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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.


Nucleosomal histone and DNA elements critical for SWR1 activity and model for SWR1-mediated H2A-H2B displacement.(A) Yeast nucleosome structure PDB 1ID3 was modeled to show one face of the nucleosome and the histone-fold elements that are critical for SWR1 activation. The SWR1 footprint is shown in blue. The gap-sensitive region, 17–22 nt from dyad, is shown in cyan. Residues of H2A that affect SWR1 activity are shown in magenta. (B) Nucleosome model showing histone-DNA and histone–histone interactions that hold H2A-H2B within the nucleosome. Also shown is the gap-sensitive region, where SWR1 interacts with nucleosome DNA leading to eviction of H2A/H2B and concomitant deposition of H2A.Z/H2B.DOI:http://dx.doi.org/10.7554/eLife.06845.011
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fig3s2: Nucleosomal histone and DNA elements critical for SWR1 activity and model for SWR1-mediated H2A-H2B displacement.(A) Yeast nucleosome structure PDB 1ID3 was modeled to show one face of the nucleosome and the histone-fold elements that are critical for SWR1 activation. The SWR1 footprint is shown in blue. The gap-sensitive region, 17–22 nt from dyad, is shown in cyan. Residues of H2A that affect SWR1 activity are shown in magenta. (B) Nucleosome model showing histone-DNA and histone–histone interactions that hold H2A-H2B within the nucleosome. Also shown is the gap-sensitive region, where SWR1 interacts with nucleosome DNA leading to eviction of H2A/H2B and concomitant deposition of H2A.Z/H2B.DOI:http://dx.doi.org/10.7554/eLife.06845.011

Mentions: We have identified elements of the canonical nucleosome that activate the SWR1 complex for histone H2A.Z replacement. A DNA site at SHL2 on the nucleosome, in a region identified for DNA translocation by chromatin remodelers RSC, SWI/SNF, ISW2, and ISW1, is also important for histone exchange by SWR1. The ATPase domains of the SNF2 and ISW2 nucleosome sliding complexes are known to interact with the nucleosome at SHL2 (Dang and Bartholomew, 2007; Dechassa et al., 2012), and we envision that the catalytic Swr1 ATPase also contacts the SHL2 site. Footprinting experiments show that other chromatin remodelers contact the nucleosome core particle at either the linker-proximal side or both sides of the dyad axis; however, SWR1 contacts the core particle on the linker-distal side of the dyad. This distinction between SWR1 and other remodelers may reflect the unique requirements of dimer eviction and deposition as opposed to nucleosome sliding. Within the nucleosome core particle, each H2A-H2B dimer is stabilized by histone–DNA interactions (at three minor groove locations SHL3.5, SHL4.5, and SHL5.5) and histone–histone interactions (the α2 and α3 helices of H2B interact with α2 and α3 helices of H4 in a four-helix bundle). For histone exchange, SWR1 must disrupt either one or both of these interactions, coordinated with H2A.Z-H2B deposition. This might be initiated by transient, confined DNA translocation by the SWR1 ATPase essentially as indicated for other remodelers (Clapier and Cairns, 2009; Mueller-Planitz et al., 2013), but without propagation as histone exchange is not accompanied by repositioning of the histone octamer on DNA. Alternatively, histone replacement could be initiated by a local, ATP-driven DNA conformational change near SHL2 that alters the path of the DNA superhelix, resulting in destabilization of H2A-H2B contacts with DNA or with the H3-H4 tetramer (Figure 3—figure supplement 2).


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)

Nucleosomal histone and DNA elements critical for SWR1 activity and model for SWR1-mediated H2A-H2B displacement.(A) Yeast nucleosome structure PDB 1ID3 was modeled to show one face of the nucleosome and the histone-fold elements that are critical for SWR1 activation. The SWR1 footprint is shown in blue. The gap-sensitive region, 17–22 nt from dyad, is shown in cyan. Residues of H2A that affect SWR1 activity are shown in magenta. (B) Nucleosome model showing histone-DNA and histone–histone interactions that hold H2A-H2B within the nucleosome. Also shown is the gap-sensitive region, where SWR1 interacts with nucleosome DNA leading to eviction of H2A/H2B and concomitant deposition of H2A.Z/H2B.DOI:http://dx.doi.org/10.7554/eLife.06845.011
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Related In: Results  -  Collection

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fig3s2: Nucleosomal histone and DNA elements critical for SWR1 activity and model for SWR1-mediated H2A-H2B displacement.(A) Yeast nucleosome structure PDB 1ID3 was modeled to show one face of the nucleosome and the histone-fold elements that are critical for SWR1 activation. The SWR1 footprint is shown in blue. The gap-sensitive region, 17–22 nt from dyad, is shown in cyan. Residues of H2A that affect SWR1 activity are shown in magenta. (B) Nucleosome model showing histone-DNA and histone–histone interactions that hold H2A-H2B within the nucleosome. Also shown is the gap-sensitive region, where SWR1 interacts with nucleosome DNA leading to eviction of H2A/H2B and concomitant deposition of H2A.Z/H2B.DOI:http://dx.doi.org/10.7554/eLife.06845.011
Mentions: We have identified elements of the canonical nucleosome that activate the SWR1 complex for histone H2A.Z replacement. A DNA site at SHL2 on the nucleosome, in a region identified for DNA translocation by chromatin remodelers RSC, SWI/SNF, ISW2, and ISW1, is also important for histone exchange by SWR1. The ATPase domains of the SNF2 and ISW2 nucleosome sliding complexes are known to interact with the nucleosome at SHL2 (Dang and Bartholomew, 2007; Dechassa et al., 2012), and we envision that the catalytic Swr1 ATPase also contacts the SHL2 site. Footprinting experiments show that other chromatin remodelers contact the nucleosome core particle at either the linker-proximal side or both sides of the dyad axis; however, SWR1 contacts the core particle on the linker-distal side of the dyad. This distinction between SWR1 and other remodelers may reflect the unique requirements of dimer eviction and deposition as opposed to nucleosome sliding. Within the nucleosome core particle, each H2A-H2B dimer is stabilized by histone–DNA interactions (at three minor groove locations SHL3.5, SHL4.5, and SHL5.5) and histone–histone interactions (the α2 and α3 helices of H2B interact with α2 and α3 helices of H4 in a four-helix bundle). For histone exchange, SWR1 must disrupt either one or both of these interactions, coordinated with H2A.Z-H2B deposition. This might be initiated by transient, confined DNA translocation by the SWR1 ATPase essentially as indicated for other remodelers (Clapier and Cairns, 2009; Mueller-Planitz et al., 2013), but without propagation as histone exchange is not accompanied by repositioning of the histone octamer on DNA. Alternatively, histone replacement could be initiated by a local, ATP-driven DNA conformational change near SHL2 that alters the path of the DNA superhelix, resulting in destabilization of H2A-H2B contacts with DNA or with the H3-H4 tetramer (Figure 3—figure supplement 2).

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.