A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing

Abstract

Recent studies have implicated the nucleosome acidic patch in the activity of ATP-dependent chromatin remodeling machines. We employed a photocrosslinking-based nucleosome profiling technology-'photoscanning'-to identify a conserved basic motif within the catalytic subunit of ISWI remodelers, SNF2h, which engages this nucleosomal epitope. This region of SNF2h is essential for chromatin remodeling activity in a reconstituted biochemical system and in cells. Our studies suggest that the basic motif in SNF2h plays a critical role in anchoring the remodeler to the nucleosomal surface. We also examine the functional consequences of several cancer-associated histone mutations that map to the nucleosome acidic patch. Kinetic studies employing physiologically relevant heterotypic nucleosomal substrates ('Janus' nucleosomes) indicate that these cancer mutations can disrupt regularly spaced chromatin structure by inducing ISWImediated unidirectional nucleosome sliding. These results imply a potential mechanistic link between oncogenic histones and alterations to the chromatin landscape. Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation

“…5e, see H380, H2A89, and H2A113). Similar to our data, binding of the mammalian homolog of Isw1, Snf2h, to the acidic pocket is required to stimulate the remodeling activity of the ISWI complex by relieving auto-inhibition [16][17][18] . Two changes in ISW1a interactions with nucleosomes are required to deactivate ISW1a when remodeling mononucleosomes that are switched with dinucleosomes.…”

“…The backtracking motion is only observed with ISW1a (not Isw1) on mononucleosomes and not on dinucleosomes. The importance of Isw1 contact with the acidic pocket of nucleosomes is consistent with the acidic patch of nucleosomes shown previously to be required for relieving auto-inhibition of mammalian ISWI and a part of the ISWI catalytic subunit outside of the ATPase domain to contact the acidic pocket [16][17][18] .…”

“…Z and H2A is the extended acidic patch of H2A.Z 15 . Mammalian ISWI complexes have been shown to bind the acidic patch of nucleosomes and to be required for efficient remodeling [16][17][18] . Expanding the acidic patch by incorporation of H2A.Z also stimulates mammalian ISWI nucleosome remodeling activity 19 .…”

The Mechanism of Chromatin Remodeler SMARCAD1/Fun30 in Response to DNA Damage

“…Despite these advances in recent years, some questions still need to be further answered, for example, how the remodeling activity of SMARCAD1 is activated by ubiquitinated nucleosomes or ssDNA and how SMARCAD1 removes the obstacles (such as 53BP1 and nucleosomes) through its histone dimer exchange activity. Take advantage of the recent advances in chemical protein synthesis ( McGinty et al, 2008 ; Fang et al, 2011 , 2012 ; Fierz et al, 2011 ; Siman et al, 2013 ; Li et al, 2014 , 2018 ; Morgan et al, 2016 ; Ai et al, 2019 ; Chu et al, 2019 ; Pan et al, 2019 ) and cryo-electron microscopy techniques, the biochemical and structural studies of ubiquitinated nucleosomes have recently received increasing attention ( Zhou L. et al, 2016 ; Anderson et al, 2019 ; Hsu et al, 2019 ; Jang et al, 2019 ; Park et al, 2019 ; Valencia-Sanchez et al, 2019 ; Worden and Wolberger, 2019 ; Worden et al, 2019 ; Xue et al, 2019 ; Yao et al, 2019 ; Dao et al, 2020 ). Both the in vitro reconstruction experiments and the structural analysis of the SMARCAD1-nucleosome complex may provide new insights into the remodeling mechanism of SMARCAD1.…”

Structural insights into assembly and function of the RSC chromatin remodeling complex

“…6a). A recent study showed that ISWI also contains a small basic stretch C-terminal to the ATPase domain that mediates binding to the acidic patch 39 . This motif is conserved in ISWI orthologs and mutating it reduces the rate of remodeling, as we have reported here.…”