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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.


Nucleosome structure showing critical H2A residues that effect SWR1 activity.(A) Left: The yeast nucleosome crystal structure 1ID3 in Protein Data Bank was modeled to show histones on one face of nucleosome. Histone H2A is yellow, H2B is black and H3, H4 are gray. The domains of H2A that affect SWR1 activity-M3A (cyan), M4 (magenta), and M5 (blue) are marked. Center and right: Buried residues of histone H2A are shown by removing other histones and rotating on X-axis by 45°. (B) The H2A surface residue G47 in 1ID3 is shown in magenta. Bottom left: Zoom-in view shows that G47 is at the bottom of a cleft. Bottom right: Replacing Glycine for Lysine in H2A.Z histone shows the long side-chain of Lysine filling the cleft.DOI:http://dx.doi.org/10.7554/eLife.06845.006
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fig1s3: Nucleosome structure showing critical H2A residues that effect SWR1 activity.(A) Left: The yeast nucleosome crystal structure 1ID3 in Protein Data Bank was modeled to show histones on one face of nucleosome. Histone H2A is yellow, H2B is black and H3, H4 are gray. The domains of H2A that affect SWR1 activity-M3A (cyan), M4 (magenta), and M5 (blue) are marked. Center and right: Buried residues of histone H2A are shown by removing other histones and rotating on X-axis by 45°. (B) The H2A surface residue G47 in 1ID3 is shown in magenta. Bottom left: Zoom-in view shows that G47 is at the bottom of a cleft. Bottom right: Replacing Glycine for Lysine in H2A.Z histone shows the long side-chain of Lysine filling the cleft.DOI:http://dx.doi.org/10.7554/eLife.06845.006

Mentions: Earlier work has shown that the structures of H2A- and H2A.Z-containing nucleosomes show prominent differences in the region C-terminal to the histone-fold domain (Suto et al., 2000). This C-terminal region is important for binding of the free H2A.Z-H2B dimer to specific chaperones (Luk et al., 2007; Zhou et al., 2008; Hong et al., 2014), and for effector interactions post-incorporation (Clarkson et al., 1999; Adam et al., 2001). For histone H2A.Z replacement, our analysis shows that SWR1 utilizes other unique and conserved features of the H2A nucleosome for substrate specificity. Of the three SWR1-activating regions of the H2A histone-fold, the α2 helix and loop 2 are exposed on the nucleosome surface for contact with SWR1, whereas the α1 helix is buried and may act by allostery (Figure 1—figure supplement 3A). Residue G47 of the H2A α2 helix is highly conserved and is located at the bottom of a cleft (∼8 Å deep) on the H2A nucleosome surface (Figure 1—figure supplement 3B). This cleft might serve as a structural feature for recognition by SWR1; the presence of a Lysine residue at this position in H2A.Z would fill it (Figure 1—figure supplement 3B). It would be of interest to determine structural interactions of SWR1 with this local nucleosome surface. Our findings provide new insights on the structural basis by which canonical and H2A.Z-nucleosomes are recognized by SWR1 and should facilitate future studies of the histone H2A.Z replacement mechanism.


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)

Nucleosome structure showing critical H2A residues that effect SWR1 activity.(A) Left: The yeast nucleosome crystal structure 1ID3 in Protein Data Bank was modeled to show histones on one face of nucleosome. Histone H2A is yellow, H2B is black and H3, H4 are gray. The domains of H2A that affect SWR1 activity-M3A (cyan), M4 (magenta), and M5 (blue) are marked. Center and right: Buried residues of histone H2A are shown by removing other histones and rotating on X-axis by 45°. (B) The H2A surface residue G47 in 1ID3 is shown in magenta. Bottom left: Zoom-in view shows that G47 is at the bottom of a cleft. Bottom right: Replacing Glycine for Lysine in H2A.Z histone shows the long side-chain of Lysine filling the cleft.DOI:http://dx.doi.org/10.7554/eLife.06845.006
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4508883&req=5

fig1s3: Nucleosome structure showing critical H2A residues that effect SWR1 activity.(A) Left: The yeast nucleosome crystal structure 1ID3 in Protein Data Bank was modeled to show histones on one face of nucleosome. Histone H2A is yellow, H2B is black and H3, H4 are gray. The domains of H2A that affect SWR1 activity-M3A (cyan), M4 (magenta), and M5 (blue) are marked. Center and right: Buried residues of histone H2A are shown by removing other histones and rotating on X-axis by 45°. (B) The H2A surface residue G47 in 1ID3 is shown in magenta. Bottom left: Zoom-in view shows that G47 is at the bottom of a cleft. Bottom right: Replacing Glycine for Lysine in H2A.Z histone shows the long side-chain of Lysine filling the cleft.DOI:http://dx.doi.org/10.7554/eLife.06845.006
Mentions: Earlier work has shown that the structures of H2A- and H2A.Z-containing nucleosomes show prominent differences in the region C-terminal to the histone-fold domain (Suto et al., 2000). This C-terminal region is important for binding of the free H2A.Z-H2B dimer to specific chaperones (Luk et al., 2007; Zhou et al., 2008; Hong et al., 2014), and for effector interactions post-incorporation (Clarkson et al., 1999; Adam et al., 2001). For histone H2A.Z replacement, our analysis shows that SWR1 utilizes other unique and conserved features of the H2A nucleosome for substrate specificity. Of the three SWR1-activating regions of the H2A histone-fold, the α2 helix and loop 2 are exposed on the nucleosome surface for contact with SWR1, whereas the α1 helix is buried and may act by allostery (Figure 1—figure supplement 3A). Residue G47 of the H2A α2 helix is highly conserved and is located at the bottom of a cleft (∼8 Å deep) on the H2A nucleosome surface (Figure 1—figure supplement 3B). This cleft might serve as a structural feature for recognition by SWR1; the presence of a Lysine residue at this position in H2A.Z would fill it (Figure 1—figure supplement 3B). It would be of interest to determine structural interactions of SWR1 with this local nucleosome surface. Our findings provide new insights on the structural basis by which canonical and H2A.Z-nucleosomes are recognized by SWR1 and should facilitate future studies of the histone H2A.Z replacement mechanism.

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.