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Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence.

van Vugt JJ, de Jager M, Murawska M, Brehm A, van Noort J, Logie C - PLoS ONE (2009)

Bottom Line: Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps.Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA.This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, NCMLS, Radboud University, Nijmegen, The Netherlands. j.vanvugt@ncmls.ru.nl;

ABSTRACT

Background: Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted.

Methodology/principal findings: We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps.

Conclusions/significance: Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.

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Quantification of remodeled nucleosome position.The nucleosome position was determined relative to the normalized DNA contour length. The histograms show the relative nucleosome displacement when remodeling without (top) or with (bottom) ATP. We could not discriminate to which DNA arm each nucleosome was translocated. The relative nucleosome displacement is 0 for the DNA center from where the nucleosome translocation is initiated and 1 for the DNA end. A) Mononucleosome with 240 bp arms with (N = 124) or without (N = 112) ATP. Bin size 48 bp. B) Mononucleosome with 1200 bp arms with (N = 204) or without (N = 194) ATP. Bin size 120 bp. C) AFM image of mononucleosomes with 1200 bp arms of which one with RSC bound to a DNA end. Scale bare is 100 nm, z-range 4 nm.
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pone-0006345-g003: Quantification of remodeled nucleosome position.The nucleosome position was determined relative to the normalized DNA contour length. The histograms show the relative nucleosome displacement when remodeling without (top) or with (bottom) ATP. We could not discriminate to which DNA arm each nucleosome was translocated. The relative nucleosome displacement is 0 for the DNA center from where the nucleosome translocation is initiated and 1 for the DNA end. A) Mononucleosome with 240 bp arms with (N = 124) or without (N = 112) ATP. Bin size 48 bp. B) Mononucleosome with 1200 bp arms with (N = 204) or without (N = 194) ATP. Bin size 120 bp. C) AFM image of mononucleosomes with 1200 bp arms of which one with RSC bound to a DNA end. Scale bare is 100 nm, z-range 4 nm.

Mentions: The remodeling potency of RSC is further demonstrated by its ability to reposition a single nucleosome over at least 1200 bp (Figure 3). The accumulation of nucleosomes at the DNA end indicates that RSC does not move nucleosomes away from the DNA end. Careful tracing of the DNA contour revealed that DNA in remodeled nucleosomal templates appeared on average 13 nm, or 38 bp, longer than that in centrally positioned nucleosomes (197±26 nm (N = 49) vs. 184±26 nm (N = 62), Figure S2). We observed a 5% decrease in nucleosome volume (420±81 nm3 vs 402±94 nm3). This indicates that no histone proteins were lost as H2A-H2B dimer dissociation results in a much larger volume loss [50], [51]. It has been reported before that RSC, like SWI/SNF, positions nucleosomes slightly over the DNA end [38], [43], [52], [53]. The fact that RSC is apparently not able to translocate the nucleosomes from the DNA ends suggests that RSC needs free DNA upstream of the nucleosome translocation direction and thus ‘pushes’ nucleosomes rather than ‘pulling’ them.


Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence.

van Vugt JJ, de Jager M, Murawska M, Brehm A, van Noort J, Logie C - PLoS ONE (2009)

Quantification of remodeled nucleosome position.The nucleosome position was determined relative to the normalized DNA contour length. The histograms show the relative nucleosome displacement when remodeling without (top) or with (bottom) ATP. We could not discriminate to which DNA arm each nucleosome was translocated. The relative nucleosome displacement is 0 for the DNA center from where the nucleosome translocation is initiated and 1 for the DNA end. A) Mononucleosome with 240 bp arms with (N = 124) or without (N = 112) ATP. Bin size 48 bp. B) Mononucleosome with 1200 bp arms with (N = 204) or without (N = 194) ATP. Bin size 120 bp. C) AFM image of mononucleosomes with 1200 bp arms of which one with RSC bound to a DNA end. Scale bare is 100 nm, z-range 4 nm.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2710519&req=5

pone-0006345-g003: Quantification of remodeled nucleosome position.The nucleosome position was determined relative to the normalized DNA contour length. The histograms show the relative nucleosome displacement when remodeling without (top) or with (bottom) ATP. We could not discriminate to which DNA arm each nucleosome was translocated. The relative nucleosome displacement is 0 for the DNA center from where the nucleosome translocation is initiated and 1 for the DNA end. A) Mononucleosome with 240 bp arms with (N = 124) or without (N = 112) ATP. Bin size 48 bp. B) Mononucleosome with 1200 bp arms with (N = 204) or without (N = 194) ATP. Bin size 120 bp. C) AFM image of mononucleosomes with 1200 bp arms of which one with RSC bound to a DNA end. Scale bare is 100 nm, z-range 4 nm.
Mentions: The remodeling potency of RSC is further demonstrated by its ability to reposition a single nucleosome over at least 1200 bp (Figure 3). The accumulation of nucleosomes at the DNA end indicates that RSC does not move nucleosomes away from the DNA end. Careful tracing of the DNA contour revealed that DNA in remodeled nucleosomal templates appeared on average 13 nm, or 38 bp, longer than that in centrally positioned nucleosomes (197±26 nm (N = 49) vs. 184±26 nm (N = 62), Figure S2). We observed a 5% decrease in nucleosome volume (420±81 nm3 vs 402±94 nm3). This indicates that no histone proteins were lost as H2A-H2B dimer dissociation results in a much larger volume loss [50], [51]. It has been reported before that RSC, like SWI/SNF, positions nucleosomes slightly over the DNA end [38], [43], [52], [53]. The fact that RSC is apparently not able to translocate the nucleosomes from the DNA ends suggests that RSC needs free DNA upstream of the nucleosome translocation direction and thus ‘pushes’ nucleosomes rather than ‘pulling’ them.

Bottom Line: Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps.Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA.This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, NCMLS, Radboud University, Nijmegen, The Netherlands. j.vanvugt@ncmls.ru.nl;

ABSTRACT

Background: Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted.

Methodology/principal findings: We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps.

Conclusions/significance: Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.

Show MeSH