Research Topics
| Craig PetersonSummaryAffiliation: University of Massachusetts Medical School Country: USA Publications
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Publications
Promoter targeting and chromatin remodeling by the SWI/SNF complexC L Peterson
Department of Biochemistry and Molecular Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA
Curr Opin Genet Dev 10:187-92. 2000....- Transcriptional activation: getting a grip on condensed chromatinCraig L Peterson
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Biotech 2, Suite 210, Worcester, MA 01605, USA
Curr Biol 13:R195-7. 2003..A recent study, however, suggests a different and surprising viewpoint in which these protein assemblies are quite dynamic and individual subunits play key roles in chromatin remodeling... 
Transcriptional memory: mothers SET the table for daughtersCraig L Peterson
Program in Molecular Medicine, 373 Plantation Street, University of Massachusetts Medical School, Worcester, MA 01605, USA
Curr Biol 20:R240-2. 2010..A recent study, however, shows that mothers and their daughters share similar transcriptional frequencies, and inheritance of mother's transcriptional tendencies requires methylation of histone H3 by a Set1 methyltransferase...- Genome integrity: a HAT needs a chaperoneCraig L Peterson
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Curr Biol 17:R324-6. 2007..Four groups have now identified protein Rtt109p as the catalytic subunit of a novel histone H3 acetylase complex that harbors a histone chaperone subunit essential for significant activity... 
Chromatin remodeling enzymes: taming the machines. Third in review series on chromatin dynamicsCraig L Peterson
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
EMBO Rep 3:319-22. 2002....- Chromatin remodeling: nucleosomes bulging at the seamsCraig L Peterson
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
Curr Biol 12:R245-7. 2002..Recent mechanistic studies suggest that these enzymes generate localized changes in DNA topology that drive formation of multiple, remodeled nucleosomal states... - Cellular machineries for chromosomal DNA repairCraig L Peterson
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester 01605, USA
Genes Dev 18:602-16. 2004 - Transcription. Unlocking the gates to gene expressionChristopher J Fry
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Science 295:1847-8. 2002 - Chromatin dynamics during repair of chromosomal DNA double-strand breaksManisha Sinha
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
Epigenomics 1:371-85. 2009..In particular, we discuss recent studies implicating specialized roles for several, distinct ATP-dependent chromatin remodeling enzymes in facilitating multiple steps within the homologous recombination process... - Histones and histone modificationsCraig L Peterson
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Curr Biol 14:R546-51. 2004 - Chromatin: mysteries solved?C L Peterson
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester 01605, USA
Biochem Cell Biol 79:219-25. 2001..This view could not be further from the truth! Here I briefly outline four areas of chromatin research where new paradigms and mysteries are still waiting to be discovered... - ATP-dependent chromatin remodeling: going mobileC L Peterson
Program in Molecular Medicine and Department of Biochemistry and Molecular Biology, Biotech 2, Suite 301, 373 Plantation St, 01605, Worcester, MA, USA
FEBS Lett 476:68-72. 2000..Here the biochemical properties of these enzymes are reviewed and the manner in which ATP-driven nucleosome movements might account for many of these diverse activities is discussed... - Recruitment of chromatin remodeling machinesC L Peterson
Program in Molecular Medicine and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
J Cell Biochem 78:179-85. 2000..Here we review these recent observations and discuss the implications for gene-specific regulation by chromatin remodeling machines... - Histone H4-K16 acetylation controls chromatin structure and protein interactionsMichael Shogren-Knaak
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Science 311:844-7. 2006.... - Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymesLaurie A Boyer
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Mol Cell 10:935-42. 2002..Our results are consistent with a general role for SANT domains in functional interactions with histone N-terminal tails... - ATP-dependent and ATP-independent roles for the Rad54 chromatin remodeling enzyme during recombinational repair of a DNA double strand breakBranden Wolner
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St, Worcester, Massachusetts 01605, USA
J Biol Chem 280:10855-60. 2005..We also identify a novel Rad54-dependent chromatin remodeling event that occurs in vivo during the DNA strand invasion step of HR. This ATP-dependent remodeling activity of Rad54 appears to control subsequent steps in the HR process... - Molecular biology. Chromatin higher order folding--wrapping up transcriptionPeter J Horn
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
Science 297:1824-7. 2002..We also discuss evidence suggesting that adenosine-5'-triphosphate-dependent chromatin-remodeling enzymes and histone-modifying enzymes may regulate transcription by controlling the extent and dynamics of chromatin higher order folding... - Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatinMariela Jaskelioff
Interdisciplinary Graduate Program and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
J Biol Chem 278:9212-8. 2003..Taken together, our results indicate that Rad54p is a chromatin-remodeling enzyme that promotes homologous DNA pairing events within the context of chromatin... - Dominant role for signal transduction in the transcriptional memory of yeast GAL genesSharmistha Kundu
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
Mol Cell Biol 30:2330-40. 2010.... - The SIN domain of the histone octamer is essential for intramolecular folding of nucleosomal arraysPeter J Horn
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Nat Struct Biol 9:167-71. 2002..Our results suggest that Sin- versions of histones may alleviate the need for SWI/SNF in vivo by disrupting higher-order chromatin folding... - SWI/SNF is required for transcriptional memory at the yeast GAL gene clusterSharmistha Kundu
Interdisciplinary Graduate Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genes Dev 21:997-1004. 2007..Genetic studies indicate that SWI/SNF controls transcriptional memory by antagonizing ISWI-like chromatin remodeling enzymes... - Modulating acetyl-CoA binding in the GCN5 family of histone acetyltransferasesMichael R Langer
Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97201-3098, USA
J Biol Chem 277:27337-44. 2002..In each case, the A190T derivative behaved similarly to wild type GCN5, suggesting that the efficacy of HAT activity by GCN5 is not limited by the availability of nuclear acetyl-CoA pools... - Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacementXiaofang Yang
Interdisciplinary Graduate Program, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Nat Struct Mol Biol 14:540-7. 2007..Our data indicate that H2A-H2B dimer loss is not an obligatory consequence of ATP-dependent DNA translocation, and furthermore they suggest that SWI/SNF is composed of at least four interdependent modules... - A Rad51 presynaptic filament is sufficient to capture nucleosomal homology during recombinational repair of a DNA double-strand breakManisha Sinha
Program in Molecular Medicine, Interdisciplinary Graduate Program, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
Mol Cell 30:803-10. 2008..Thus, contrary to popular belief, nucleosomes do not pose a potent barrier for successful recognition and capture of homology by an invading presynaptic filament... - A native peptide ligation strategy for deciphering nucleosomal histone modificationsMichael A Shogren-Knaak
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
J Biol Chem 278:15744-8. 2003..This difference between peptide and array substrates suggests that the ability to generate specifically modified nucleosomal arrays should provide a powerful tool for understanding the effects of post-translational histone modifications... - Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymesPeter J Horn
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Nat Struct Biol 9:263-7. 2002..These results suggest that linker histones exert a global, genome-wide control over remodeling activities, implicating a new, obligatory coupling between linker histone kinases and ATP-dependent remodeling enzymes... - Structural characterization of H3K56Q nucleosomes and nucleosomal arraysShinya Watanabe
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St, Worcester, MA 01605, USA
Biochim Biophys Acta 1799:480-6. 2010..Our data suggests that H3K56 acetylation is one of the molecular mechanisms employed to keep chromatin with nucleosome-free regions accessible to the DNA replication and repair machinery... - Architecture of the SWI/SNF-nucleosome complexMekonnen Lemma Dechassa
Department of Biochemistry and Molecular Biology, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL 62901 4413, USA
Mol Cell Biol 28:6010-21. 2008..The highly conserved Snf5 subunit associates with the histone octamer and not with nucleosomal DNA. The model of the binding trough of SWI/SNF illustrates how nucleosomal DNA can be mobilized while SWI/SNF remains bound... - The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencingChristopher J Fry
Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, Suite 210, Worcester, MA 01605, USA
Mol Cell Biol 26:9045-59. 2006..Our study shows that structurally similar nucleosomal surfaces provide distinct functionalities in vivo and in vitro... - Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damageManolis Papamichos-Chronakis
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genes Dev 20:2437-49. 2006..We propose that Ino80 and Swr1 function antagonistically at chromatin surrounding a DSB, and that they regulate the incorporation of different histone H2A variants that can either promote or block cell cycle checkpoint adaptation... - The ins and outs of heterochromatic DNA repairCraig L Peterson
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
Dev Cell 20:285-7. 2011..A recent study by Chiolo et al. (2011) published in Cell finds that DNA double-strand breaks formed within heterochromatin are shuttled to adjacent sites that are "safe" to complete repair by recombination... - ATP-dependent chromatin remodelingCorey L Smith
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Curr Top Dev Biol 65:115-48. 2005..This chapter provides an introduction to the structure of chromatin and then describes how special classes of enzymes modulate chromatin structure to allow access to DNA... - A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodelingCorey L Smith
Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, Suite 210, Worcester, Massachusetts 01605, USA
Mol Cell Biol 25:5880-92. 2005..Interestingly, motif V of the human Swi2p/Snf2p homolog, Brg1p, has been shown to be a possible hot spot for mutational alterations associated with cancers... - Structural analysis of the yeast SWI/SNF chromatin remodeling complexCorey L Smith
University of Massachusetts Medical School, Program in Molecular Medicine, Worcester 01605, USA
Nat Struct Biol 10:141-5. 2003..We also report a three-dimensional reconstruction of yeast SWI/SNF derived from electron micrographs... - Recombinational repair within heterochromatin requires ATP-dependent chromatin remodelingManisha Sinha
University of Massachusetts Medical School, Worcester, MA 01605, USA
Cell 138:1109-21. 2009..These results suggest that recombinational repair in the context of heterochromatin presents additional constraints that can be overcome by ATP-dependent chromatin-remodeling enzymes... - Role of chromatin states in transcriptional memorySharmistha Kundu
Interdisciplinary Graduate Program and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Biochim Biophys Acta 1790:445-55. 2009..We also discuss illuminating cases of cellular memory in budding yeast and evaluate whether transcriptional memory in yeast is nuclear or cytoplasmically inherited... - Mechanisms that regulate localization of a DNA double-strand break to the nuclear peripheryPranav Oza
Program in Molecular Medicine, Interdisciplinary Graduate Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genes Dev 23:912-27. 2009..Based on these findings, we propose that sequestration of unrepaired or slowly repaired DSBs to the nuclear periphery reflects a competition between alternative repair pathways... - Switching on chromatin: mechanistic role of histone H4-K16 acetylationMichael Shogren-Knaak
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
Cell Cycle 5:1361-5. 2006..The potential significance of this finding for in vivo chromatin structure, establishment of euchromatic domains, and promotion of gene transcription is examined... - Effects of HMGN1 on chromatin structure and SWI/SNF-mediated chromatin remodelingDavid A Hill
Department of Cell Biology at the University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
J Biol Chem 280:41777-83. 2005..We further demonstrate that HMGN1 does not affect SWI/SNF-dependent chromatin remodeling on either mononucleosomes or nucleosomal arrays, indicating that SWI/SNF functions independently of HMGN1... - Chromatin and transcription: histones continue to make their marksMariela Jaskelioff
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St, Worcester, MA 01605, USA
Nat Cell Biol 5:395-9. 2003 - HDAC's at work: everyone doing their partCraig L Peterson
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Mol Cell 9:921-2. 2002..A recent report of genome-wide, microarray maps of histone acetylation has uncovered the intragenic targets for six different yeast HDACs and has led to the discovery of new heterochromatin-like domains... - Opening the DNA repair toolbox: localization of DNA double strand breaks to the nuclear peripheryPranav Oza
Interdisciplinary Graduate Program, University of Massachusetts Medical School, Worcester, MA, USA
Cell Cycle 9:43-9. 2010..In this Extra View, we discuss these recent reports, and we show that the Est1 component of the telomerase machinery plays an essential role in anchoring DSB chromatin to the nuclear envelope protein, Mps3... - Recruitment of the recombinational repair machinery to a DNA double-strand break in yeastBranden Wolner
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Mol Cell 12:221-32. 2003..These studies provide a near comprehensive view of the molecular events required for the in vivo assembly of a functional Rad51p presynaptic filament... - Heterochromatin assembly: a new twist on an old modelPeter J Horn
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St, Biotech 2, Suite 210, Worcester, 01605, USA
Chromosome Res 14:83-94. 2006..Recent studies have also identified a novel E3 ubiquitin ligase universally required for H3 K9 methylation. Here we outline these studies and propose several models for the role of this E3 ligase in heterochromatin assembly... - Coupling tandem affinity purification and quantitative tyrosine iodination to determine subunit stoichiometry of protein complexesCorey L Smith
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Biotech II Suite 210, Worcester, MA 01605, USA
Methods 31:104-9. 2003.... - The Ino80 chromatin-remodeling enzyme regulates replisome function and stabilityManolis Papamichos-Chronakis
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Biotechnology 2, Suite 210, Worcester, Massachusetts 01605, USA
Nat Struct Mol Biol 15:338-45. 2008..Our data indicate that the chromatin-remodeling activity of Ino80 regulates efficient progression of replication forks and that Ino80 has a crucial role in stabilizing a stalled replisome to ensure proper restart of DNA replication... - Polyamine analogues: potent inducers of nucleosomal array oligomerization and inhibitors of yeast cell growthLenny M Carruthers
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Drive, Biotech 2, Suite 210, Worcester, MA 01605, USA
Biochem J 405:541-5. 2007..We find that a class of long-chain polyamines called oligoamines are potent inducers of nucleosomal array oligomerization in vitro and that these same polyamine analogues rapidly block yeast cell growth... - Creating designer histones by native chemical ligationMichael A Shogren-Knaak
University of Massachusetts Medical School, Worchester, Massachusetss 01605, USA
Methods Enzymol 375:62-76. 2004 - A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formationPeter J Horn
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Genes Dev 19:1705-14. 2005..These studies provide evidence for a novel Rik1-associated E3 ubiquitin ligase that is required for heterochromatin formation... - Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNABrent D Brower-Toland
Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
Proc Natl Acad Sci U S A 99:1960-5. 2002..When arrays were relaxed before the dissociated state was reached, nucleosomes were able to reassemble and to repeat the disassembly process. The kinetic parameters for nucleosome disassembly also have been determined... - DNA instructed displacement of histones H2A and H2B at an inducible promoterGuillermo P Vicent
, Universitat Pompeu Fabra, , E-08003 Barcelona, Spain
Mol Cell 16:439-52. 2004..In MMTV nucleosome arrays, SWI/SNF displaces H2A and H2B from nucleosome B and not from the adjacent nucleosome. Thus, the outcome of nucleosome remodeling by SWI/SNF depends on DNA sequence... - Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyaseHélène Gaillard
Institut für Zellbiologie and Institut für Molekularbiologie, Departement Biologie, ETH Honggerberg, CH 8093 Zurich, Switzerland
J Biol Chem 278:17655-63. 2003..Similar activities might relieve the inhibitory effect of nucleosomes on DNA repair processes in living cells... - DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSCYongli Zhang
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
Mol Cell 24:559-68. 2006..Such loop formation may provide a molecular basis for the biological functions of remodelers... - Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA moleculesAlla Shundrovsky
Cornell University, Department of Physics, Laboratory of Atomic and Solid State Physics, Ithaca, New York 14853, USA
Nat Struct Mol Biol 13:549-54. 2006..These results impose substantial constraints on the mechanism of SWI/SNF remodeling... - Phosphorylation of histone H4 serine 1 during DNA damage requires casein kinase II in S. cerevisiaeWang L Cheung
Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland 21210, USA
Curr Biol 15:656-60. 2005..CK2 has been implicated in regulating a DNA-damage response; our data suggest that histone H4 S1 is one of its physiological substrates. These data suggest that this modification is a part of the DNA-repair histone code... - gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repairDipanjan Chowdhury
CBR Institute for Biomedical Research and The Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
Mol Cell 20:801-9. 2005..The effect of PP2A on gamma-H2AX levels is independent of ATM, ATR, or DNA-PK activity... - The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genomeYutao Fu
Bioinformatics Program, Boston University, Boston, Massachusetts, USA
PLoS Genet 4:e1000138. 2008..We suggest that binding of CTCF provides an anchor point for positioning nucleosomes, and chromatin remodeling is an important component of CTCF function... - The SANT domain: a unique histone-tail-binding module?Laurie A Boyer
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
Nat Rev Mol Cell Biol 5:158-63. 2004 - Profound challenges do remain in our understanding of the mechanisms of gene regulationSteven J Triezenberg
Biochim Biophys Acta 1779:1-2. 2008
Research Grants
- Yeast Chromatin Structure and FunctionCraig Peterson; Fiscal Year: 2005..These studies will test the hypothesis that these histone variants create specialized chromatin structures. ..
- Analysis of SWI1, SWI2, amd SWI3 proteinsCraig Peterson; Fiscal Year: 2005..This aim also describes a conditional degron strategy to define the role(s) of individual SWI/SNF subunits for both in vivo and in vitro functions ..
- Analysis of yeast chromatin structure and functionCraig Peterson; Fiscal Year: 2007..The fourth aim will investigate the role of a novel casein kinase 2-dependent phosphorylation of histone H4 Serine 1 in DSB repair. ..
- Analysis of the yeast SWI1, SWI2, and SWI3 proteinsCraig Peterson; Fiscal Year: 2007..This machine is essential for mammalian development and inactivation of human SWI/SNF leads to a variety of cancers. ..
- Analysis of yeast chromatin structure and functionCraig Peterson; Fiscal Year: 2009..The fourth aim will investigate the role of a novel casein kinase 2-dependent phosphorylation of histone H4 Serine 1 in DSB repair. ..
- YEAST SWI1, SWI2, AND SWI3 PROTEINSCraig Peterson; Fiscal Year: 1993..The results from the proposed studies will enrich our knowledge of the global role that SWI products play in transcription and provide valuable insights into the mechanisms for regulating transcription by RNA polymerase II...
- YEAST CHROMATIN STRUCTURE/FUNCTIONCraig Peterson; Fiscal Year: 2000....
- YEAST SWI1, SWI2, AND SWI3 PROTEINSCraig Peterson; Fiscal Year: 2001..The fifth aim will use in vivo labeling and in vitro association assays to investigate the subunit organization of SWI/SNF. ..
- Yeast Chromatin Structure and FunctionCraig L Peterson; Fiscal Year: 2010..Consequently, defects in these pathways can impact cell survival and maintenance of genome integrity. The studies described here will investigate the role of key enzymes and structural proteins that regulate these events. ..