Readout of Epigenetic Modifications

Structural Biology Department, Memorial Sloan-Kettering Cancer Center, New York, NY 10021
Annual review of biochemistry (Impact Factor: 30.28). 04/2013; 82(1). DOI: 10.1146/annurev-biochem-072711-165700
Source: PubMed


This review focuses on a structure-based analysis of histone posttranslational modification (PTM) readout, where the PTMs serve as docking sites for reader modules as part of larger complexes displaying chromatin modifier and remodeling activities, with the capacity to alter chromatin architecture and templated processes. Individual topics addressed include the diversity of reader-binding pocket architectures and common principles underlying readout of methyl-lysine and methy-larginine marks, their unmodified counterparts, as well as acetyl-lysine and phosphoserine marks. The review also discusses the impact of multivalent readout of combinations of PTMs localized at specific genomic sites by linked binding modules on processes ranging from gene transcription to repair. Additional topics include cross talk between histone PTMs, histone mimics, epigenetic-based diseases, and drug-based therapeutic intervention. The review ends by highlighting new initiatives and advances, as well as future challenges, toward the promise of enhancing our structural and mechanistic understanding of the readout of histone PTMs at the nucleosomal level. Expected final online publication date for the Annual Review of Biochemistry Volume 82 is June 02, 2013. Please see for revised estimates.

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    • "The histone octamer is composed by two copies of H2A, H2B, H3 and H4 histone proteins. The histone tails are modified by dynamic post-translational modifications (PTMs) including methylation/demethylation, acetylation/deacetylation, and so on (Patel and Wang, 2013). Various histone modifications, which are termed as the " histone code, " collectively build up an enriched and complicated pattern of chromatin structure and powerful function modulations (Strahl and Allis, 2000). "
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    ABSTRACT: In eukaryotes, histone acetylation and methylation have been known to be involved in regulating diverse developmental processes and plant defense. These histone modification events are controlled by a series of histone modification gene families. To date, there is no study regarding genome-wide characterization of histone modification related genes in citrus species. Based on the two recent sequenced sweet orange genome databases, a total of 136 CsHMs (Citrus sinensis histone modification genes), including 47 CsHMTs (histone methyltransferase genes), 23 CsHDMs (histone demethylase genes), 50 CsHATs (histone acetyltransferase genes), and 16 CsHDACs (histone deacetylase genes) were identified. These genes were categorized to 11 gene families. A comprehensive analysis of these 11 gene families was performed with chromosome locations, phylogenetic comparison, gene structures, and conserved domain compositions of proteins. In order to gain an insight into the potential roles of these genes in citrus fruit development, 42 CsHMs with high mRNA abundance in fruit tissues were selected to further analyze their expression profiles at six stages of fruit development. Interestingly, a numbers of genes were expressed highly in flesh of ripening fruit and some of them showed the increasing expression levels along with the fruit development. Furthermore, we analyzed the expression patterns of all 136 CsHMs response to the infection of blue mold (Penicillium digitatum), which is the most devastating pathogen in citrus post-harvest process. The results indicated that 20 of them showed the strong alterations of their expression levels during the fruit-pathogen infection. In conclusion, this study presents a comprehensive analysis of the histone modification gene families in sweet orange and further elucidates their behaviors during the fruit development and the blue mold infection responses.
    Full-text · Article · Aug 2015 · Frontiers in Plant Science
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    • "Specificity analysis of H3K9me3 binders on histone peptide arrays Histone PTMs exert their biological effects mainly through the regulated binding of HMIDs, which are critical constituents of many chromatin-modifying complexes (Taverna et al. 2007; Patel and Wang 2013). HMIDs are often small domains with a stable fold that can be easily expressed in E. coli and purified with high yield by affinity chromatography (Supplemental Fig. 2A). "
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    ABSTRACT: Post-translational modifications (PTMs) of histones constitute a major chromatin indexing mechanism, and their proper characterization is of highest biological importance. So far, PTM-specific antibodies have been the standard reagent for studying histone PTMs despite caveats such as lot-to-lot variability of specificity and binding affinity. Herein, we successfully employed naturally occurring and engineered histone modification interacting domains for detection and identification of histone PTMs and ChIP-like enrichment of different types of chromatin. Our results demonstrate that histone interacting domains are robust and highly specific reagents that can replace or complement histone modification antibodies. These domains can be produced recombinantly in Escherichia coli at low cost and constant quality. Protein design of reading domains allows for generation of novel specificities, addition of affinity tags, and preparation of PTM binding pocket variants as matching negative controls, which is not possible with antibodies.
    Full-text · Article · Oct 2014 · Genome Research
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    • "Residues on the surface of the binding pocket may mediate sequence-specific interactions with nearby residues on the histone tail, conferring lysine specificity [21]. Bromodomains often occur within proteins as tandem units, allowing for proteins that recognize multiple acetyl marks on the same or adjacent nucleosomes [7]. The bromodomain was originally identified as a conserved sequence element of unknown function in a handful of genes including the Drosophila Brm and fsh genes, the S. cerevisiae swi2/snf2 and spt7 genes, and two human genes, ccg1 and ring3 [22] [23]. "
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    ABSTRACT: Chromatin dynamics play an essential role in regulating the accessibility of genomic DNA for a variety of nuclear processes, including gene transcription and DNA repair. The posttranslational modification of the core histones and the action of ATP-dependent chromatin remodeling enzymes represent two primary mechanisms by which chromatin dynamics are controlled and linked to nuclear events. Although there are examples in which a histone modification or a remodeling enzyme may be sufficient to drive a chromatin transition, these mechanisms typically work in concert to integrate regulatory inputs, leading to a coordinated alteration in chromatin structure and function. Indeed, site-specific histone modifications can facilitate the recruitment of chromatin remodeling enzymes to particular genomic regions, or they can regulate the efficiency or the outcome of a chromatin remodeling reaction. Conversely, chromatin remodeling enzymes can also influence, and sometimes directly modulate, the modification state of histones. These functional interactions are generally complex, frequently transient, and often require the association of myriad additional factors. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
    Full-text · Article · Aug 2014 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
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