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Craig L Peterson PhD

InstitutionUMass Chan Medical School
DepartmentProgram in Molecular Medicine
AddressUMass Chan Medical School
373 Plantation Street Two Biotech Suite 210
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
    DepartmentProgram in Molecular Medicine

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentPostbaccalaureate Research Education Program

    Collapse Biography 
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    University of Washington, Seattle, WA, United StatesBSMolecular Biology
    University of California, Los Angeles, Los Angeles, CA, United StatesPH DMolecular Biology

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    Academic Background

    Peterson Lab Web Page

    Craig Peterson received his BS from the University of Washington in 1983 and his PhD from the University of California, Los Angeles in 1988. He was a Helen Hay Whitney Foundation postdoctoral fellow from 1988-1991, in the Department of Biochemistry and Biophysics at the University of California, San Francisco. In 1992, he joined the University of Massachusetts Medical School as a faculty member in the Program in Molecular Medicine.

    How chromosome structure influences nuclear processes

    craig peterson's picture The overall objective of our research is to determine how chromosome structure influences nuclear processes and to identify and characterize the cellular machines that contend with this structure.Over the years, our general strategy has been to employ yeast molecular genetics to develop detailed models that describe complex nuclear events that can then be directly tested and expanded by subsequent biophysical and biochemical approaches. Much of our efforts over the past few years have focused on ATP-dependent chromatin remodeling enzymes (e.g. SWI/SNF and INO80) that hydrolyze ~1,000 ATPs per minute to alter chromatin structure and thereby regulate transcription, DNA repair, or replication. Our studies are centered on both the regulation and mechanism of this chromatin "remodeling" reaction. Since most of these enzymes are enormous (>1 MDa), multi-subunit enzymes, we are also interested in understanding how these enzymes are assembled and what roles are played by individual subunits. To address these goals we use a broad spectrum of methodologies, including yeast molecular and classical genetics, modern analytical ultracentrifugation, molecular biology, and traditional biochemistry. Notably, these remodeling enzymes are conserved from yeast to mammals, play key roles in gene expression and the maintenance of genome integrity, and loss of their function leads to various disease states.

    In addition to our studies on chromatin remodeling enzymes, we also wish to understand the dynamics of chromatin fibers and how fiber condensation influences DNA repair, transcription, and DNA replication. These projects involve the biochemical reconstitution of defined nucleosomal arrays from recombinant histones and DNA templates that contain head-to-tail repeats of nucleosome positioning sequences. Typically, we perform sedimentation velocity experiments in the analytical ultracentrifuge to investigate how histone modifications (e.g. H4 K16 acetylation), histone variants, or heterochromatin proteins (e.g. HP1, Sir3) influence the folding dynamics of these reconstituted chromatin fibers. These biophysical studies are complemented by powerful biochemical assays where we assess how the structure of a chromatin fiber regulates various steps of DNA double strand break repair or DNA replication.

    As we learn more about the dynamics of chromatin fibers and the basic mechanics of DNA repair and DNA replication, we have initiated in vivo studies that probe how these processes are coordinated and regulated within cells. For instance, we have recently, found that a DNA double strand break can induce the re-localization of a chromosomal domain to the nuclear envelope and that this compartmentalization inhibits recombinational repair. Interestingly, localization to the nuclear periphery requires components of the telomerase complex and seems to be due to an attempt to heal the chromosome by formation of a new telomere. Similar types of chromosome healing events may also occur at stalled replication forks. We are currently using a variety of cell biological and molecular genetic approaches to dissect the complex decision-making processes that a cell employs in its attempts to maintain genome integrity.


    Research Figure

    Figure Legend

    3 dimensional EM reconstruction of the 1.15 MDa yeast SWI/SNF chromatin remodeling complex (image courtesy of C. Woodcock and R. Horowitz). Top two panels show two views of yeast SWI/SNF -- dimensions are 27 nm by 8 nm. Bottom two panels show a theoretical docking of a mononucleosome core particle into the presumptive active site. Note the large cavity that provides a perfect fit for the nucleosome core when it is oriented with the entry/exit strands of DNA facing away from the SWI/SNF surface.

    Peterson Lab Web Page

    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.
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    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. Chio US, Rechiche O, Bryll AR, Zhu J, Leith EM, Feldman JL, Peterson CL, Tan S, Armache JP. Cryo-EM structure of the human Sirtuin 6-nucleosome complex. Sci Adv. 2023 04 14; 9(15):eadf7586. PMID: 37058572.
      Citations:    Fields:    Translation:HumansCells
    2. Chio US, Rechiche O, Bryll AR, Zhu J, Feldman JL, Peterson CL, Tan S, Armache JP. Cryo-EM structure of the human Sirtuin 6-nucleosome complex. bioRxiv. 2023 Mar 18. PMID: 36993468.
    3. Bryll AR, Peterson CL. The circular logic of mRNA homeostasis. Transcription. 2023 11; 14(1-2):18-26. PMID: 36843061.
      Citations: 1     Fields:    Translation:Cells
    4. Fan J, Moreno AT, Baier AS, Loparo JJ, Peterson CL. H2A.Z deposition by SWR1C involves multiple ATP-dependent steps. Nat Commun. 2022 11 17; 13(1):7052. PMID: 36396651.
      Citations: 4     Fields:    Translation:AnimalsCells
    5. Baier AS, Peterson CL. Fluorescence approaches for biochemical analysis of ATP-dependent chromatin remodeling enzymes. Methods Enzymol. 2022; 673:1-17. PMID: 35965003.
      Citations: 1     Fields:    Translation:Cells
    6. Gutierrez JI, Brittingham GP, Karadeniz Y, Tran KD, Dutta A, Holehouse AS, Peterson CL, Holt LJ. SWI/SNF senses carbon starvation with a pH-sensitive low-complexity sequence. Elife. 2022 02 07; 11. PMID: 35129437.
      Citations: 9     Fields:    Translation:Animals
    7. Bryll AR, Peterson CL. Functional interaction between the RNA exosome and the sirtuin deacetylase Hst3 maintains transcriptional homeostasis. Genes Dev. 2022 01 01; 36(1-2):17-22. PMID: 34916303.
      Citations: 3     Fields:    
    8. Oberbeckmann E, Niebauer V, Watanabe S, Farnung L, Moldt M, Schmid A, Cramer P, Peterson CL, Eustermann S, Hopfner KP, Korber P. Ruler elements in chromatin remodelers set nucleosome array spacing and phasing. Nat Commun. 2021 05 28; 12(1):3232. PMID: 34050140.
      Citations: 13     Fields:    Translation:AnimalsCells
    9. Liu WH, Zheng J, Feldman JL, Klein MA, Kuznetsov VI, Peterson CL, Griffin PR, Denu JM. Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6. Nat Commun. 2020 10 16; 11(1):5244. PMID: 33067423.
      Citations: 11     Fields:    Translation:HumansCells
    10. Topal S, Van C, Xue Y, Carey MF, Peterson CL. INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins. Cell Rep. 2020 09 08; 32(10):108106. PMID: 32905765.
      Citations: 1     Fields:    Translation:HumansCells
    11. Wang A, Kolhe JA, Gioacchini N, Baade I, Brieher WM, Peterson CL, Freeman BC. Mechanism of Long-Range Chromosome Motion Triggered by Gene Activation. Dev Cell. 2020 02 10; 52(3):309-320.e5. PMID: 31902656.
      Citations: 14     Fields:    Translation:AnimalsCells
    12. Topal S, Vasseur P, Radman-Livaja M, Peterson CL. Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle in Yeast. Nat Commun. 2019 09 26; 10(1):4372. PMID: 31558720.
      Citations: 22     Fields:    Translation:AnimalsCells
    13. Feldman JL, Peterson CL. Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability. Cell Rep. 2019 06 04; 27(10):2978-2989.e5. PMID: 31167142.
      Citations: 15     Fields:    Translation:AnimalsCells
    14. Singh RK, Fan J, Gioacchini N, Watanabe S, Bilsel O, Peterson CL. Transient Kinetic Analysis of SWR1C-Catalyzed H2A.Z Deposition Unravels the Impact of Nucleosome Dynamics and the Asymmetry of Histone Exchange. Cell Rep. 2019 04 09; 27(2):374-386.e4. PMID: 30970243.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    15. Swygert SG, Senapati S, Bolukbasi MF, Wolfe SA, Lindsay S, Peterson CL. SIR proteins create compact heterochromatin fibers. Proc Natl Acad Sci U S A. 2018 12 04; 115(49):12447-12452. PMID: 30455303.
      Citations: 9     Fields:    Translation:AnimalsCells
    16. Gioacchini N, Peterson CL. Chromatin remodeling: a complex affair. EMBO Rep. 2017 10; 18(10):1673-1674. PMID: 28835548.
      Citations: 5     Fields:    Translation:Cells
    17. Xue Y, Pradhan SK, Sun F, Chronis C, Tran N, Su T, Van C, Vashisht A, Wohlschlegel J, Peterson CL, Timmers HTM, Kurdistani SK, Carey MF. Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals. Mol Cell. 2017 Aug 17; 67(4):594-607.e4. PMID: 28735899.
      Citations: 23     Fields:    Translation:AnimalsCells
    18. Clapier CR, Iwasa J, Cairns BR, Peterson CL. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol. 2017 07; 18(7):407-422. PMID: 28512350.
      Citations: 395     Fields:    Translation:HumansAnimalsCells
    19. Azmi IF, Watanabe S, Maloney MF, Kang S, Belsky JA, MacAlpine DM, Peterson CL, Bell SP. Nucleosomes influence multiple steps during replication initiation. Elife. 2017 03 21; 6. PMID: 28322723.
      Citations: 30     Fields:    Translation:AnimalsCells
    20. Adkins NL, Swygert SG, Kaur P, Niu H, Grigoryev SA, Sung P, Wang H, Peterson CL. Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair. J Biol Chem. 2017 Mar 31; 292(13):5271-5281. PMID: 28202543.
      Citations: 23     Fields:    Translation:AnimalsCells
    21. Echtenkamp FJ, Gvozdenov Z, Adkins NL, Zhang Y, Lynch-Day M, Watanabe S, Peterson CL, Freeman BC. Hsp90 and p23 Molecular Chaperones Control Chromatin Architecture by Maintaining the Functional Pool of the RSC Chromatin Remodeler. Mol Cell. 2016 12 01; 64(5):888-899. PMID: 27818141.
      Citations: 26     Fields:    Translation:AnimalsCells
    22. Krietenstein N, Wal M, Watanabe S, Park B, Peterson CL, Pugh BF, Korber P. Genomic Nucleosome Organization Reconstituted with Pure Proteins. Cell. 2016 Oct 20; 167(3):709-721.e12. PMID: 27768892.
      Citations: 105     Fields:    Translation:AnimalsCells
    23. Yu L, Rege M, Peterson CL, Volkert MR. RNA polymerase II depletion promotes transcription of alternative mRNA species. BMC Mol Biol. 2016 08 30; 17(1):20. PMID: 27578267.
      Citations: 4     Fields:    Translation:AnimalsCells
    24. Watanabe S, Peterson CL. Response to Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme". Science. 2016 Jul 22; 353(6297):358. PMID: 27463666.
      Citations: 6     Fields:    Translation:AnimalsCells
    25. Rege M, Subramanian V, Zhu C, Hsieh TH, Weiner A, Friedman N, Clauder-M?nster S, Steinmetz LM, Rando OJ, Boyer LA, Peterson CL. Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Cell Rep. 2015 Nov 24; 13(8):1610-22. PMID: 26586442.
      Citations: 24     Fields:    Translation:AnimalsCells
    26. Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TM, Birck C, Brautigam CA, Brennerman W, Byron O, Bzowska A, Chaires JB, Chaton CT, C?lfen H, Connaghan KD, Crowley KA, Curth U, Daviter T, Dean WL, D?ez AI, Ebel C, Eckert DM, Eisele LE, Eisenstein E, England P, Escalante C, Fagan JA, Fairman R, Finn RM, Fischle W, de la Torre JG, Gor J, Gustafsson H, Hall D, Harding SE, Cifre JG, Herr AB, Howell EE, Isaac RS, Jao SC, Jose D, Kim SJ, Kokona B, Kornblatt JA, Kosek D, Krayukhina E, Krzizike D, Kusznir EA, Kwon H, Larson A, Laue TM, Le Roy A, Leech AP, Lilie H, Luger K, Luque-Ortega JR, Ma J, May CA, Maynard EL, Modrak-Wojcik A, Mok YF, M?cke N, Nagel-Steger L, Narlikar GJ, Noda M, Nourse A, Obsil T, Park CK, Park JK, Pawelek PD, Perdue EE, Perkins SJ, Perugini MA, Peterson CL, Peverelli MG, Piszczek G, Prag G, Prevelige PE, Raynal BD, Rezabkova L, Richter K, Ringel AE, Rosenberg R, Rowe AJ, Rufer AC, Scott DJ, Seravalli JG, Solovyova AS, Song R, Staunton D, Stoddard C, Stott K, Strauss HM, Streicher WW, Sumida JP, Swygert SG, Szczepanowski RH, Tessmer I, Toth RT, Tripathy A, Uchiyama S, Uebel SF, Unzai S, Gruber AV, von Hippel PH, Wandrey C, Wang SH, Weitzel SE, Wielgus-Kutrowska B, Wolberger C, Wolff M, Wright E, Wu YS, Wubben JM, Schuck P. A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. PLoS One. 2015; 10(5):e0126420. PMID: 25997164.
      Citations: 44     Fields:    
    27. Watanabe S, Tan D, Lakshminarasimhan M, Washburn MP, Hong EJ, Walz T, Peterson CL. Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C. Nat Commun. 2015 May 12; 6:7108. PMID: 25964121.
      Citations: 44     Fields:    Translation:AnimalsCells
    28. Jeronimo C, Watanabe S, Kaplan CD, Peterson CL, Robert F. The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations. Mol Cell. 2015 Jun 18; 58(6):1113-23. PMID: 25959393.
      Citations: 64     Fields:    Translation:AnimalsCells
    29. Bennett G, Peterson CL. SWI/SNF recruitment to a DNA double-strand break by the NuA4 and Gcn5 histone acetyltransferases. DNA Repair (Amst). 2015 Jun; 30:38-45. PMID: 25869823.
      Citations: 26     Fields:    Translation:AnimalsCells
    30. Xue Y, Van C, Pradhan SK, Su T, Gehrke J, Kuryan BG, Kitada T, Vashisht A, Tran N, Wohlschlegel J, Peterson CL, Kurdistani SK, Carey MF. The Ino80 complex prevents invasion of euchromatin into silent chromatin. Genes Dev. 2015 Feb 15; 29(4):350-5. PMID: 25691465.
      Citations: 31     Fields:    Translation:AnimalsCells
    31. Manning BJ, Peterson CL. Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):17827-32. PMID: 25453095.
      Citations: 10     Fields:    Translation:AnimalsCells
    32. Van C, Williams JS, Kunkel TA, Peterson CL. Deposition of histone H2A.Z by the SWR-C remodeling enzyme prevents genome instability. DNA Repair (Amst). 2015 Jan; 25:9-14. PMID: 25463393.
      Citations: 10     Fields:    Translation:AnimalsCells
    33. Swygert SG, Manning BJ, Senapati S, Kaur P, Lindsay S, Demeler B, Peterson CL. Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres. Nat Commun. 2014 Aug 28; 5:4751. PMID: 25163529.
      Citations: 11     Fields:    Translation:Cells
    34. Swygert SG, Peterson CL. Chromatin dynamics: interplay between remodeling enzymes and histone modifications. Biochim Biophys Acta. 2014 Aug; 1839(8):728-36. PMID: 24583555.
      Citations: 97     Fields:    Translation:HumansAnimalsCells
    35. Peterson CL, Almouzni G. Nucleosome dynamics as modular systems that integrate DNA damage and repair. Cold Spring Harb Perspect Biol. 2013 Sep 01; 5(9). PMID: 24003210.
      Citations: 25     Fields:    Translation:Cells
    36. Carey MF, Peterson CL, Smale ST. PCR-mediated site-directed mutagenesis. Cold Spring Harb Protoc. 2013 Aug 01; 2013(8):738-42. PMID: 23906918.
      Citations: 18     Fields:    Translation:Cells
    37. Watanabe S, Peterson CL. Chromatin dynamics: flipping the switch on a chromatin remodeling machine. Cell Cycle. 2013 Aug 01; 12(15):2337-8. PMID: 23856580.
      Citations: 4     Fields:    Translation:AnimalsCells
    38. Carey MF, Peterson CL, Smale ST. Electrophoretic mobility-shift assays. Cold Spring Harb Protoc. 2013 Jul 01; 2013(7):636-9. PMID: 23818676.
      Citations: 6     Fields:    Translation:Cells
    39. Adkins NL, Niu H, Sung P, Peterson CL. Nucleosome dynamics regulates DNA processing. Nat Struct Mol Biol. 2013 Jul; 20(7):836-42. PMID: 23728291.
      Citations: 81     Fields:    Translation:AnimalsCells
    40. Carey MF, Peterson CL, Smale ST. DNase I footprinting. Cold Spring Harb Protoc. 2013 May 01; 2013(5):469-78. PMID: 23637368.
      Citations: 7     Fields:    Translation:Cells
    41. Carey MF, Peterson CL, Smale ST. Preparation of (32)P-end-labeled DNA fragments for performing DNA-binding experiments. Cold Spring Harb Protoc. 2013 May 01; 2013(5):464-8. PMID: 23637369.
      Citations: 1     Fields:    Translation:Cells
    42. Watanabe S, Radman-Livaja M, Rando OJ, Peterson CL. A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme. Science. 2013 Apr 12; 340(6129):195-9. PMID: 23580526.
      Citations: 107     Fields:    Translation:AnimalsCells
    43. Carey MF, Peterson CL, Smale ST. The RNase protection assay. Cold Spring Harb Protoc. 2013 Mar 01; 2013(3). PMID: 23457339.
      Citations: 8     Fields:    Translation:Cells
    44. Carey MF, Peterson CL, Smale ST. The primer extension assay. Cold Spring Harb Protoc. 2013 Feb 01; 2013(2):164-73. PMID: 23378648.
      Citations: 14     Fields:    Translation:Cells
    45. Papamichos-Chronakis M, Peterson CL. Chromatin and the genome integrity network. Nat Rev Genet. 2013 Jan; 14(1):62-75. PMID: 23247436.
      Citations: 124     Fields:    Translation:Cells
    46. Manning BJ, Peterson CL. Releasing the brakes on a chromatin-remodeling enzyme. Nat Struct Mol Biol. 2013 Jan; 20(1):5-7. PMID: 23288358.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    47. Bennett G, Papamichos-Chronakis M, Peterson CL. DNA repair choice defines a common pathway for recruitment of chromatin regulators. Nat Commun. 2013; 4:2084. PMID: 23811932.
      Citations: 48     Fields:    Translation:AnimalsCells
    48. Carey MF, Peterson CL, Smale ST. Confirming the functional importance of a protein-DNA interaction. Cold Spring Harb Protoc. 2012 Jul 01; 2012(7):733-57. PMID: 22753608.
      Citations: 5     Fields:    Translation:Cells
    49. Sanz AB, Garc?a R, Rodr?guez-Pe?a JM, D?ez-Mu?iz S, Nombela C, Peterson CL, Arroyo J. Chromatin remodeling by the SWI/SNF complex is essential for transcription mediated by the yeast cell wall integrity MAPK pathway. Mol Biol Cell. 2012 Jul; 23(14):2805-17. PMID: 22621902.
      Citations: 20     Fields:    Translation:AnimalsCells
    50. Carey MF, Peterson CL, Smale ST. Identifying cis-acting DNA elements within a control region. Cold Spring Harb Protoc. 2012 Mar 01; 2012(3):279-96. PMID: 22383646.
      Citations: 3     Fields:    Translation:Cells
    51. Carey MF, Peterson CL, Smale ST. Experimental strategies for cloning or identifying genes encoding DNA-binding proteins. Cold Spring Harb Protoc. 2012 Feb 01; 2012(2):183-92. PMID: 22301659.
      Citations: 1     Fields:    Translation:Cells
    52. Carey MF, Peterson CL, Smale ST. Experimental strategies for the identification of DNA-binding proteins. Cold Spring Harb Protoc. 2012 Jan 01; 2012(1):18-33. PMID: 22194258.
      Citations: 13     Fields:    Translation:Cells
    53. Liu N, Peterson CL, Hayes JJ. SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes. Mol Cell Biol. 2011 Oct; 31(20):4165-75. PMID: 21859889.
      Citations: 10     Fields:    Translation:AnimalsCells
    54. Peterson CL. The ins and outs of heterochromatic DNA repair. Dev Cell. 2011 Mar 15; 20(3):285-7. PMID: 21397838.
      Citations: 4     Fields:    
    55. Wippo CJ, Israel L, Watanabe S, Hochheimer A, Peterson CL, Korber P. The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes. EMBO J. 2011 Apr 06; 30(7):1277-88. PMID: 21343911.
      Citations: 33     Fields:    Translation:AnimalsCells
    56. Peterson CL. Chromatin: a ubiquitin crowbar opens chromatin. Nat Chem Biol. 2011 Feb; 7(2):68-9. PMID: 21245855.
      Citations: 1     Fields:    Translation:Cells
    57. Papamichos-Chronakis M, Watanabe S, Rando OJ, Peterson CL. Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity. Cell. 2011 Jan 21; 144(2):200-13. PMID: 21241891.
      Citations: 212     Fields:    Translation:AnimalsCells
    58. Carey MF, Peterson CL, Smale ST. Magnesium-agarose electrophoretic mobility shift assay (EMSA) of transcription factor IID binding to DNA. Cold Spring Harb Protoc. 2010 Nov 01; 2010(11):pdb.prot5514. PMID: 21041387.
      Citations: 2     Fields:    Translation:Cells
    59. Carey MF, Peterson CL, Smale ST. Potassium permanganate probing of Pol II open complexes. Cold Spring Harb Protoc. 2010 Aug 01; 2010(8):pdb.prot5479. PMID: 20679388.
      Citations: 1     Fields:    Translation:HumansCells
    60. Carey MF, Peterson CL, Smale ST. Protein complex binding to promoter DNA: immobilized template assay. Cold Spring Harb Protoc. 2010 Aug 01; 2010(8):pdb.prot5465. PMID: 20679374.
      Citations: 1     Fields:    Translation:HumansCells
    61. Carey MF, Peterson CL, Smale ST. Purification of mediator from HeLa cell lines expressing a flag-tagged mediator subunit. Cold Spring Harb Protoc. 2010 Jul 01; 2010(7):pdb.prot5451. PMID: 20647355.
      Citations:    Fields:    Translation:HumansCells
    62. Carey MF, Peterson CL, Smale ST. Purification of epitope-tagged transcription factor IID. Cold Spring Harb Protoc. 2010 Jul 01; 2010(7):pdb.prot5450. PMID: 20647354.
      Citations: 1     Fields:    Translation:HumansCells
    63. Peterson CL. Transcriptional memory: mothers SET the table for daughters. Curr Biol. 2010 Mar 09; 20(5):R240-2. PMID: 20219175.
      Citations: 1     Fields:    Translation:AnimalsCells
    64. Kundu S, Peterson CL. Dominant role for signal transduction in the transcriptional memory of yeast GAL genes. Mol Cell Biol. 2010 May; 30(10):2330-40. PMID: 20212085.
      Citations: 38     Fields:    Translation:AnimalsCells
    65. Carey MF, Peterson CL, Smale ST. G-less cassette in vitro transcription using HeLa cell nuclear extracts. Cold Spring Harb Protoc. 2010 Mar; 2010(3):pdb.prot5387. PMID: 20194456.
      Citations: 2     Fields:    Translation:HumansCells
    66. Watanabe S, Resch M, Lilyestrom W, Clark N, Hansen JC, Peterson C, Luger K. Structural characterization of H3K56Q nucleosomes and nucleosomal arrays. Biochim Biophys Acta. 2010 May-Jun; 1799(5-6):480-6. PMID: 20100606.
      Citations: 28     Fields:    Translation:Cells
    67. Oza P, Peterson CL. Opening the DNA repair toolbox: localization of DNA double strand breaks to the nuclear periphery. Cell Cycle. 2010 Jan 01; 9(1):43-9. PMID: 20016273.
      Citations: 18     Fields:    Translation:AnimalsCells
    68. Carey MF, Peterson CL, Smale ST. Dignam and Roeder nuclear extract preparation. Cold Spring Harb Protoc. 2009 Dec; 2009(12):pdb.prot5330. PMID: 20150077.
      Citations: 30     Fields:    Translation:HumansCells
    69. Sinha M, Peterson CL. Chromatin dynamics during repair of chromosomal DNA double-strand breaks. Epigenomics. 2009 Dec; 1(2):371-85. PMID: 20495614.
      Citations: 39     Fields:    Translation:HumansCells
    70. Carey MF, Peterson CL, Smale ST. In vitro transcription using HeLa cell extracts and primer extension. Cold Spring Harb Protoc. 2009 Dec; 2009(12):pdb.prot5331. PMID: 20150078.
      Citations: 3     Fields:    Translation:HumansCells
    71. Sinha M, Watanabe S, Johnson A, Moazed D, Peterson CL. Recombinational repair within heterochromatin requires ATP-dependent chromatin remodeling. Cell. 2009 Sep 18; 138(6):1109-21. PMID: 19766565.
      Citations: 46     Fields:    Translation:AnimalsCells
    72. Carey MF, Peterson CL, Smale ST. In vivo dimethyl sulfate (DMS) footprinting via ligation-mediated polymerase chain reaction (LM-PCR). Cold Spring Harb Protoc. 2009 Sep; 2009(9):pdb.prot5278. PMID: 20147263.
      Citations: 1     Fields:    Translation:Animals
    73. Carey MF, Peterson CL, Smale ST. In vivo DNase I, MNase, and restriction enzyme footprinting via ligation-mediated polymerase chain reaction (LM-PCR). Cold Spring Harb Protoc. 2009 Sep; 2009(9):pdb.prot5277. PMID: 20147262.
      Citations: 5     Fields:    Translation:AnimalsCells
    74. Carey MF, Peterson CL, Smale ST. Chromatin immunoprecipitation (ChIP). Cold Spring Harb Protoc. 2009 Sep; 2009(9):pdb.prot5279. PMID: 20147264.
      Citations: 118     Fields:    Translation:AnimalsCells
    75. Oza P, Jaspersen SL, Miele A, Dekker J, Peterson CL. Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev. 2009 Apr 15; 23(8):912-27. PMID: 19390086.
      Citations: 171     Fields:    Translation:AnimalsCells
    76. Peterson CL. Purification of recombinant Drosophila ACF. Cold Spring Harb Protoc. 2009 Apr; 2009(4):pdb.prot5115. PMID: 20147124.
      Citations: 1     Fields:    Translation:AnimalsCells
    77. Peterson CL. Purification of recombinant Drosophila NAP1. Cold Spring Harb Protoc. 2009 Apr; 2009(4):pdb.prot5116. PMID: 20147125.
      Citations:    Fields:    Translation:AnimalsCells
    78. Peterson CL. Reconstitution of nucleosomal arrays using recombinant Drosophila ACF and NAP1. Cold Spring Harb Protoc. 2009 Apr; 2009(4):pdb.prot5114. PMID: 20147123.
      Citations: 3     Fields:    Translation:AnimalsCells
    79. Kundu S, Peterson CL. Role of chromatin states in transcriptional memory. Biochim Biophys Acta. 2009 Jun; 1790(6):445-55. PMID: 19236904.
      Citations: 22     Fields:    Translation:AnimalsCells
    80. Peterson CL. Salt gradient dialysis reconstitution of nucleosomes. CSH Protoc. 2008 Dec 01; 2008:pdb.prot5113. PMID: 21356758.
    81. Peterson CL, Hansen JC. Chicken erythrocyte histone octamer preparation. CSH Protoc. 2008 Dec 01; 2008:pdb.prot5112. PMID: 21356757.
    82. Fu Y, Sinha M, Peterson CL, Weng Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 2008 Jul 25; 4(7):e1000138. PMID: 18654629.
      Citations: 209     Fields:    Translation:HumansCells
    83. Dechassa ML, Zhang B, Horowitz-Scherer R, Persinger J, Woodcock CL, Peterson CL, Bartholomew B. Architecture of the SWI/SNF-nucleosome complex. Mol Cell Biol. 2008 Oct; 28(19):6010-21. PMID: 18644858.
      Citations: 86     Fields:    Translation:AnimalsCells
    84. Sinha M, Peterson CL. A Rad51 presynaptic filament is sufficient to capture nucleosomal homology during recombinational repair of a DNA double-strand break. Mol Cell. 2008 Jun 20; 30(6):803-10. PMID: 18570881.
      Citations: 23     Fields:    Translation:HumansAnimalsCells
    85. Papamichos-Chronakis M, Peterson CL. The Ino80 chromatin-remodeling enzyme regulates replisome function and stability. Nat Struct Mol Biol. 2008 Apr; 15(4):338-45. PMID: 18376411.
      Citations: 87     Fields:    Translation:HumansCells
    86. Triezenberg SJ, Peterson CL. Profound challenges do remain in our understanding of the mechanisms of gene regulation. Biochim Biophys Acta. 2008 Jan; 1779(1):1-2. PMID: 18082153.
      Citations:    Fields:    
    87. Carruthers LM, Marton LJ, Peterson CL. Polyamine analogues: potent inducers of nucleosomal array oligomerization and inhibitors of yeast cell growth. Biochem J. 2007 Aug 01; 405(3):541-5. PMID: 17428198.
      Citations: 5     Fields:    Translation:AnimalsCells
    88. Yang X, Zaurin R, Beato M, Peterson CL. Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement. Nat Struct Mol Biol. 2007 Jun; 14(6):540-7. PMID: 17496903.
      Citations: 58     Fields:    Translation:Cells
    89. Peterson CL. Genome integrity: a HAT needs a chaperone. Curr Biol. 2007 May 01; 17(9):R324-6. PMID: 17470345.
      Citations: 6     Fields:    Translation:AnimalsCells
    90. Kundu S, Horn PJ, Peterson CL. SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster. Genes Dev. 2007 Apr 15; 21(8):997-1004. PMID: 17438002.
      Citations: 80     Fields:    Translation:AnimalsCells
    91. Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell. 2006 Nov 17; 24(4):559-68. PMID: 17188033.
      Citations: 120     Fields:    Translation:AnimalsCells
    92. Fry CJ, Norris A, Cosgrove M, Boeke JD, Peterson CL. The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing. Mol Cell Biol. 2006 Dec; 26(23):9045-59. PMID: 17015465.
      Citations: 21     Fields:    Translation:AnimalsCells
    93. Papamichos-Chronakis M, Krebs JE, Peterson CL. Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage. Genes Dev. 2006 Sep 01; 20(17):2437-49. PMID: 16951256.
      Citations: 96     Fields:    Translation:AnimalsCells
    94. Shogren-Knaak M, Peterson CL. Switching on chromatin: mechanistic role of histone H4-K16 acetylation. Cell Cycle. 2006 Jul; 5(13):1361-5. PMID: 16855380.
      Citations: 43     Fields:    Translation:HumansAnimalsCells
    95. Shundrovsky A, Smith CL, Lis JT, Peterson CL, Wang MD. Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nat Struct Mol Biol. 2006 Jun; 13(6):549-54. PMID: 16732285.
      Citations: 54     Fields:    Translation:Cells
    96. Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science. 2006 Feb 10; 311(5762):844-7. PMID: 16469925.
      Citations: 847     Fields:    Translation:HumansCells
    97. Horn PJ, Peterson CL. Heterochromatin assembly: a new twist on an old model. Chromosome Res. 2006; 14(1):83-94. PMID: 16506098.
      Citations: 25     Fields:    Translation:HumansAnimalsCells
    98. Chowdhury D, Keogh MC, Ishii H, Peterson CL, Buratowski S, Lieberman J. gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair. Mol Cell. 2005 Dec 09; 20(5):801-9. PMID: 16310392.
      Citations: 217     Fields:    Translation:HumansAnimalsCells
    99. Hill DA, Peterson CL, Imbalzano AN. Effects of HMGN1 on chromatin structure and SWI/SNF-mediated chromatin remodeling. J Biol Chem. 2005 Dec 16; 280(50):41777-83. PMID: 16253989.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    100. Horn PJ, Bastie JN, Peterson CL. A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev. 2005 Jul 15; 19(14):1705-14. PMID: 16024659.
      Citations: 101     Fields:    Translation:AnimalsCells
    101. Smith CL, Peterson CL. A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling. Mol Cell Biol. 2005 Jul; 25(14):5880-92. PMID: 15988005.
      Citations: 50     Fields:    Translation:HumansAnimalsCells
    102. Cheung WL, Turner FB, Krishnamoorthy T, Wolner B, Ahn SH, Foley M, Dorsey JA, Peterson CL, Berger SL, Allis CD. Phosphorylation of histone H4 serine 1 during DNA damage requires casein kinase II in S. cerevisiae. Curr Biol. 2005 Apr 12; 15(7):656-60. PMID: 15823538.
      Citations: 66     Fields:    Translation:AnimalsCells
    103. Wolner B, Peterson CL. ATP-dependent and ATP-independent roles for the Rad54 chromatin remodeling enzyme during recombinational repair of a DNA double strand break. J Biol Chem. 2005 Mar 18; 280(11):10855-60. PMID: 15653683.
      Citations: 50     Fields:    Translation:HumansCells
    104. Smith CL, Peterson CL. ATP-dependent chromatin remodeling. Curr Top Dev Biol. 2005; 65:115-48. PMID: 15642381.
      Citations: 94     Fields:    Translation:AnimalsCells
    105. Vicent GP, Nacht AS, Smith CL, Peterson CL, Dimitrov S, Beato M. DNA instructed displacement of histones H2A and H2B at an inducible promoter. Mol Cell. 2004 Nov 05; 16(3):439-52. PMID: 15525516.
      Citations: 41     Fields:    Translation:HumansCells
    106. Peterson CL, Laniel MA. Histones and histone modifications. Curr Biol. 2004 Jul 27; 14(14):R546-51. PMID: 15268870.
      Citations: 421     Fields:    Translation:Cells
    107. Peterson CL, C?t? J. Cellular machineries for chromosomal DNA repair. Genes Dev. 2004 Mar 15; 18(6):602-16. PMID: 15075289.
      Citations: 106     Fields:    Translation:HumansAnimalsCells
    108. Boyer LA, Latek RR, Peterson CL. The SANT domain: a unique histone-tail-binding module? Nat Rev Mol Cell Biol. 2004 Feb; 5(2):158-63. PMID: 15040448.
      Citations: 193     Fields:    Translation:HumansAnimalsCells
    109. Shogren-Knaak MA, Peterson CL. Creating designer histones by native chemical ligation. Methods Enzymol. 2004; 375:62-76. PMID: 14870659.
      Citations: 20     Fields:    Translation:AnimalsCells
    110. Smith CL, Peterson CL. Coupling tandem affinity purification and quantitative tyrosine iodination to determine subunit stoichiometry of protein complexes. Methods. 2003 Sep; 31(1):104-9. PMID: 12893180.
      Citations: 2     Fields:    Translation:Animals
    111. Wolner B, van Komen S, Sung P, Peterson CL. Recruitment of the recombinational repair machinery to a DNA double-strand break in yeast. Mol Cell. 2003 Jul; 12(1):221-32. PMID: 12887907.
      Citations: 90     Fields:    Translation:AnimalsCells
    112. Jaskelioff M, Peterson CL. Chromatin and transcription: histones continue to make their marks. Nat Cell Biol. 2003 May; 5(5):395-9. PMID: 12724776.
      Citations: 28     Fields:    Translation:HumansAnimalsCells
    113. Gaillard H, Fitzgerald DJ, Smith CL, Peterson CL, Richmond TJ, Thoma F. Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase. J Biol Chem. 2003 May 16; 278(20):17655-63. PMID: 12637512.
      Citations: 25     Fields:    Translation:Cells
    114. Peterson CL. Transcriptional activation: getting a grip on condensed chromatin. Curr Biol. 2003 Mar 04; 13(5):R195-7. PMID: 12620212.
      Citations: 3     Fields:    Translation:AnimalsCells
    115. Shogren-Knaak MA, Fry CJ, Peterson CL. A native peptide ligation strategy for deciphering nucleosomal histone modifications. J Biol Chem. 2003 May 02; 278(18):15744-8. PMID: 12595522.
      Citations: 44     Fields:    Translation:AnimalsCells
    116. Smith CL, Horowitz-Scherer R, Flanagan JF, Woodcock CL, Peterson CL. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat Struct Biol. 2003 Feb; 10(2):141-5. PMID: 12524530.
      Citations: 83     Fields:    Translation:AnimalsCells
    117. Jaskelioff M, Van Komen S, Krebs JE, Sung P, Peterson CL. Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J Biol Chem. 2003 Mar 14; 278(11):9212-8. PMID: 12514177.
      Citations: 86     Fields:    Translation:Cells
    118. Horn PJ, Peterson CL. Molecular biology. Chromatin higher order folding--wrapping up transcription. Science. 2002 Sep 13; 297(5588):1824-7. PMID: 12228709.
      Citations: 127     Fields:    Translation:AnimalsCells
    119. Langer MR, Fry CJ, Peterson CL, Denu JM. Modulating acetyl-CoA binding in the GCN5 family of histone acetyltransferases. J Biol Chem. 2002 Jul 26; 277(30):27337-44. PMID: 11994311.
      Citations: 30     Fields:    Translation:AnimalsCells
    120. Peterson CL. Chromatin remodeling: nucleosomes bulging at the seams. Curr Biol. 2002 Apr 02; 12(7):R245-7. PMID: 11937040.
      Citations: 26     Fields:    Translation:HumansCells
    121. Peterson CL. Chromatin remodeling enzymes: taming the machines. Third in review series on chromatin dynamics. EMBO Rep. 2002 Apr; 3(4):319-22. PMID: 11943761.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    122. Horn PJ, Carruthers LM, Logie C, Hill DA, Solomon MJ, Wade PA, Imbalzano AN, Hansen JC, Peterson CL. Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes. Nat Struct Biol. 2002 Apr; 9(4):263-7. PMID: 11887184.
      Citations: 59     Fields:    Translation:HumansAnimalsCells
    123. Fry CJ, Peterson CL. Transcription. Unlocking the gates to gene expression. Science. 2002 Mar 08; 295(5561):1847-8. PMID: 11884741.
      Citations: 16     Fields:    Translation:HumansCells
    124. Brower-Toland BD, Smith CL, Yeh RC, Lis JT, Peterson CL, Wang MD. Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc Natl Acad Sci U S A. 2002 Feb 19; 99(4):1960-5. PMID: 11854495.
      Citations: 188     Fields:    Translation:AnimalsCells
    125. Peterson CL. Chromatin: mysteries solved? Biochem Cell Biol. 2001; 79(3):219-25. PMID: 11467736.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    126. Peterson CL. ATP-dependent chromatin remodeling: going mobile. FEBS Lett. 2000 Jun 30; 476(1-2):68-72. PMID: 10878253.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    127. Peterson CL, Logie C. Recruitment of chromatin remodeling machines. J Cell Biochem. 2000 May; 78(2):179-85. PMID: 10842313.
      Citations: 19     Fields:    Translation:AnimalsCells
    128. Peterson CL, Workman JL. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr Opin Genet Dev. 2000 Apr; 10(2):187-92. PMID: 10753786.
      Citations: 177     Fields:    Translation:HumansAnimalsCells
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