Volume 12, Issue 6, Pages (December 2003)

Slides:



Advertisements
Similar presentations
Volume 13, Issue 2, Pages (January 2004)
Advertisements

Volume 6, Issue 3, Pages (September 2000)
Generation and Interconversion of Multiple Distinct Nucleosomal States as a Mechanism for Catalyzing Chromatin Fluidity  Geeta J. Narlikar, Michael L.
Stimulation of V(D)J recombination by histone acetylation
Nucleosome Sliding via TBP DNA Binding In Vivo
Reconstitution of a Functional Core Polycomb Repressive Complex
Volume 3, Issue 1, Pages (January 1999)
Spontaneous Sharp Bending of Double-Stranded DNA
Volume 9, Issue 4, Pages (April 2002)
Volume 90, Issue 1, Pages (July 1997)
Replication-Independent Histone Deposition by the HIR Complex and Asf1
Ben B. Hopkins, Tanya T. Paull  Cell 
Characterization of a Triple DNA Polymerase Replisome
John D. Leonard, Geeta J. Narlikar  Molecular Cell 
ClpX-Mediated Remodeling of Mu Transpososomes
Volume 30, Issue 1, Pages (April 2008)
Regulation of CSF1 Promoter by the SWI/SNF-like BAF Complex
Volume 35, Issue 1, Pages (July 2009)
Stephen Schuck, Arne Stenlund  Molecular Cell 
Direct Observation of Single MuB Polymers
Volume 6, Issue 5, Pages (November 2000)
The Rpd3 Core Complex Is a Chromatin Stabilization Module
Distinct Strategies to Make Nucleosomal DNA Accessible
Mu Transpososome Architecture Ensures that Unfolding by ClpX or Proteolysis by ClpXP Remodels but Does Not Destroy the Complex  Briana M. Burton, Tania.
Jun Y. Fan, Danny Rangasamy, Karolin Luger, David J. Tremethick 
Xinyang Zhao, P.Shannon Pendergrast, Nouria Hernandez  Molecular Cell 
Programmable RNA Cleavage and Recognition by a Natural CRISPR-Cas9 System from Neisseria meningitidis  Beth A. Rousseau, Zhonggang Hou, Max J. Gramelspacher,
Vidya Subramanian, Pascal Ducept, Robert M. Williams, Karolin Luger 
Volume 6, Issue 5, Pages (November 2000)
Direct Observation of DNA Distortion by the RSC Complex
Nature of the Nucleosomal Barrier to RNA Polymerase II
Volume 37, Issue 6, Pages (March 2010)
HMGN Proteins Act in Opposition to ATP-Dependent Chromatin Remodeling Factors to Restrict Nucleosome Mobility  Barbara P. Rattner, Timur Yusufzai, James.
NAD+-Dependent Modulation of Chromatin Structure and Transcription by Nucleosome Binding Properties of PARP-1  Mi Young Kim, Steven Mauro, Nicolas Gévry,
Ahmed H. Hassan, Kristen E. Neely, Jerry L. Workman  Cell 
Volume 12, Issue 2, Pages (August 2003)
Volume 24, Issue 3, Pages (November 2006)
Volume 1, Issue 1, Pages (December 1997)
Volume 16, Issue 3, Pages (November 2004)
Mikhail Grigoriev, Peggy Hsieh  Molecular Cell 
Joshua C. Black, Janet E. Choi, Sarah R. Lombardo, Michael Carey 
Progressive Structural Transitions within Mu Transpositional Complexes
Volume 43, Issue 4, Pages (August 2011)
Volume 10, Issue 5, Pages (November 2002)
Volume 35, Issue 3, Pages (August 2009)
Volume 13, Issue 2, Pages (January 2004)
Mechanism of 5′-Directed Excision in Human Mismatch Repair
Chromatin Constrains the Initiation and Elongation of DNA Replication
Hansen Du, Haruhiko Ishii, Michael J. Pazin, Ranjan Sen  Molecular Cell 
Xuetong Shen, Ryan Ranallo, Eugene Choi, Carl Wu  Molecular Cell 
Jongbum Kwon, Anthony N Imbalzano, Adam Matthews, Marjorie A Oettinger 
Gaku Mizuguchi, Toshio Tsukiyama, Jan Wisniewski, Carl Wu 
Replication-Independent Histone Deposition by the HIR Complex and Asf1
RSC Unravels the Nucleosome
Chul-Hwan Lee, Jun Wu, Bing Li  Molecular Cell 
Nucleosome Remodeling Induced by RNA Polymerase II
Nucleosomes assembled with FACT have similar MNase digestion pattern as salt-reconstituted nucleosomes. Nucleosomes assembled with FACT have similar MNase.
Site-Specific Ribonuclease Activity of Eukaryotic DNA Topoisomerase I
FACT has moderate nucleosome assembly activity.
Excision of the Drosophila Mariner Transposon Mos1
Replication-Coupled Nucleosome Assembly and Positioning by ATP-Dependent Chromatin-Remodeling Enzymes  Tejas Yadav, Iestyn Whitehouse  Cell Reports  Volume.
SWI/SNF Chromatin Remodeling Requires Changes in DNA Topology
An Early Developmental Transcription Factor Complex that Is More Stable on Nucleosome Core Particles Than on Free DNA  Lisa Ann Cirillo, Kenneth S Zaret 
Transcriptional Regulation by p53 through Intrinsic DNA/Chromatin Binding and Site- Directed Cofactor Recruitment  Joaquin M Espinosa, Beverly M Emerson 
J.Russell Lipford, Stephen P Bell  Molecular Cell 
Ali Hamiche, Raphael Sandaltzopoulos, David A Gdula, Carl Wu  Cell 
ISWI Is an ATP-Dependent Nucleosome Remodeling Factor
Volume 9, Issue 12, Pages (December 2001)
Volume 64, Issue 5, Pages (December 2016)
Volume 3, Issue 1, Pages (January 1999)
Presentation transcript:

Volume 12, Issue 6, Pages 1599-1606 (December 2003) Histone H2A/H2B Dimer Exchange by ATP-Dependent Chromatin Remodeling Activities  Michael Bruno, Andrew Flaus, Chris Stockdale, Chantal Rencurel, Helder Ferreira, Tom Owen-Hughes  Molecular Cell  Volume 12, Issue 6, Pages 1599-1606 (December 2003) DOI: 10.1016/S1097-2765(03)00499-4

Figure 1 The Movement of Nucleosomes beyond DNA Ends Is Expected to Destabilize the Association of One Histone Dimer (A) Nucleosome positioning on the 219 bp MMTV LTR-derived DNA fragment 54A18 was monitored by site directed mapping. Nucleosomes (100 nM) initially positioned at +70 (lane 1) were transformed to a series of new upstream cleavage sites following incubation with RSC (6 nM) and 1 mM Mg:ATP for 20, 40, and 80 min (lanes 2–4). (B) Native gel electrophoresis of samples in (A) shows increased mobility after RSC action, consistent with the relocation toward DNA ends (lanes 1–4). (C) Extended electrophoresis of mapping products from (A) with G ladder and deduced nucleosome positions up to 38 bp beyond the end of the DNA fragment. (D) Orthogonal views of nucleosome with 30 bp DNA removed from one edge. Histone-DNA contacts stabilizing the association of one histone dimer (yellow) are lost. (E) Chromatin assembled onto the 219 bp 54A18 fragment and the 116 bp 0A-31 fragment was purified by native gel electrophoresis and the histone content assessed by SDS PAGE. Molecular Cell 2003 12, 1599-1606DOI: (10.1016/S1097-2765(03)00499-4)

Figure 2 ATP-Dependent Histone H2A/H2B Dimer Transfer by the RSC Complex Nucleosomes (200 nM) comprising Cy5 labeled 54A18 DNA were incubated in the presence or absence of a 4-fold molar excess of tetramer on Cy5 labeled 0A0 DNA, 7 nM RSC, and 1 mM Mg:ATP as indicated. (A) shows the Cy5 signal from DNA and (B) the Oregon Green labeled histones. Transfer of Oregon Green fluorescence from the remodeled 54A18 nucleosomes onto 0A0/tetramer is detected in the presence of RSC and ATP (lane 7). Transfer also occurs when Oregon green is attached to H2B, but not when it is attached to H4 (lanes 9 and 11). (C) monitors the fate of Oregon Green H2A during remodeling by RSC (20 nM) for 0, 10s, 30s, 1.5 min, 5 min, 15 min, 45 min, and 120 min in lanes 1–8, respectively. The signal is lost from the initial position and appears at intermediate locations before accumulating as a more discrete species that is likely to represent nucleosomes at and beyond the end of the fragment (see Figure 1). The majority of the H2A/H2B transfer onto 0A0 occurs late in the reaction. The temporal relationship between the different species is illustrated in (D). In order to confirm that attachment of dyes did not affect the positioning or movement of nucleosomes, a comparison of the variant octamers was made (Supplemental Figure S1). Molecular Cell 2003 12, 1599-1606DOI: (10.1016/S1097-2765(03)00499-4)

Figure 3 Dimer Exchange by Other ATP-Dependent Remodeling Activities (A) Dimer exchange assays were performed using 54A18 nucleosomes (200 nM) labeled with Oregon Green on H2A and a 4-fold molar excess of 0A0/tetramer (as described in Figure 2), 1 mM Mg:ATP, and increasing concentrations of Drosophila ISWI protein (0, 50 and 100 nM, lanes 1–3, respectively) and yeast SWI/SNF complex (0, 14, and 28 nM, lanes 4–6, respectively). (B) The IOC2 containing ISW1b and IOC3 containing ISW1a complexes were also tested for dimer exchange activity as in (A). Lanes 1 to 4 contain 0, 3.5, 7, and 35 nM ISW1b complex and 1 mM Mg:ATP as indicated. Lanes 6–9 contain 0, 3.5, 7, and 35 nM ISW1a complex and 1 mM Mg:ATP. Lanes 5 and 10 contain 35 nM ISW1b and ISW1a but no Mg:ATP. ISW1b causes an increase in nucleosome mobility consistent with the relocation of nucleosomes toward DNA ends and a modest exchange of dimer. ISW1a causes a subtle decrease in nucleosome mobility consistent with the movement of nucleosomes to a more central location and does not significantly increase dimer exchange. Molecular Cell 2003 12, 1599-1606DOI: (10.1016/S1097-2765(03)00499-4)

Figure 4 Dimer Transfer on Multinucleosome Templates (A) In order to assay dimer exchange between nucleosomes, a 10-mer tandem repeat of a 177 bp NucA positioning sequence was reconstituted with wild-type histone octamer, and used as an acceptor (10× NucA array) in exchange reactions. Remodeling reactions were performed in the presence of 200 nM Oregon Green labeled 54A18 nucleosome, 17.5 nM RSC, and 1 mM Mg:ATP as indicated and the products resolved on a 1% agarose 1×TBE gel. Dimer transfer was observed in the presence of 0.8 μM acceptor (lanes 3 and 4) and 4 μM (lanes 5 and 6), but not observed in its absence (lanes 1 and 2). (B) Circular plasmid DNA (5 kb) reconstituted with Oregon Green H2A labeled histone octamer (800 nM) was incubated with a 8 μM 10× NucA array in the presence of 1 mM Mg:ATP and increasing concentrations of RSC complex (0, 3.5, 7, and 35 nM RSC, lanes 1, 2, 3, and 4, respectively). Histone H4 occupancy was monitored by preparing an identical series of reactions as lanes 1–5 except that Oregon Green was labeled at H4 on the reconstituted plasmid (lanes 6–10). (C) The integrity of plasmid DNA was monitored during the course of remodeling in the presence of RSC complex. Chromatin assembled plasmid DNA was incubated with RSC complex as in (B). Following remodeling protein was removed by digestion with proteinase K and the plasmid DNA analyzed by agarose gel electrophoresis. No linear DNA could be detected. Molecular Cell 2003 12, 1599-1606DOI: (10.1016/S1097-2765(03)00499-4)