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H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast.

Ranjan A, Wang F, Mizuguchi G, Wei D, Huang Y, Wu C - Elife (2015)

Bottom Line: We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity.Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site.Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition.

View Article: PubMed Central - PubMed

Affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.

ABSTRACT
The histone variant H2A.Z is a universal mark of gene promoters, enhancers, and regulatory elements in eukaryotic chromatin. The chromatin remodeler SWR1 mediates site-specific incorporation of H2A.Z by a multi-step histone replacement reaction, evicting histone H2A-H2B from the canonical nucleosome and depositing the H2A.Z-H2B dimer. Binding of both substrates, the canonical nucleosome and the H2A.Z-H2B dimer, is essential for activation of SWR1. We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity. Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site. Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition.

No MeSH data available.


Position of SWR1 footprint on linker-distal face of nucleosome.The 601 DNA-containing nucleosome structure PDB 3MVD was modeled to highlight the position of the SWR1 footprint in blue on the linker-distal side of the dyad axis. The H2A on the linker-distal face is in yellow.DOI:http://dx.doi.org/10.7554/eLife.06845.008
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fig2s1: Position of SWR1 footprint on linker-distal face of nucleosome.The 601 DNA-containing nucleosome structure PDB 3MVD was modeled to highlight the position of the SWR1 footprint in blue on the linker-distal side of the dyad axis. The H2A on the linker-distal face is in yellow.DOI:http://dx.doi.org/10.7554/eLife.06845.008

Mentions: We next investigated the role of nucleosomal DNA. Previous studies have established the importance of specific DNA contacts by ATP-dependent chromatin remodelers (Mueller-Planitz et al., 2013; Bartholomew, 2014). In vitro, SWR1 is known to bind preferentially to long linker DNA adjacent to a nucleosome core particle (Ranjan et al., 2013). To favor SWR1 binding in one orientation, we reconstituted mono-nucleosomes bearing only one 60 bp linker and subjected bound nucleosomes to hydroxyl radical footprinting (Figure 2A). Notably, we observed protection at superhelix locations (SHLs) SHL0, SHL+1, and SHL+2 on the linker-distal side of the nucleosome dyad (Figure 2B,C; Figure 2—figure supplement 1). Strongest protection was observed at SHL2, where other ATP-dependent chromatin remodelers have been shown to interact with the nucleosome, but on the linker-proximal or both sides of dyad (Bartholomew, 2014). We also observed broad protection from hydroxyl radical cleavage of long linker DNA by SWR1 (Figure 2D), consistent with previous findings (Ranjan et al., 2013).10.7554/eLife.06845.007Figure 2.Hydroxyl radical footprinting of SWR1 on nucleosomal DNA.


H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast.

Ranjan A, Wang F, Mizuguchi G, Wei D, Huang Y, Wu C - Elife (2015)

Position of SWR1 footprint on linker-distal face of nucleosome.The 601 DNA-containing nucleosome structure PDB 3MVD was modeled to highlight the position of the SWR1 footprint in blue on the linker-distal side of the dyad axis. The H2A on the linker-distal face is in yellow.DOI:http://dx.doi.org/10.7554/eLife.06845.008
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508883&req=5

fig2s1: Position of SWR1 footprint on linker-distal face of nucleosome.The 601 DNA-containing nucleosome structure PDB 3MVD was modeled to highlight the position of the SWR1 footprint in blue on the linker-distal side of the dyad axis. The H2A on the linker-distal face is in yellow.DOI:http://dx.doi.org/10.7554/eLife.06845.008
Mentions: We next investigated the role of nucleosomal DNA. Previous studies have established the importance of specific DNA contacts by ATP-dependent chromatin remodelers (Mueller-Planitz et al., 2013; Bartholomew, 2014). In vitro, SWR1 is known to bind preferentially to long linker DNA adjacent to a nucleosome core particle (Ranjan et al., 2013). To favor SWR1 binding in one orientation, we reconstituted mono-nucleosomes bearing only one 60 bp linker and subjected bound nucleosomes to hydroxyl radical footprinting (Figure 2A). Notably, we observed protection at superhelix locations (SHLs) SHL0, SHL+1, and SHL+2 on the linker-distal side of the nucleosome dyad (Figure 2B,C; Figure 2—figure supplement 1). Strongest protection was observed at SHL2, where other ATP-dependent chromatin remodelers have been shown to interact with the nucleosome, but on the linker-proximal or both sides of dyad (Bartholomew, 2014). We also observed broad protection from hydroxyl radical cleavage of long linker DNA by SWR1 (Figure 2D), consistent with previous findings (Ranjan et al., 2013).10.7554/eLife.06845.007Figure 2.Hydroxyl radical footprinting of SWR1 on nucleosomal DNA.

Bottom Line: We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity.Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site.Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition.

View Article: PubMed Central - PubMed

Affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.

ABSTRACT
The histone variant H2A.Z is a universal mark of gene promoters, enhancers, and regulatory elements in eukaryotic chromatin. The chromatin remodeler SWR1 mediates site-specific incorporation of H2A.Z by a multi-step histone replacement reaction, evicting histone H2A-H2B from the canonical nucleosome and depositing the H2A.Z-H2B dimer. Binding of both substrates, the canonical nucleosome and the H2A.Z-H2B dimer, is essential for activation of SWR1. We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity. Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site. Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition.

No MeSH data available.