1. Department of Biochemistry and Molecular Genetics,
2. Department of Pharmacology and
3. Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, Virginia 22908, USA
4. Argonne National Laboratory, Biosciences Division/Structural Biology Center, Argonne, Illinois 60439, USA
5. Present address: Department of Pathology, Harvard Medical School and The CBR Institute for Biomedical Research, Inc., 200 Longwood Avenue, Boston, Massachusetts 02115, USA

Correspondence to: Fraydoon Rastinejad^1,2Sepideh Khorasanizadeh¹ Correspondence and requests for materials should be addressed to S.K. (Email: khorasan@virginia.edu) or F.R. (Email: fr9c@virginia.edu). The atomic coordinates have been deposited in the Protein Data Bank with the accession numbers 2B2Y, 2B2W, 2B2V, 2B2U and 2B2T.

Abstract

Chromodomains are modules implicated in the recognition of lysine-methylated histone tails and nucleic acids^{1, 2}. CHD (for chromo-ATPase/helicase-DNA-binding) proteins regulate ATP-dependent nucleosome assembly and mobilization through their conserved double chromodomains and SWI2/SNF2 helicase/ATPase domain^{3, 4, 5}. The Drosophila CHD1 localizes to the interb

ands and puffs of the polytene chromosomes, which are classic sites of transcriptional activity⁶. Other CHD isoforms (CHD3/4 or Mi-2) are important for nucleosome remodelling in histone deacetylase complexes^{7, 8}. Deletion of chromodomains impairs nucleosome binding and remodelling by CHD proteins⁴. Here we describe the structure of the tandem arrangement of the human CHD1 chromodomains, and its interactions with histone tails. Unlike HP1 and Polycomb proteins that use single chromodomains to bind to their respective methylated histone H3 tails, the two chromodomains of CHD1 cooperate to interact with one methylated H3 tail. We show that the human CHD1 double chromodomains target the lysine 4-methylated histone H3 tail (H3K4me), a hallmark of active chromatin⁹. Methylammonium recognition involves two aromatic residues, not the three-residue aromatic cage used by chromodomains of HP1 and Polycomb proteins^{10, 11, 12, 13}. Furthermore, unique inserts within chromodomain 1 of CHD1 block the expected site of H3 tail binding seen in HP1 and Polycomb, instead directing H3 binding to a groove at the inter-chromodomain junction.

1. Department of Biochemistry and Molecular Genetics,
2. Department of Pharmacology and
3. Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, Virginia 22908, USA
4. Argonne National Laboratory, Biosciences Division/Structural Biology Center, Argonne, Illinois 60439, USA
5. Present address: Department of Pathology, Harvard Medical School and The CBR Institute for Biomedical Research, Inc., 200 Longwood Avenue, Boston, Massachusetts 02115, USA

Correspondence to: Fraydoon Rastinejad^1,2Sepideh Khorasanizadeh¹ Correspondence and requests for materials should be addressed to S.K. (Email: khorasan@virginia.edu) or F.R. (Email: fr9c@virginia.edu). The atomic coordinates have been deposited in the Protein Data Bank with the accession numbers 2B2Y, 2B2W, 2B2V, 2B2U and 2B2T.

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