ATR-X (alpha-thalassemia/mental retardation, X-linked) syndrome is a human congenital disease whose clinical manifestations are α-thalassemia and mental retardation. Approximately 50% of the missense mutations in affected persons are clustered in the ADD (ATRX-DNMT3-DNMT3) domain of the syndrome’s key gene ATRX. However, the function of ATRX ADD (ADDATRX)  domain has remained elusive. In collaboration with Dr. Yang Shi at the Harvard Medical School, a group led by Dr. Haitao Li from the Center for Structural Biology, Tsinghua University conducted structural and functional studies on ADDATRX and demonstrated that  ADDATRX is a new type of histone H3-binding module that is able to combinatorially sense the methylation state at both H3K4 and H3K9. This work has been published in Nat Struct & Mol Biol in June, 2011.

Recognition of H3K9me3 by ATRX ADD

At beamline 3W1A of Beijing Synchrotron Radiation Facility (BSRF), Dr. Li group achieved 0.93Å atomic resolution co-crystal structure of ADDATRX bound to H3K9 trimethylated (H3K9me3) peptide. The structure revealed the following new mechanisms in the recognition of histone lysine methylation:

1) ADDATRX adopts an atypical polar pocket for H3K9me3 readout, in which recognition of trimethyllysine is notably contributed by a set of unconventional “C-O” hydrogen bonds. Such a polar pocket is distinct from the classical “aromatic cage” that has been widely reported for trimethyllysine binding.

2) The H3K9me3-binding pocket is formed at the interface of a GATA-like finger and a PHD finger of ADDATRX. The usage of a “composite” pocket for histone methylation readout highlights the strategy of module integration to create a functional reader pocket.

3) Effective binding of H3K9me3 by ADDATRX not only depends on trimethylated H3K9 but also on non-methylated H3K4 as well as a free amino terminus, representative of a combinatorial readout mode of histone H3 methylation.

ATRX is the key etiologic factor for ATR-X syndrome. This work identified ADDATRX as an important H3K9me3 “reader”, which is essential for the recruitment of ATRX to heterochromatic regions like pericentromeric heterochromatin or telomere for optimal chromatin remodeling function excelled by ATRX. This study has revealed a unique histone-recognition mechanism underlying the ATR-X etiology, and may have also provided a new avenue for therapeutic intervention in ATR-X syndrome.

The synchrotron radiation light source at BSRF played a vital role in the structure determination of the ADDATRX –H3K9me3 complex. It is the high intensity and small beam size of the synchrotron radiation light that allows the complex structure determination at atomic resolution and enables the elucidation of such an atypical histone methylation recognition mechanism to the public.

Article:

Shigeki Iwase, Bin Xiang, Sharmistha Ghosh, Ting Ren, Peter W Lewis, Jesse C Cochrane, C David Allis, David J Picketts, Dinshaw J Patel^*, Haitao Li^* & Yang Shi^*, ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome. Nature Structural & Molecular Biology, 2011,18,769-776.