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Search Results to Craig L Peterson PhD

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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.

Figure

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 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 Roles of the histone H2A-H2B dimers and the (H3-H4)(2) tetramer in nucleosome remodeling by the SWI-SNF complex.
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 Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.
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 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 Phosphorylation of histone H4 serine 1 during DNA damage requires casein kinase II in S. cerevisiae.
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 Promoter targeting and chromatin remodeling by the SWI/SNF complex.
Academic Article Functional delineation of three groups of the ATP-dependent family of chromatin remodeling enzymes.
Academic Article ATP-dependent chromatin remodeling: going mobile.
Academic Article The Ino80 chromatin-remodeling enzyme regulates replisome function and stability.
Academic Article Chromatin: mysteries solved?
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 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 Chromatin immunoprecipitation (ChIP).
Academic Article The INO80 family of chromatin-remodeling enzymes: regulators of histone variant dynamics.
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 Chromatin and the genome integrity network.
Academic Article Transcriptional activation: getting a grip on condensed chromatin.
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 Chromatin and transcription: histones continue to make their marks.
Academic Article The SWI-SNF complex: a chromatin remodeling machine?
Academic Article Cellular machineries for chromosomal DNA repair.
Academic Article Histones and histone modifications.
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 Effects of HMGN1 on chromatin structure and SWI/SNF-mediated chromatin remodeling.
Academic Article Histone H4-K16 acetylation controls chromatin structure and protein interactions.
Academic Article Switching on chromatin: mechanistic role of histone H4-K16 acetylation.
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 Profound challenges do remain in our understanding of the mechanisms of gene regulation.
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 In vivo DNase I, MNase, and restriction enzyme footprinting via ligation-mediated polymerase chain reaction (LM-PCR).
Academic Article Dominant role for signal transduction in the transcriptional memory of yeast GAL genes.
Academic Article Chromatin dynamics during repair of chromosomal DNA double-strand breaks.
Academic Article Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity.
Academic Article Chromatin: a ubiquitin crowbar opens chromatin.
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 Releasing the brakes on a chromatin-remodeling enzyme.
Academic Article Nucleosome dynamics regulates DNA processing.
Academic Article Nucleosome dynamics as modular systems that integrate DNA damage and repair.
Academic Article The SMC family: novel motor proteins for chromosome condensation?
Concept Gene Expression Regulation, Fungal
Concept Chromatin Immunoprecipitation
Concept Chromatin
Concept Gene Expression Regulation
Concept Gene Expression Regulation, Enzymologic
Concept Chromatin Assembly and Disassembly
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 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 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 Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis.
Academic Article Response to Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme".
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 Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes.
Academic Article Chromatin remodeling: a complex affair.
Academic Article Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals.
Academic Article Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6.

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