The Essential Role of the Nucleosomal Acidic Patch in H2A.Z Deposition by the SWR1C Chromatin Remodeling Complex

Concetti Chiave

The SWR1C chromatin remodeling complex requires engagement of the nucleosomal acidic patch on both faces of the nucleosome to catalyze efficient deposition of the histone variant H2A.Z.

Sintesi

The SWR1C chromatin remodeling complex catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, which is involved in various nuclear functions. This study investigates the role of the nucleosomal acidic patch in the H2A.Z exchange reaction by SWR1C.
Key highlights:

Disruption of even a single nucleosomal acidic patch severely impairs the ability of SWR1C to bind nucleosomes and catalyze H2A.Z deposition, suggesting SWR1C must engage both acidic patches simultaneously in a "pincer-like" conformation.
Loss of a single acidic patch results in the loss of high-affinity nucleosome binding and nucleosomal stimulation of SWR1C's ATPase activity.
An arginine-rich motif within the Swc5 subunit of SWR1C binds the acidic patch and is essential for dimer exchange activity.
A cryo-EM structure of the Swc5-nucleosome complex confirms the acidic patch interaction and also reveals contacts with the histone H4 N-terminal tail and the H2B C-terminal helix.
The Swc5 arginine-rich motif is critical for SWR1C function in vivo, as mutations in this region lead to severe growth defects.
Together, these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.

Statistiche

The SWR1C-catalyzed dimer exchange reaction was reduced 10-fold when the nucleosomal acidic patch was disrupted.
Disruption of a single nucleosomal acidic patch decreased the binding affinity of SWR1C for nucleosomes by at least 10-fold.
Incorporation of an H2A.Z/H2B dimer on the contralateral nucleosomal face stimulated the rate of H2A.Z deposition by ~20%.

Citazioni

"Surprisingly, we find that loss of even a single acidic patch results in the loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity, suggesting SWR1C must engage both acidic patches simultaneously in a 'pincer-like' conformation to carry out dimer exchange."
"Efforts to identify potential SWR1C subunits responsible for acidic patch interactions led us to identify an arginine rich motif within the Swc5 subunit of SWR1C, and we show that this domain is essential for dimer exchange in vitro, the function of SWR1C in vivo, and Swc5 binding to the nucleosome."

Approfondimenti chiave tratti da

Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C

by Gioacchini,N... alle www.biorxiv.org 12-09-2021

https://www.biorxiv.org/content/10.1101/2021.12.08.471801v5

Domande più approfondite

How might the interactions between Swc5 and the H4 N-terminal tail or H2B C-terminal helix regulate H2A.Z deposition by SWR1C?

The interactions between Swc5 and the H4 N-terminal tail or H2B C-terminal helix play a crucial role in regulating H2A.Z deposition by SWR1C. Swc5 forms multivalent interactions with the nucleosome, including contacts with the H4 N-terminal tail and the H2B C-terminal helix. These interactions are essential for anchoring SWR1C to the nucleosome and facilitating the deposition of H2A.Z.

H4 N-terminal Tail Interaction: Swc5 interacts with the H4 N-terminal tail, which is known to undergo post-translational modifications like acetylation. This interaction may influence SWR1C recruitment and activity. Acetylation of the H4 tail can modulate SWR1C function, potentially by affecting the stability of the Swc5-nucleosome complex.

H2B C-terminal Helix Interaction: Swc5 also interacts with the H2B C-terminal helix, specifically with H2B-K123. This residue is subject to ubiquitination by the Bre1-Rad6 ubiquitin ligase complex. H2B-K123ub is enriched at the +1 nucleosome, the target site for H2A.Z deposition by SWR1C. The interaction between Swc5 and H2B-K123 may be disrupted by ubiquitination, leading to modulation of H2A.Z deposition.

Overall, the interactions between Swc5 and these histone regions provide structural support and stability for SWR1C on the nucleosome, facilitating the efficient deposition of H2A.Z.

How might the interactions between Swc5 and the H4 N-terminal tail or H2B C-terminal helix regulate H2A.Z deposition by SWR1C?

The interactions between Swc5 and the H4 N-terminal tail or H2B C-terminal helix play a crucial role in regulating H2A.Z deposition by SWR1C. Swc5 forms multivalent interactions with the nucleosome, including contacts with the H4 N-terminal tail and the H2B C-terminal helix. These interactions are essential for anchoring SWR1C to the nucleosome and facilitating the deposition of H2A.Z.

H4 N-terminal Tail Interaction: Swc5 interacts with the H4 N-terminal tail, which is known to undergo post-translational modifications like acetylation. This interaction may influence SWR1C recruitment and activity. Acetylation of the H4 tail can modulate SWR1C function, potentially by affecting the stability of the Swc5-nucleosome complex.

H2B C-terminal Helix Interaction: Swc5 also interacts with the H2B C-terminal helix, specifically with H2B-K123. This residue is subject to ubiquitination by the Bre1-Rad6 ubiquitin ligase complex. H2B-K123ub is enriched at the +1 nucleosome, the target site for H2A.Z deposition by SWR1C. The interaction between Swc5 and H2B-K123 may be disrupted by ubiquitination, leading to modulation of H2A.Z deposition.

Overall, the interactions between Swc5 and these histone regions provide structural support and stability for SWR1C on the nucleosome, facilitating the efficient deposition of H2A.Z.

How might the interactions between Swc5 and the H4 N-terminal tail or H2B C-terminal helix regulate H2A.Z deposition by SWR1C?

The interactions between Swc5 and the H4 N-terminal tail or H2B C-terminal helix are crucial for regulating H2A.Z deposition by SWR1C. These interactions play a significant role in anchoring SWR1C to the nucleosome and facilitating the efficient deposition of H2A.Z.

H4 N-terminal Tail Interaction: Swc5 interacts with the H4 N-terminal tail, which is subject to post-translational modifications such as acetylation. This interaction may influence the recruitment and activity of SWR1C. Acetylation of the H4 tail can modulate SWR1C function, potentially affecting the stability of the Swc5-nucleosome complex and the deposition of H2A.Z.

H2B C-terminal Helix Interaction: Swc5 also interacts with the H2B C-terminal helix, particularly with H2B-K123. This residue can be ubiquitinated by the Bre1-Rad6 ubiquitin ligase complex. H2B-K123ub is enriched at the +1 nucleosome, the site targeted by SWR1C for H2A.Z deposition. Disruption of the Swc5-H2B-K123 interaction due to ubiquitination may modulate H2A.Z deposition by SWR1C.

These interactions provide structural stability and support for SWR1C on the nucleosome, enabling the enzyme to efficiently catalyze the deposition of H2A.Z. The dynamic interplay between Swc5 and the histone regions is essential for the proper functioning of SWR1C in regulating chromatin structure and gene expression.