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Thomas G Fazzio PhD

InstitutionUMass Chan Medical School
DepartmentMolecular, Cell and Cancer Biology
AddressUMass Chan Medical School
364 Plantation Street LRB-519
Worcester MA 01605
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionT.H. Chan School of Medicine
    DepartmentMolecular, Cell and Cancer Biology

    InstitutionT.H. Chan School of Medicine
    DepartmentProgram in Molecular Medicine

    InstitutionT.H. Chan School of Medicine
    DepartmentSystems Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentPostbaccalaureate Research Education Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentSystems Computational and Quantitative Biology

    InstitutionUMass Chan Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative Biology

    Collapse Biography 
    Collapse education and training
    University of Utah, Salt Lake City, UT, United StatesBSBiology
    University of Washington, Seattle, WA, United StatesPHDMolecular & Cellular Biology

    Collapse Overview 
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    Academic Information

    Thomas Fazzio received his B.S. degree from the University of Utah in 1997, where he studied the genetics of Vitamin B12 metabolism in Salmonella typhimurium, in the laboratory of John Roth. Tom received his Ph.D. from the University of Washington and Fred Hutchinson Cancer Research Center in 2004 for work on yeast chromatin regulation in the lab of Toshio Tsukiyama. Tom did postdoctoral work on chromatin regulation in stem cells at the University of California, San Francisco in the labs of Barbara Panning and J. Michael Bishop. This work was supported by a postdoctoral fellowship from the Jane Coffin Childs Memorial Fund for Medical Research and a Pathway to Independence Award from the NIH. Tom joined the Program in Gene Function and Expression at the University of Massachusetts Medical School in spring 2010.

    Chromatin Regulation in Stem Cells

    Thomas FazzioIn eukaryotes, relatively large amounts of DNA must be packed into microscopic nuclei within each cell. This is achieved via the formation of highly-organized, yet dynamic chromatin structure in cells. Chromatin affects nuclear processes like gene expression, DNA replication and recombination by several mechanisms, including inhibition of transcription factor binding and localization of genes to transcriptionally active or inactive regions of the nucleus.

    Stem cells – cells that are capable of generating any cell type of a tissue or organism – need to remain developmentally flexible in order to be able to self-renew (generate more stem cells) or differentiate into various somatic cell types. To maintain this flexibility, embryonic stem cells maintain a unique chromatin structure that is unusually dynamic and exhibits an atypical pattern of histone modifications at the regulatory sequences of some developmentally regulated genes. In spite of this, the functions of chromatin structure in regulation of stem cell fate remain largely unknown.

    We are interested in the mechanisms by which chromatin structure and chromatin regulatory proteins impact gene expression, self-renewal and differentiation in stem cells. To study these processes, we utilize an array of molecular, cellular, genetic, biochemical and systems level approaches.

    Chromatin Regulation and Embryonic Stem Cell Self-Renewal

    Chromatin structure in embryonic stem (ES) cells is distinct from differentiated cells. ES cells lack large domains of heterochromatin and have unusual patterns of histone modifications at the regulatory regions of some genes. In addition, the chromatin of ES cells is extremely dynamic, exhibiting rapid exchange of chromatin proteins on and off of DNA. However, the functions of this unusual chromatin structure in ES cell self-renewal and differentiation are mysterious.

    In an RNA-interference (RNAi) screen of most chromatin proteins in mouse, we recently identified a number of chromatin regulatory proteins necessary for ES cell proliferation or self-renewal. However, the targets of these proteins, along with their cellular functions in ES cell self-renewal, remain largely unknown. Currently, we are examining the functions of some of these chromatin regulators, their regulation, and how they fit into the known transcriptional network governing ES cell pluripotency.

    Functions and Regulation of the Tip60-p400 Chromatin Remodeling Complex

    One important chromatin regulator in ES cells is the Tip60-p400 complex. Tip60-p400 has both histone exchange and histone acetyltransferase (HAT) activities, and functions in gene regulation and DNA damage repair.

    We found that RNAi-mediated knockdown (KD) of any of the 17 subunits of the Tip60-p400 complex in ES cells inhibited self-renewal. However, the molecular functions of Tip60-p400 necessary for self-renewal remain unclear. Although the Tip60 HAT activity has been implicated in gene activation in somatic cells, the primary effect of Tip60 KD in ES cells was activation of genes induced during differentiation. The promoters of many of these genes are directly bound and acetylated by Tip60-p400, raising the question of how this complex might be repressing transcription (Figure 1). We are currently working to dissect the mechanisms by which Tip60-p400 regulates genes in ES cells, and how Tip60-p400 activity is regulated upon ES cell differentiation.

    Figure 1. Possible mechanisms for Tip60-p400-mediated repression.

    Figure 1. Possible mechanisms for Tip60-p400-mediated repression. (A) Acetylation-mediated activation of a repressor. Tip60, which also acetylates non-histone proteins, may activate a transcriptional repressor (TR) by acetylation, causing it to bind its target sequence and repress transcription. (B) Dual-modification repressor binding. Tip60-mediated histone acetylation, plus a second chromatin modification (or alternatively, a specific DNA sequence), might recruit a repressor specific for chromatin harboring both modifications. HMC: histone modifying complex. Adapted from Fazzio et al., Cell Cycle 7:21, 3302-3306.

    Chromatin Regulation and Cancer Stem Cells

    While embryonic stem cells, adult stem cells and cancer stem cells (cells within some tumors that can self-renew indefinitely and reconstitute the entire tumor on their own) have very different cellular properties, their chromatin structures share some common features. One example is the polycomb repressive complex 1 (PRC1) protein Bmi-1, which is required for self-renewal in a number of stem cell types. It is unclear whether there are many other chromatin regulators are similarly required for maintenance of developmental potency. We are addressing this question by testing whether chromatin regulators necessary for proliferation or self-renewal of ES cells are also essential in cancer stem cells. Our goals for these experiments are to learn more about the common features of chromatin structure in developmentally plastic cells, as well as identify potential new targets for drugs that target stem cells within tumors.

    Collapse Rotation Projects

    Rotation Projects

    Rotation projects are available on any of the main topics being studied in the lab. Our recent RNAi screen identifying chromatin regulators necessary for ES cell self-renewal has opened up several new potential projects aimed at identification of the important functions of these regulators in ES cells. Alternatively, projects focusing on the mechanisms of action and regulation of Tip60-p400 complex, or examining the functions of chromatin regulators in cancer stem cells are also possible, depending on the student’s interests. Rotation projects will usually involve some combination of mammalian cell culture, cell and molecular biology, biochemistry, and genomic approaches.

    Collapse Post Docs

    A postdoctoral position is available to study in this laboratory. Please contact Dr. Fazzio for details.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Huang L, Ravi M, Zhang XO, Verdejo-Torres O, Shendy NAM, Nezhady MAM, Gopalan S, Wang G, Durbin AD, Fazzio TG, Wu Q. PRMT5 orchestrates EGFR and AKT networks to activate NF?B and promote EMT. bioRxiv. 2024 Jan 04. PMID: 38260418.
    2. Yin Q, Yang CH, Strelkova OS, Wu J, Sun Y, Gopalan S, Yang L, Dekker J, Fazzio TG, Li XZ, Gibcus J, Rando OJ. Revisiting chromatin packaging in mouse sperm. Genome Res. 2023 Dec 21. PMID: 38129076.
      Citations: 3     Fields:    
    3. Chibaya L, Murphy KC, DeMarco KD, Gopalan S, Liu H, Parikh CN, Lopez-Diaz Y, Faulkner M, Li J, Morris JP, Ho YJ, Chana SK, Simon J, Luan W, Kulick A, de Stanchina E, Simin K, Zhu LJ, Fazzio TG, Lowe SW, Ruscetti M. EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance. Nat Cancer. 2023 06; 4(6):872-892. PMID: 37142692.
      Citations: 5     Fields:    Translation:AnimalsCells
    4. Godbole AA, Gopalan S, Nguyen TK, Munden AL, Lui DS, Fanelli MJ, Vo P, Lewis CA, Spinelli JB, Fazzio TG, Walker AK. S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress. Elife. 2023 02 09; 12. PMID: 36756948.
      Citations: 1     Fields:    Translation:Animals
    5. Conti MM, Li R, Narv?ez Ramos MA, Zhu LJ, Fazzio TG, Benanti JA. Phosphosite Scanning reveals a complex phosphorylation code underlying CDK-dependent activation of Hcm1. Nat Commun. 2023 01 19; 14(1):310. PMID: 36658165.
      Citations: 2     Fields:    Translation:AnimalsCells
    6. Daneshpour H, van den Bersselaar P, Chao CH, Fazzio TG, Youk H. Macroscopic quorum sensing sustains differentiating embryonic stem cells. Nat Chem Biol. 2023 05; 19(5):596-606. PMID: 36635563.
      Citations: 2     Fields:    Translation:AnimalsCells
    7. Gopalan S, Fazzio TG. Multiomic chromatin and transcription profiling with EpiDamID. Cell Rep Methods. 2022 05 23; 2(5):100219. PMID: 35637908.
    8. Gura MA, Relovsk? S, Abt KM, Seymour KA, Wu T, Kaya H, Turner JMA, Fazzio TG, Freiman RN. TAF4b transcription networks regulating early oocyte differentiation. Development. 2022 02 01; 149(3). PMID: 35043944.
      Citations: 1     Fields:    Translation:AnimalsCells
    9. Gopalan S, Fazzio TG. Multi-CUT&Tag to simultaneously profile multiple chromatin factors. STAR Protoc. 2022 03 18; 3(1):101100. PMID: 35098158.
      Citations: 1     Fields:    Translation:HumansCells
    10. Gopalan S, Wang Y, Harper NW, Garber M, Fazzio TG. Simultaneous profiling of multiple chromatin proteins in the same cells. Mol Cell. 2021 11 18; 81(22):4736-4746.e5. PMID: 34637755.
      Citations: 32     Fields:    Translation:AnimalsCells
    11. Wu T, Nance J, Chu F, Fazzio TG. Characterization of R-Loop-Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression. Mol Cell Proteomics. 2021; 20:100142. PMID: 34478875.
      Citations: 7     Fields:    Translation:AnimalsCells
    12. Fazzio TG. Preface. Curr Top Dev Biol. 2020; 138:xi-xviii. PMID: 32220300.
      Citations:    Fields:    Translation:HumansCells
    13. Tavera-Monta?ez C, Hainer SJ, Cangussu D, Gordon SJV, Xiao Y, Reyes-Gutierrez P, Imbalzano AN, Navea JG, Fazzio TG, Padilla-Benavides T. The classic metal-sensing transcription factor MTF1 promotes myogenesis in response to copper. FASEB J. 2019 12; 33(12):14556-14574. PMID: 31690123.
      Citations: 24     Fields:    Translation:AnimalsCells
    14. Hainer SJ, Bo?kovic A, McCannell KN, Rando OJ, Fazzio TG. Profiling of Pluripotency Factors in Single Cells and Early Embryos. Cell. 2019 05 16; 177(5):1319-1329.e11. PMID: 30955888.
      Citations: 87     Fields:    Translation:AnimalsCells
    15. Hainer SJ, Fazzio TG. High-Resolution Chromatin Profiling Using CUT&RUN. Curr Protoc Mol Biol. 2019 04; 126(1):e85. PMID: 30688406.
      Citations: 45     Fields:    Translation:Cells
    16. Amrani N, Gao XD, Liu P, Edraki A, Mir A, Ibraheim R, Gupta A, Sasaki KE, Wu T, Donohoue PD, Settle AH, Lied AM, McGovern K, Fuller CK, Cameron P, Fazzio TG, Zhu LJ, Wolfe SA, Sontheimer EJ. NmeCas9 is an intrinsically high-fidelity genome-editing platform. Genome Biol. 2018 12 05; 19(1):214. PMID: 30518407.
      Citations: 54     Fields:    Translation:HumansAnimalsCells
    17. Acharya D, Nera B, Milstone ZJ, Bourke L, Yoon Y, Rivera-P?rez JA, Trivedi CM, Fazzio TG. TIP55, a splice isoform of the KAT5 acetyltransferase, is essential for developmental gene regulation and organogenesis. Sci Rep. 2018 10 08; 8(1):14908. PMID: 30297694.
      Citations: 2     Fields:    Translation:AnimalsCells
    18. Yan J, Tie G, Wang S, Tutto A, DeMarco N, Khair L, Fazzio TG, Messina LM. Diabetes impairs wound healing by Dnmt1-dependent dysregulation of hematopoietic stem cells differentiation towards macrophages. Nat Commun. 2018 01 02; 9(1):33. PMID: 29295997.
      Citations: 80     Fields:    Translation:AnimalsCells
    19. Wang F, McCannell KN, Bo?kovic A, Zhu X, Shin J, Yu J, Gallant J, Byron M, Lawrence JB, Zhu LJ, Jones SN, Rando OJ, Fazzio TG, Bach I. Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs. Cell Rep. 2017 12 26; 21(13):3691-3699. PMID: 29281819.
      Citations: 11     Fields:    Translation:AnimalsCells
    20. Ee LS, McCannell KN, Tang Y, Fernandes N, Hardy WR, Green MR, Chu F, Fazzio TG. An Embryonic Stem Cell-Specific NuRD Complex Functions through Interaction with WDR5. Stem Cell Reports. 2017 06 06; 8(6):1488-1496. PMID: 28528697.
      Citations: 14     Fields:    Translation:AnimalsCells
    21. Acharya D, Hainer SJ, Yoon Y, Wang F, Bach I, Rivera-P?rez JA, Fazzio TG. KAT-Independent Gene Regulation by Tip60 Promotes ESC Self-Renewal but Not Pluripotency. Cell Rep. 2017 04 25; 19(4):671-679. PMID: 28445719.
      Citations: 17     Fields:    Translation:AnimalsCells
    22. Tie G, Yan J, Khair L, Messina JA, Deng A, Kang J, Fazzio T, Messina LM. Hypercholesterolemia Increases Colorectal Cancer Incidence by Reducing Production of NKT and ?d T Cells from Hematopoietic Stem Cells. Cancer Res. 2017 05 01; 77(9):2351-2362. PMID: 28249902.
      Citations: 29     Fields:    Translation:HumansAnimalsCells
    23. Hainer SJ, McCannell KN, Yu J, Ee LS, Zhu LJ, Rando OJ, Fazzio TG. DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells. Elife. 2016 11 16; 5. PMID: 27849519.
      Citations: 15     Fields:    Translation:AnimalsCells
    24. Fazzio TG. Regulation of chromatin structure and cell fate by R-loops. Transcription. 2016 08 07; 7(4):121-6. PMID: 27327157.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    25. Chen PB, Chen HV, Acharya D, Rando OJ, Fazzio TG. R loops regulate promoter-proximal chromatin architecture and cellular differentiation. Nat Struct Mol Biol. 2015 Dec; 22(12):999-1007. PMID: 26551076.
      Citations: 87     Fields:    Translation:AnimalsCells
    26. Hainer SJ, Fazzio TG. Regulation of Nucleosome Architecture and Factor Binding Revealed by Nuclease Footprinting of the ESC Genome. Cell Rep. 2015 Oct 06; 13(1):61-69. PMID: 26411677.
      Citations: 13     Fields:    Translation:AnimalsCells
    27. Hainer SJ, Gu W, Carone BR, Landry BD, Rando OJ, Mello CC, Fazzio TG. Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF. Genes Dev. 2015 Feb 15; 29(4):362-78. PMID: 25691467.
      Citations: 46     Fields:    Translation:AnimalsCells
    28. Chen PB, Zhu LJ, Hainer SJ, McCannell KN, Fazzio TG. Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo. BMC Genomics. 2014 Dec 15; 15:1104. PMID: 25494698.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    29. Carone BR, Hung JH, Hainer SJ, Chou MT, Carone DM, Weng Z, Fazzio TG, Rando OJ. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Dev Cell. 2014 Jul 14; 30(1):11-22. PMID: 24998598.
      Citations: 117     Fields:    Translation:AnimalsCells
    30. Chen PB, Hung JH, Hickman TL, Coles AH, Carey JF, Weng Z, Chu F, Fazzio TG. Hdac6 regulates Tip60-p400 function in stem cells. Elife. 2013 Dec 03; 2:e01557. PMID: 24302573.
      Citations: 34     Fields:    Translation:HumansAnimalsCells
    31. Fazzio TG, Rando OJ. NURDs are required for diversity. EMBO J. 2012 May 11; 31(14):3036-7. PMID: 22580827.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    32. Yildirim O, Li R, Hung JH, Chen PB, Dong X, Ee LS, Weng Z, Rando OJ, Fazzio TG. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell. 2011 Dec 23; 147(7):1498-510. PMID: 22196727.
      Citations: 265     Fields:    Translation:HumansAnimalsCells
    33. Fazzio TG, Panning B. Control of embryonic stem cell identity by nucleosome remodeling enzymes. Curr Opin Genet Dev. 2010 Oct; 20(5):500-4. PMID: 20800472.
      Citations: 7     Fields:    Translation:AnimalsCells
    34. Fazzio TG, Panning B. Condensin complexes regulate mitotic progression and interphase chromatin structure in embryonic stem cells. J Cell Biol. 2010 Feb 22; 188(4):491-503. PMID: 20176923.
      Citations: 36     Fields:    Translation:AnimalsCells
    35. Fazzio TG, Huff JT, Panning B. Chromatin regulation Tip(60)s the balance in embryonic stem cell self-renewal. Cell Cycle. 2008 Nov 01; 7(21):3302-6. PMID: 18948739.
      Citations: 16     Fields:    Translation:HumansAnimalsCells
    36. Fazzio TG, Huff JT, Panning B. An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity. Cell. 2008 Jul 11; 134(1):162-74. PMID: 18614019.
      Citations: 255     Fields:    Translation:AnimalsCells
    37. Nusinow DA, Hern?ndez-Mu?oz I, Fazzio TG, Shah GM, Kraus WL, Panning B. Poly(ADP-ribose) polymerase 1 is inhibited by a histone H2A variant, MacroH2A, and contributes to silencing of the inactive X chromosome. J Biol Chem. 2007 Apr 27; 282(17):12851-9. PMID: 17322296.
      Citations: 57     Fields:    Translation:Cells
    38. Fazzio TG, Gelbart ME, Tsukiyama T. Two distinct mechanisms of chromatin interaction by the Isw2 chromatin remodeling complex in vivo. Mol Cell Biol. 2005 Nov; 25(21):9165-74. PMID: 16227570.
      Citations: 40     Fields:    Translation:AnimalsCells
    39. Price-Carter M, Fazzio TG, Vallbona EI, Roth JR. Polyphosphate kinase protects Salmonella enterica from weak organic acid stress. J Bacteriol. 2005 May; 187(9):3088-99. PMID: 15838036.
      Citations: 25     Fields:    Translation:Cells
    40. Vary JC, Fazzio TG, Tsukiyama T. Assembly of yeast chromatin using ISWI complexes. Methods Enzymol. 2004; 375:88-102. PMID: 14870661.
      Citations: 30     Fields:    Translation:AnimalsCells
    41. Fazzio TG, Tsukiyama T. Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism. Mol Cell. 2003 Nov; 12(5):1333-40. PMID: 14636590.
      Citations: 61     Fields:    Translation:AnimalsCells
    42. Carey JF, Schultz SJ, Sisson L, Fazzio TG, Champoux JJ. DNA relaxation by human topoisomerase I occurs in the closed clamp conformation of the protein. Proc Natl Acad Sci U S A. 2003 May 13; 100(10):5640-5. PMID: 12711735.
      Citations: 19     Fields:    Translation:HumansCells
    43. Kooperberg C, Fazzio TG, Delrow JJ, Tsukiyama T. Improved background correction for spotted DNA microarrays. J Comput Biol. 2002; 9(1):55-66. PMID: 11911795.
      Citations: 35     Fields:    Translation:HumansAnimals
    44. Goldmark JP, Fazzio TG, Estep PW, Church GM, Tsukiyama T. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell. 2000 Oct 27; 103(3):423-33. PMID: 11081629.
      Citations: 130     Fields:    Translation:AnimalsCells
    45. Fazzio TG, Roth JR. Evidence that the CysG protein catalyzes the first reaction specific to B12 synthesis in Salmonella typhimurium, insertion of cobalt. J Bacteriol. 1996 Dec; 178(23):6952-9. PMID: 8955319.
      Citations: 14     Fields:    Translation:Cells
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