How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers

How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers

2007 November | Sean D Taverna#, Haitao Li#, Alexander J Ruthenburg1, C David Allis1, and Dinshaw J Patel2
The article discusses how chromatin-binding modules interpret histone modifications, focusing on the structural and functional mechanisms by which these modules recognize specific histone post-translational modifications (PTMs). Histones, which are the core proteins of chromatin, undergo various PTMs, particularly on their flexible tails, which may form a 'histone code' that helps regulate epigenetic information. These modifications are read by effector modules, which are involved in defining functional states of chromatin and regulating chromatin-templated processes. Structural and functional data show how these modules target their cognate PTMs, and the article summarizes key features of molecular recognition by 'reader pockets' that bind different histone PTMs. The article highlights the recognition of acetyllysine marks by bromodomains, which are protein modules found in chromatin-associated proteins. The Gcn5p bromodomain specifically targets acetyllysine in the H4 Lys16 context, while the TAF1 double bromodomains target diacetylated H4 tails. The Rsc4p tandem bromodomains target both histone and non-histone protein acetylation marks. The article also discusses the recognition of methylation marks, including the chromodomains that target di- and trimethyllysine in H3 Lys9 and Lys27 contexts, and the Royal superfamily members that recognize higher lysine methylation states. The PHD-finger family is also discussed, with examples of how they recognize methyllysine marks. The article concludes with a discussion of the recognition of unmodified basic amino acids and the WD40 protein WDR5, which targets arginine in the H3 Arg2 context. Overall, the article provides insights into the molecular mechanisms by which chromatin-binding modules interpret histone modifications and their implications for human biology and disease.The article discusses how chromatin-binding modules interpret histone modifications, focusing on the structural and functional mechanisms by which these modules recognize specific histone post-translational modifications (PTMs). Histones, which are the core proteins of chromatin, undergo various PTMs, particularly on their flexible tails, which may form a 'histone code' that helps regulate epigenetic information. These modifications are read by effector modules, which are involved in defining functional states of chromatin and regulating chromatin-templated processes. Structural and functional data show how these modules target their cognate PTMs, and the article summarizes key features of molecular recognition by 'reader pockets' that bind different histone PTMs. The article highlights the recognition of acetyllysine marks by bromodomains, which are protein modules found in chromatin-associated proteins. The Gcn5p bromodomain specifically targets acetyllysine in the H4 Lys16 context, while the TAF1 double bromodomains target diacetylated H4 tails. The Rsc4p tandem bromodomains target both histone and non-histone protein acetylation marks. The article also discusses the recognition of methylation marks, including the chromodomains that target di- and trimethyllysine in H3 Lys9 and Lys27 contexts, and the Royal superfamily members that recognize higher lysine methylation states. The PHD-finger family is also discussed, with examples of how they recognize methyllysine marks. The article concludes with a discussion of the recognition of unmodified basic amino acids and the WD40 protein WDR5, which targets arginine in the H3 Arg2 context. Overall, the article provides insights into the molecular mechanisms by which chromatin-binding modules interpret histone modifications and their implications for human biology and disease.
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