On December 6th, 2016, Zhucheng Chen’s group at Tsinghua University published their work “Structure and regulation of the chromatin remodeller ISWI” in NATURE. In this work, they solved the high-resolution structure of thermophilic yeast ISWI and its complex with histone H4 using X-ray crystallography. Combining with biochemical analysis, they uncovered the mechanisms on how ISWI is autoinhibited, activated by histone H4, and exerts its nucleosome-centering activity to assemble chromatin.
Chromatin is the life blueprint of eukaryotes. Chromatin remodellers utilize the energy of ATP hydrolysis to move, destabilize, eject, or restructure nucleosomes, building and rebuilding the blueprint of lives. ISWI is the catalytic subunit of several chromatin remodelling complexes which mobilize nucleosomes along genomic DNA, regulating gene transcription, heterochromatin formation, X-chromosome inactivation and many other important chromatin processes. The ATPase motor of ISWI (Fig. a, Core) is an autonomous remodelling machine, the activity of which is under tight control. ISWI is inhibited by AutoN domain and NegC domain, avoiding futile ATP hydrolysis in the absent of substrate. Nucleosomal H4 and extranucleosomal DNA activate ISWI by antagonizing these inhibitory effects, yet acetylation of histone H4 impairs ISWI activation. These multilevel regulations of ISWI ensure the appropriate chromatin landscape in cells.
The study by Chen and his colleagues shows that the amino (N)-terminal AutoN domain contains two inhibitory elements (Fig. b, L3 and a4), which collectively bind the second RecA-like domain (core2), holding the enzyme in an inactive conformation. The H4 peptide binds to the core2 domain coincident with one of the AutoN-binding sites (Fig. c), explaining the ISWI activation by H4 and the fine-tuning of ISWI activity by H4 acetylation. Furthermore, they show that the C-terminal NegC domain is involved in binding to the core2 domain, functioning as an allosteric element for ISWI to sense the extranucleosomal DNA length (Fig. d-f).
This work is an important part of the series studies on chromatin remodellers in Chen’s lab. Lijuan Yan and Li Wang are the co-first authors, and Zhucheng Chen is the corresponding author. This work was funded by the Chinese Key Research Plan- Protein Sciences, the National Natural Science Foundation of China, the ‘Junior One Thousand Talents’ program and the Beijing Advanced Innovation Center for Structural Biology (Tsinghua University, Beijing). The Center of Structure Biology (Tsinghua University) and the staff at beamline BL17U of Shanghai Synchrotron Radiation provided facility support and help.
Structure and regulation of the chromatin remodeller ISWI
a, Domain architecture of MtISWI. b, The overall structure of MtISWI. c, Superimposition of the structures of the core2 domain in the peptide-bound (cyan) and the auto-inhibited (grey) states. H4 peptide, yellow; L3 loop, magenta. d, Cartoon image of ISWI in the auto-inhibited state. The tethering HSS domain is omitted. e, Proposed model of ISWI bound to the nucleosome with long linker DNA. The dotted line illustrates NegC in the stressed condition. ISWI is activated. f, Proposed model of ISWI bound to the nucleosome with short linker DNA, in which the Brace helix is partly disrupted and NegC binds to core2 intramolecularly. ISWI lost its remodelling activity.