Direct Observation of DNA Distortion by the RSC Complex

Lia, Giuseppe; Praly, Elise; Ferreira, Helder; Stockdale, Chris; Tse-Dinh, Yuk Ching; Dunlap, David; Croquette, Vincent; Bensimon, David; Owen-Hughes, Tom

doi:10.1016/j.molcel.2005.12.013

Cited by 149 publications

(171 citation statements)

References 28 publications

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“…Translocation ceased at tensions >12 pN, the motor 'stall force'. Interestingly, as in the magnetic-tweezers study 49 , there was evidence of pausing and reverse translocation, the ATP-dependent retraction of the DNA loop. Thus, SWI/SNF and RSC translocate DNA loops onto nucleosomes, and they impart sufficient force to disrupt several histone-DNA contacts, but not a 'rip force' that can disrupt all the contacts at once (requiring >20 pN).…”

Section: Optical Tweezersmentioning

confidence: 57%

“…This type of analysis demonstrated that loops confined by RSC contained negative supercoils 49 , as RSC translocation imparted positive supercoils or twist to the flanking region (not depicted in Fig. 2a).…”

Section: Magnetic Tweezersmentioning

confidence: 88%

“…In recent single-molecule studies, the DNA translocation and force parameters of the remodelers SWI/SNF, RSC and Rad54 have been measured directly. Each study used a different single-molecule technique: two studies monitored the ability of the remodeler to form DNA loops (via translocation) within a single DNA molecule (or single nucleosome) in real time 49,50 , two studies imaged remodeler movement along DNA in real time 46,51 , and one study analyzed single nucleosomes after SWI/SNF action 52 (see Fig. 2 legend for an explanation of each method).…”

Section: Single-molecule Analysis Of Remodeler Mechanismsmentioning

confidence: 99%

“…Lia et al 49 used magnetic tweezers with a tethered single DNA molecule (Fig. 2a) to show that a single RSC complex creates a confined, negatively supercoiled DNA loop.…”

Section: Magnetic Tweezersmentioning

confidence: 99%

“…Movement of the translocase domain creates a confined DNA loop that shortens the apparent end-to-end length of the DNA molecule. The studies of Lia et al 49 provided the first direct observations of DNA translocation by a remodeler in a single-molecule experiment. RSC translocated DNA at high speeds (200 bp per second) and for considerable distances (averaging ∼420 bp) under conditions of very low tension (0.3 pN).…”

Section: Magnetic Tweezersmentioning

confidence: 99%

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Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

227

208

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Chromatin remodelers are ATP-hydrolyzing machines specialized to restructure, mobilize or eject nucleosomes, allowing regulated exposure of DNA in chromatin. Recently, remodelers have been analyzed using single-molecule techniques in real time, revealing them to be complex DNA-pumping machines. The results both support and challenge aspects of current models of remodeling, supporting the idea that the remodeler translocates or pumps DNA loops into and around the nucleosome, while also challenging earlier concepts about loop formation, the character of the loop and how it propagates. Several complex behaviors were observed, such as reverse translocation and long translocation bursts of the remodeler, without appreciable DNA twist. This review presents and discusses revised models for nucleosome sliding and ejection that integrate this new information with the earlier biochemical studies.Many processes involving chromosomes are guided by DNA-binding proteins, and the access of these proteins to DNA is regulated by chromatin. Nucleosomes, the primary repeating unit of chromatin, package DNA by wrapping 147 base pairs (bp) around an octamer of histone proteins in ∼1.7 helical turns 1-3 . This packaging provides topological order but occludes one face of the DNA, which slows or prevents the recognition of DNA sequences by DNA-binding proteins. To maintain topological order, and also to allow rapid and regulated access to the DNA, cells have evolved a set of chromatin-remodeling machines that alter nucleosome position, presence and structure.Remodelers can be separated into several families on the basis of their composition and activities: SWI/SNF, ISWI, NURD/Mi-2/CHD and the 'split ATPases' INO80 and SWR1 (which bear an insertion within their ATPase domains). Rad54 may represent an additional family, as it perturbs chromatin in vitro, but it apparently lacks specific nucleosome-interacting domains 4,5 . The participation of remodelers in various chromosomal processes has been the subject of many reviews 6-9 . The present work focuses solely on remodeler mechanisms, and primarily on the function of their conserved catalytic subunit, a superfamily 2 (SF2) ATPdependent DNA translocase. Recently, single-molecule approaches have been used to examine several remodelers, providing many new insights into their behavior. Here I discuss these recent studies, compare them with previous biochemical studies and suggest refinements to existing models to account for some of the observations. Remodelers slide, eject and restructure nucleosomesRemodelers can affect nucleosomes in at least four ways ( Fig. 1): (i) sliding, or moving the histone octamer to a new position, which exposes DNA 10-12 ; (ii) ejection, or completely displacing the octamer to expose DNA [13][14][15][16] ; (iii) removal of H2A-H2B dimers, leaving only the central H3-H4 tetramer, which exposes DNA and destabilizes the nucleosome 17,18 ; and (iv) dimer replacement-for example, exchanging the resident H2A-H2B dimers for dimers NIH Public Access

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Section: Optical Tweezersmentioning

confidence: 57%

Section: Magnetic Tweezersmentioning

confidence: 88%

Section: Single-molecule Analysis Of Remodeler Mechanismsmentioning

confidence: 99%

“…Lia et al 49 used magnetic tweezers with a tethered single DNA molecule (Fig. 2a) to show that a single RSC complex creates a confined, negatively supercoiled DNA loop.…”

Section: Magnetic Tweezersmentioning

confidence: 99%

Section: Magnetic Tweezersmentioning

confidence: 99%

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Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

227

208

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Chromatin Remodeling and Nucleosome Positioning

Längst

Teif

Rippe

2011

Genome Organization and Function in the Cell Nucleus

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ATP‐dependent looping of DNA by ISWI

Lia

Indrieri

Owen-Hughes

et al. 2008

Journal of Biophotonics

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Snf2 related chromatin remodelling enzymes possess an ATPase subunit similar to that of the SF-II helicases which hydrolyzes ATP to track along DNA. Translocation and any resulting torque in the DNA could drive chromatin remodeling. To determine whether the ISWI protein can translocate and generate torque, tethered particle motion experiments and atomic force microscopy have been performed using recombinant ISWI expressed in E. coli. In the absence of ATP, ISWI bound to and wrapped DNA thereby shortening the overall contour length measured in atomic force micrographs. Although naked DNA only weakly stimulates ATP hydrolysis by ISWI, both atomic force microscopy and tethered particle motion data indicate that the protein generated loops in the presence of ATP. The duration of the looped state of the DNA measured using tethered particle motion was ATP-dependent. Finally, ISWI relaxed positively supercoiled plasmids visualized by atomic force microscopy. While other chromatin remodeling ATPases catalyze either DNA wrapping or looping, both are catalyzed by ISWI.

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Direct Observation of DNA Distortion by the RSC Complex

Cited by 149 publications

References 28 publications

Chromatin remodeling: insights and intrigue from single-molecule studies

Chromatin remodeling: insights and intrigue from single-molecule studies

Chromatin Remodeling and Nucleosome Positioning

ATP‐dependent looping of DNA by ISWI

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