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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
One or more keywords matched the following items that are connected to Peterson, Craig
Item TypeName
Academic Article DNA-binding properties of the yeast SWI/SNF complex.
Academic Article Functional analysis of the DNA-stimulated ATPase domain of yeast SWI2/SNF2.
Academic Article Protein complexes for remodeling chromatin.
Academic Article Effects of Sin- versions of histone H4 on yeast chromatin structure and function.
Academic Article The yeast SWI-SNF complex facilitates binding of a transcriptional activator to nucleosomal sites in vivo.
Academic Article Role for ADA/GCN5 products in antagonizing chromatin-mediated transcriptional repression.
Academic Article Catalytic activity of the yeast SWI/SNF complex on reconstituted nucleosome arrays.
Academic Article Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family.
Academic Article Multiple SWItches to turn on chromatin?
Academic Article The core histone N-terminal domains are required for multiple rounds of catalytic chromatin remodeling by the SWI/SNF and RSC complexes.
Academic Article SWI/SNF complex: dissection of a chromatin remodeling cycle.
Academic Article SWI-SNF-mediated nucleosome remodeling: role of histone octamer mobility in the persistence of the remodeled state.
Academic Article Understanding "active" chromatin: a historical perspective of chromatin remodeling.
Academic Article Recruitment of chromatin remodeling machines.
Academic Article Actin-related proteins (Arps): conformational switches for chromatin-remodeling machines?
Academic Article Global role for chromatin remodeling enzymes in mitotic gene expression.
Academic Article SWI/SNF chromatin remodeling requires changes in DNA topology.
Academic Article Chromatin remodeling enzymes: who's on first?
Academic Article The SIN domain of the histone octamer is essential for intramolecular folding of nucleosomal arrays.
Academic Article Transcription. Unlocking the gates to gene expression.
Academic Article Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes.
Academic Article Chromatin remodeling enzymes: taming the machines. Third in review series on chromatin dynamics.
Academic Article Chromatin remodeling: a marriage between two families?
Academic Article Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin.
Academic Article Recruitment of the recombinational repair machinery to a DNA double-strand break in yeast.
Academic Article Coupling tandem affinity purification and quantitative tyrosine iodination to determine subunit stoichiometry of protein complexes.
Academic Article A role for the yeast SWI/SNF complex in DNA replication.
Academic Article The SANT domain: a unique histone-tail-binding module?
Academic Article Cell cycle-regulated histone acetylation required for expression of the yeast HO gene.
Academic Article Purification and biochemical properties of yeast SWI/SNF complex.
Academic Article DNA instructed displacement of histones H2A and H2B at an inducible promoter.
Academic Article Functional interaction between GCN5 and polyamines: a new role for core histone acetylation.
Academic Article A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling.
Academic Article Histone H3 amino-terminal tail phosphorylation and acetylation: synergistic or independent transcriptional regulatory marks?
Academic Article gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair.
Academic Article Promoter targeting and chromatin remodeling by the SWI/SNF complex.
Academic Article Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules.
Academic Article SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster.
Academic Article Genome integrity: a HAT needs a chaperone.
Academic Article The Ino80 chromatin-remodeling enzyme regulates replisome function and stability.
Academic Article The bromodomain: a regulator of ATP-dependent chromatin remodeling?
Academic Article A Rad51 presynaptic filament is sufficient to capture nucleosomal homology during recombinational repair of a DNA double-strand break.
Academic Article The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.
Academic Article Role of chromatin states in transcriptional memory.
Academic Article Recombinational repair within heterochromatin requires ATP-dependent chromatin remodeling.
Academic Article Structural characterization of H3K56Q nucleosomes and nucleosomal arrays.
Academic Article Reconstitution of nucleosomal arrays using recombinant Drosophila ACF and NAP1.
Academic Article Purification of recombinant Drosophila ACF.
Academic Article Purification of recombinant Drosophila NAP1.
Academic Article Purification of mediator from HeLa cell lines expressing a flag-tagged mediator subunit.
Academic Article Chromatin remodeling: nucleosomes bulging at the seams.
Academic Article Modulating acetyl-CoA binding in the GCN5 family of histone acetyltransferases.
Academic Article Identifying cis-acting DNA elements within a control region.
Academic Article Chromatin remodeling by the SWI/SNF complex is essential for transcription mediated by the yeast cell wall integrity MAPK pathway.
Academic Article HDAC's at work: everyone doing their part.
Academic Article Molecular biology. Chromatin higher order folding--wrapping up transcription.
Academic Article Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes.
Academic Article Structural analysis of the yeast SWI/SNF chromatin remodeling complex.
Academic Article A native peptide ligation strategy for deciphering nucleosomal histone modifications.
Academic Article A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme.
Academic Article Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase.
Academic Article DNA repair choice defines a common pathway for recruitment of chromatin regulators.
Academic Article The SWI-SNF complex: a chromatin remodeling machine?
Academic Article Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement.
Academic Article Cellular machineries for chromosomal DNA repair.
Academic Article ATP-dependent chromatin remodeling.
Academic Article ATP-dependent and ATP-independent roles for the Rad54 chromatin remodeling enzyme during recombinational repair of a DNA double strand break.
Academic Article A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation.
Academic Article Histone H4-K16 acetylation controls chromatin structure and protein interactions.
Academic Article Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage.
Academic Article The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing.
Academic Article DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC.
Academic Article Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement.
Academic Article Architecture of the SWI/SNF-nucleosome complex.
Academic Article Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery.
Academic Article Opening the DNA repair toolbox: localization of DNA double strand breaks to the nuclear periphery.
Academic Article Dominant role for signal transduction in the transcriptional memory of yeast GAL genes.
Academic Article Transcriptional memory: mothers SET the table for daughters.
Academic Article Chromatin dynamics during repair of chromosomal DNA double-strand breaks.
Academic Article Purification of epitope-tagged transcription factor IID.
Academic Article Magnesium-agarose electrophoretic mobility shift assay (EMSA) of transcription factor IID binding to DNA.
Academic Article Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity.
Academic Article The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes.
Academic Article SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes.
Academic Article Experimental strategies for the identification of DNA-binding proteins.
Academic Article Experimental strategies for cloning or identifying genes encoding DNA-binding proteins.
Academic Article Confirming the functional importance of a protein-DNA interaction.
Academic Article Releasing the brakes on a chromatin-remodeling enzyme.
Academic Article DNase I footprinting.
Academic Article Nucleosome dynamics regulates DNA processing.
Academic Article Electrophoretic mobility-shift assays.
Academic Article The SMC family: novel motor proteins for chromosome condensation?
Concept Membrane Proteins
Concept DNA-Binding Proteins
Concept MADS Domain Proteins
Concept Silent Information Regulator Proteins, Saccharomyces cerevisiae
Concept High Mobility Group Proteins
Concept Carrier Proteins
Concept Chromosomal Proteins, Non-Histone
Concept Cell Cycle Proteins
Concept Nuclear Proteins
Concept Recombinant Proteins
Concept Phosphate Transport Proteins
Concept Mutant Proteins
Concept Repressor Proteins
Concept Xenopus Proteins
Concept HSP90 Heat-Shock Proteins
Concept Schizosaccharomyces pombe Proteins
Concept Membrane Transport Proteins
Concept Cytoskeletal Proteins
Concept Recombinant Fusion Proteins
Concept Plant Proteins
Concept Fungal Proteins
Concept Saccharomyces cerevisiae Proteins
Concept Drosophila Proteins
Concept Microfilament Proteins
Concept Telomere-Binding Proteins
Concept Cullin Proteins
Concept Tumor Suppressor Proteins
Concept RNA-Binding Proteins
Academic Article Chromatin dynamics: flipping the switch on a chromatin remodeling machine.
Academic Article Chromatin dynamics: interplay between remodeling enzymes and histone modifications.
Academic Article Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres.
Academic Article Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme.
Academic Article Deposition of histone H2A.Z by the SWR-C remodeling enzyme prevents genome instability.
Academic Article The Ino80 complex prevents invasion of euchromatin into silent chromatin.
Academic Article SWI/SNF recruitment to a DNA double-strand break by the NuA4 and Gcn5 histone acetyltransferases.
Academic Article Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C.
Academic Article The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations.
Academic Article Response to Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme".
Academic Article RNA polymerase II depletion promotes transcription of alternative mRNA species.
Academic Article Genomic Nucleosome Organization Reconstituted with Pure Proteins.
Academic Article Hsp90 and p23 Molecular Chaperones Control Chromatin Architecture by Maintaining the Functional Pool of the RSC Chromatin Remodeler.
Academic Article Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair.
Academic Article SIR proteins create compact heterochromatin fibers.
Academic Article Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals.
Academic Article Transient Kinetic Analysis of SWR1C-Catalyzed H2A.Z Deposition Unravels the Impact of Nucleosome Dynamics and the Asymmetry of Histone Exchange.
Academic Article Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability.
Academic Article Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle in Yeast.
Academic Article Mechanism of Long-Range Chromosome Motion Triggered by Gene Activation.
Academic Article INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins.
Academic Article Ruler elements in chromatin remodelers set nucleosome array spacing and phasing.
Concept Ataxia Telangiectasia Mutated Proteins
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