Now showing items 1-15 of 15

    • Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells 

      Luyten, Annouck; Zang, Chongzhi; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (Cold Spring Harbor Laboratory Press, 2014)
      Tissues may adopt diverse strategies to establish specific transcriptional programs in daughter lineages. In intestinal crypts, enhancers for genes expressed in both major cell types appear broadly permissive in stem and ...
    • The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis 

      Pomerantz, Mark M.; Li, Fugen; Takeda, David; Lenci, Romina; Chonkar, Apurva; Chabot, Matthew; Cejas, Paloma; Vazquez, Francisca; Cook, Jennifer; Shivdasani, Ramesh A.; Bowden, Michaela; Lis, Rosina; Hahn, William C.; Kantoff, Philip W.; Brown, Myles; Loda, Massimo; Long, Henry W.; Freedman, Matthew L. (2015)
      Master transcription factors interact with DNA to establish cell-type identity and to regulate gene expression in mammalian cells1,2. The genome-wide map of these transcription factor binding sites has been termed the ...
    • Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity 

      Kim, Tae-Hee; Li, Fugen; Ferreiro-Neira, Isabel; Ho, Li-Lun; Luyten, Annouck; Nalapareddy, Kodandaramireddy; Long, Henry; Verzi, Michael; Shivdasani, Ramesh A. (2014)
      Cells differentiate when transcription factors (TFs) bind accessible cis-regulatory elements to establish specific gene expression programs. In differentiating embryonic stem (ES) cells, chromatin at lineage-restricted ...
    • Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers 

      Eeckhoute, J.; Lupien, M.; Meyer, Clifford; Verzi, M. P.; Shivdasani, Ramesh Arjun; Liu, Xiaole (Shirley) Shirley; Brown, Myles A. (Cold Spring Harbor Laboratory Press, 2008)
      Selective activity of a specific set of enhancers defines tissue-specific gene transcription. The pioneer factor FOXA1 has been shown to induce functional enhancer competency through chromatin openings. We have previously ...
    • Differentiation-Specific Histone Modifications Reveal Dynamic Chromatin Interactions and Partners for the Intestinal Transcription Factor CDX2 

      Verzi, Michael P.; Shin, Hyunjin; He, H. Hansen; Sulahian, Rita; Meyer, Clifford; Montgomery, Robert K.; Fleet, James C.; Brown, Myles A.; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (Elsevier BV, 2010)
      Cell differentiation requires remodeling of tissue-specific gene loci and activities of key transcriptional regulators, which are recognized for their dominant control over cellular programs. Using epigenomic methods, we ...
    • Essential and Redundant Functions of Caudal Family Proteins in Activating Adult Intestinal Genes 

      Verzi, M. P.; Shin, H.; Ho, L.-L.; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (American Society for Microbiology, 2011)
      Transcription factors that potently induce cell fate often remain expressed in the induced organ throughout life, but their requirements in adults are uncertain and varied. Mechanistically, it is unclear if they activate ...
    • Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis 

      Dulak, A. M.; Schumacher, S. E.; van Lieshout, J.; Imamura, Y.; Fox, Cameron; Shim, B.; Ramos, A. H.; Saksena, G.; Baca, Sylvan Charles; Baselga, J.; Tabernero, J.; Barretina, J.; Enzinger, Peter C.; Corso, G.; Roviello, F.; Lin, Lin; Bandla, S.; Luketich, J. D.; Pennathur, A.; Meyerson, Matthew Langer; Ogino, Shuji; Shivdasani, Ramesh Arjun; Beer, Dennis J; Godfrey, T. E.; Beroukhim, Rameen; Bass, Adam Joel (American Association for Cancer Research (AACR), 2012)
      A more detailed understanding of the somatic genetic events that drive gastrointestinal adenocarcinomas is necessary to improve diagnosis and therapy. Using data from high-density genomic profiling arrays, we conducted an ...
    • Genomic analysis identifies association of Fusobacterium with colorectal carcinoma 

      Kostic, Aleksandar David; Gevers, D.; Pedamallu, Chandra Sekhar; Michaud, Monia; Duke, F.; Earl, A. M.; Ojesina, Akinyemi Ifedapo; Jung, J.; Bass, Adam Joel; Tabernero, J.; Baselga, J.; Liu, C.; Shivdasani, Ramesh Arjun; Ogino, Shuji; Birren, B. W.; Huttenhower, Curtis; Garrett, Wendy S.; Meyerson, Matthew Langer (Cold Spring Harbor Laboratory Press, 2011)
      The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to ...
    • An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer 

      Sulahian, R; Casey, F; Shen, J; Qian, Zhirong; Shin, H; Ogino, Shuji; Weir, Barbara Ann; Vazquez, F; Liu, Xiaole (Shirley) Shirley; Hahn, William Chun; Bass, Adam Joel; Chan, Vivian; Shivdasani, Ramesh Arjun (Springer Nature, 2013)
      Lineage-restricted transcription factors (TFs) are frequently mutated or overexpressed in cancer and contribute toward malignant behaviors, but the molecular bases of their oncogenic properties are largely unknown. Because ...
    • Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding 

      Verzi, M. P.; Shin, H.; San Roman, A. K.; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (American Society for Microbiology, 2012)
      Tissue-specific gene expression requires modulation of nucleosomes, allowing transcription factors to occupy cis elements that are accessible only in selected tissues. Master transcription factors control cell-specific ...
    • NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes 

      Zang, Chongzhi; Luyten, Annouck; Chen, Justina; Liu, X. Shirley; Shivdasani, Ramesh A. (Nature Publishing Group, 2016)
      Mutations in mouse and human Nfe2, Fli1 and Runx1 cause thrombocytopenia. We applied genome-wide chromatin dynamics and ChIP-seq to determine these transcription factors’ (TFs) activities in terminal megakaryocyte (MK) ...
    • Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples 

      Campbell, Catarina D.; Kehoe, Sarah M.; Hatton, Charles; Niu, Lili; Yao, Keluo; Hanna, Megan; Mondal, Chandrani; Luongo, Lauren; Baker, Alissa C.; Philips, Juliet; Goff, Deborah J.; Rubin, Mark A.; Corso, Gianni; Roviello, Franco; MacConaill, Laura Eleanor; Bass, Adam Joel; Davis, Matthew J; Emery, Caroline Margaret; Fiorentino, Michelangelo; Polyak, Kornelia; Chan, Jennifer Ang; Wang, Yufang; Fletcher, Jonathan A.; Santagata, Sandro; Shivdasani, Ramesh Arjun; Kieran, Mark W.; Ligon, Keith Lloyd; Stiles, Charles Dean; Hahn, William C.; Meyerson, Matthew Langer; Garraway, Levi Alexander; Jones, Chris (Public Library of Science, 2009)
      Background: Detection of critical cancer gene mutations in clinical tumor specimens may predict patient outcomes and inform treatment options; however, high-throughput mutation profiling remains underdeveloped as a diagnostic ...
    • SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas 

      Bass, Adam Joel; Watanabe, Hideo; Mermel, Craig; Yu, Soyoung; Perner, Sven; Verhaak, Roel; Kim, So Jeong; Wardwell, Leslie; Tamayo, Pablo; Gat-Viks, Irit; Ramos, Alex H; Woo, Michele S; Weir, Barbara Ann; Getz, Gad A; Beroukhim, Rameen; O, Michael; Dutt, Amit; Rozenblatt-Rosen, Orit; Dziunycz, Piotr; Komisarof, Justin; Chirieac, Lucian Radu; LaFargue, Christopher J; Scheble, Veit; Wilbertz, Theresia; Ma, Changqing; Rao, Shilpa; Nakagawa, Hiroshi; Stairs, Douglas B; Lin, Lin; Giordano, Thomas J; Wagner, Patrick; Minna, John D; Gazdar, Adi F; Zhu, Chang Qi; Brose, Marcia S; Cecconello, Ivan; Jr, Ulysses Ribeiro; Marie, Suely K; Dahl, Olav; Shivdasani, Ramesh Arjun; Tsao, Ming-Sound; Rubin, Mark A; Wong, Kwok-Kin; Regev, Aviv; Hahn, William Chun; Beer, David G; Rustgi, Anil K; Meyerson, Matthew Langer (Springer Nature, 2009)
      Lineage survival oncogenes are activated by somatic DNA alterations in cancers arising from the cell lineages in which these genes play a role in normal development.1,2 Here we show that a peak of genomic amplification on ...
    • The Stem Cell Discovery Engine: An Integrated Repository and Analysis System for Cancer Stem Cell Comparisons 

      Begley, Kimberly; Reilly, Dorothy; McGovern, Ray; Rocca-Sera, Philippe; Maguire, Eamonn; Altschuler, Gabriel M.; Culhane, Aedín C.; Correll, Mick; Sansone, Susanna-Assunta; Ho Sui, Shannan; Chapman, Brad Alan; Hansen, Terah; Sompallae, Ramakrishna Rao; Krivtsov, Andrei V.; Shivdasani, Ramesh Arjun; Armstrong, Scott A.; Hofmann, Oliver Marc; Hide, Winston (Oxford University Press, 2011)
      Mounting evidence suggests that malignant tumors are initiated and maintained by a subpopulation of cancerous cells with biological properties similar to those of normal stem cells. However, descriptions of stem-like gene ...
    • TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions 

      Verzi, M. P.; Hatzis, Phillip Evangelos; Sulahian, R.; Philips, J.; Schuijers, J.; Shin, H.; Freed, E.; Lynch, J. P.; Dang, D. T.; Brown, Myles A.; Clevers, H.; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (Proceedings of the National Academy of Sciences, 2010)
      Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many mammalian tissues, including the intestinal epithelium, where ...