; Zhao, Keji
2009 Jan;19(1):24-32, Genome research
— id: 112088, year: 2009, vol: 19, page: 24, stat: Journal Article,

Transcriptional enhancer factor 1 (TEF-1/TEAD1) mediates activation of IFITM3 gene by BRGl
Cuddapah, Suresh; Cui, Kairong; Zhao, Keji
2008 Jan 23;582(2):391-397, FEBS letters
— id: 112092, year: 2008, vol: 582, page: 391, stat: Journal Article,

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
Jothi, Raja; Cuddapah, Suresh; Barski, Artem; Cui, Kairong; Zhao, Keji
2008 Sep;36(16):5221-5231, Nucleic acids research
— id: 112089, year: 2008, vol: 36, page: 5221, stat: Journal Article,

Dynamic regulation of nucleosome positioning in the human genome
Schones, Dustin E; Cui, Kairong; Cuddapah, Suresh; Roh, Tae-Young; Barski, Artem; Wang, Zhibin; Wei, Gang; Zhao, Keji
2008 Mar 7;132(5):887-898, Cell
— id: 112091, year: 2008, vol: 132, page: 887, stat: Journal Article,

Combinatorial patterns of histone acetylations and methylations in the human genome
Wang, Zhibin; Zang, Chongzhi; Rosenfeld, Jeffrey A; Schones, Dustin E; Barski, Artem; Cuddapah, Suresh; Cui, Kairong; Roh, Tae-Young; Peng, Weiqun; Zhang, Michael Q; Zhao, Keji
2008 Jul;40(7):897-903, Nature genetics
— id: 112090, year: 2008, vol: 40, page: 897, stat: Journal Article,

High-resolution profiling of histone methylations in the human genome
Barski, Artem; Cuddapah, Suresh; Cui, Kairong; Roh, Tae-Young; Schones, Dustin E; Wang, Zhibin; Wei, Gang; Chepelev, Iouri; Zhao, Keji
2007 May 18;129(4):823-837, Cell
— id: 112093, year: 2007, vol: 129, page: 823, stat: Journal Article,

Genome-wide mapping of histone modifications by GMAT
Cuddapah, Suresh; Zhao, Keji
2006 ;23:93-103, Biotechnology & genetic engineering reviews
— id: 232482, year: 2006, vol: 23, page: 93, stat: Journal Article,

The genomic landscape of histone modifications in human T cells
Roh, Tae-Young; Cuddapah, Suresh; Cui, Kairong; Zhao, Keji
2006 Oct 24;103(43):15782-15787, Proceedings of the National Academy of Sciences of the United States of America (PNAS)
— id: 112094, year: 2006, vol: 103, page: 15782, stat: Journal Article,

Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping
Roh, Tae-Young; Cuddapah, Suresh; Zhao, Keji
2005 Mar 1;19(5):542-552, Genes & development
— id: 112095, year: 2005, vol: 19, page: 542, stat: Journal Article,