Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail.

Johanna Ludwigsen,Sabrina Pfennig,Martin Zacharias,Ignasi Forné,Ashish K Singh,Nadine Harrer,Christina Schindler,Felix Mueller-Planitz

doi:10.7554/elife.21477

Abstract

ISWI-family nucleosome remodeling enzymes need the histone H4 N-terminal tail to mobilize nucleosomes. Here we mapped the H4-tail binding pocket of ISWI. Surprisingly the binding site was adjacent to but not overlapping with the docking site of an auto-regulatory motif, AutoN, in the N-terminal region (NTR) of ISWI, indicating that AutoN does not act as a simple pseudosubstrate as suggested previously. Rather, AutoN cooperated with a hitherto uncharacterized motif, termed AcidicN, to confer H4-tail sensitivity and discriminate between DNA and nucleosomes. A third motif in the NTR, ppHSA, was functionally required in vivo and provided structural stability by clamping the NTR to Lobe 2 of the ATPase domain. This configuration is reminiscent of Chd1 even though Chd1 contains an unrelated NTR. Our results shed light on the intricate structural and functional regulation of ISWI by the NTR and uncover surprising parallels with Chd1.

Highlights

Eukaryotic cells package their DNA into chromatin
We propose that AutoN does not occlude the binding pocket of the H4 tail and that inhibition by AutoN involves a more elaborate mechanism than simple mimicry of the H4 basic patch
The ppHSA motif is important for structural stability

Summary

Introduction

Eukaryotic cells package their DNA into chromatin. Chromatin organization allows cells to compact, protect and regulate their genomes. The histone H4 N-terminal tail of one nucleosome contacts the acidic patch formed by H2A and H2B of a neighboring nucleosome (Luger et al, 1997; Dorigo et al, 2004) This interaction sequesters the H4 tail, which now is no longer available for binding to and stimulating the activity of ISWI. Besides AutoN, the NTR contains additional motifs: an acidic region that we termed AcidicN, the ‘post-post-helicase-SANT-associated’ (ppHSA) motif, so named because it follows the post-HSA motif in remodelers of the Snf family (MuellerPlanitz et al, 2013; Szerlong et al, 2008), and a weakly conserved AT-hook (MuellerPlanitz et al, 2013; Aravind and Landsman, 1998) We propose that AutoN does not occlude the binding pocket of the H4 tail and that inhibition by AutoN involves a more elaborate mechanism than simple mimicry of the H4 basic patch

Results

IVERAEVK

Discussion

Materials and methods

Funding Funder Ernst Schering Foundation