Facile synthesis of site-specifically acetylated and methylated histone proteins: Reagents for evaluation of the histone code hypothesis

He, Shan; Bauman, David R.; Davis, Jamaine; Loyola, Alejandra; Nishioka, Kusuki; Gronlund, Jennifer L.; Reinberg, Danny; Meng, Fanyu; Kelleher, Neil L.; McCafferty, Dewey G.

doi:10.1073/pnas.2035256100

Cited by 114 publications

(113 citation statements)

References 31 publications

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“…Various synthesized histone N-terminal peptides, containing particular site-specific modifications, were then ligated to recombinantly produced histone C-terminal globular domains containing an engineered N-terminal cysteine residue. Those authors showed that the synthetic histones generated by this method are fully functional, as verified by the self-assembly into higher-order heterotetramers, their deposition into nucleosomes by chromatin assembly/remodeling factors, and enzymatic modifications (162). Such a method, combined with mass spectrometry and amino acid exchange analysis of potential target proteins, could be utilized for studies of poly-ADP ribosylation.…”

Section: Pargsmentioning

confidence: 96%

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Nuclear ADP-Ribosylation Reactions in Mammalian Cells: Where Are We Today and Where Are We Going?

Hassa

Haenni

Elser

et al. 2006

Microbiol Mol Biol Rev

635

644

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SUMMARY Since poly-ADP ribose was discovered over 40 years ago, there has been significant progress in research into the biology of mono- and poly-ADP-ribosylation reactions. During the last decade, it became clear that ADP-ribosylation reactions play important roles in a wide range of physiological and pathophysiological processes, including inter- and intracellular signaling, transcriptional regulation, DNA repair pathways and maintenance of genomic stability, telomere dynamics, cell differentiation and proliferation, and necrosis and apoptosis. ADP-ribosylation reactions are phylogenetically ancient and can be classified into four major groups: mono-ADP-ribosylation, poly-ADP-ribosylation, ADP-ribose cyclization, and formation of O-acetyl-ADP-ribose. In the human genome, more than 30 different genes coding for enzymes associated with distinct ADP-ribosylation activities have been identified. This review highlights the recent advances in the rapidly growing field of nuclear mono-ADP-ribosylation and poly-ADP-ribosylation reactions and the distinct ADP-ribosylating enzyme families involved in these processes, including the proposed family of novel poly-ADP-ribose polymerase-like mono-ADP-ribose transferases and the potential mono-ADP-ribosylation activities of the sirtuin family of NAD+-dependent histone deacetylases. A special focus is placed on the known roles of distinct mono- and poly-ADP-ribosylation reactions in physiological processes, such as mitosis, cellular differentiation and proliferation, telomere dynamics, and aging, as well as “programmed necrosis” (i.e., high-mobility-group protein B1 release) and apoptosis (i.e., apoptosis-inducing factor shuttling). The proposed molecular mechanisms involved in these processes, such as signaling, chromatin modification (i.e., “histone code”), and remodeling of chromatin structure (i.e., DNA damage response, transcriptional regulation, and insulator function), are described. A potential cross talk between nuclear ADP-ribosylation processes and other NAD+-dependent pathways is discussed.

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Section: Pargsmentioning

confidence: 96%

“…their amino-terminal histone tails (162). Those authors synthesized peptide thioesters corresponding to histone N termini.…”

Section: Pargsmentioning

confidence: 99%

Nuclear ADP-Ribosylation Reactions in Mammalian Cells: Where Are We Today and Where Are We Going?

Hassa

Haenni

Elser

et al. 2006

Microbiol Mol Biol Rev

635

644

View full text Add to dashboard Cite

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“…To examine the precise role of Lys acetylation at the nucleosome dyad, we generated nucleosomes bearing acetylated Lys on histone H3-K115 and/or H3-K122 by expressed protein ligation (25)(26)(27). We found that the nucleosome position was not altered by H3-K115 and/or H3-K122 acetylation.…”

mentioning

confidence: 99%

Acetylation of Histone H3 at the Nucleosome Dyad Alters DNA-Histone Binding

Manohar¹,

Mooney²,

North³

et al. 2009

Journal of Biological Chemistry

124

153

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Histone post-translational modifications are essential for regulating and facilitating biological processes such as RNA transcription and DNA repair. Fifteen modifications are located in the DNA-histone dyad interface and include the acetylation of H3-K115 (H3-K115Ac) and H3-K122 (H3-K122Ac), but the functional consequences of these modifications are unknown. We have prepared semisynthetic histone H3 acetylated at Lys-115 and/or Lys-122 by expressed protein ligation and incorporated them into single nucleosomes. Competitive reconstitution analysis demonstrated that the acetylation of H3-K115 and H3-K122 reduces the free energy of histone octamer binding. Restriction enzyme kinetic analysis suggests that these histone modifications do not alter DNA accessibility near the sites of modification. However, acetylation of H3-K122 increases the rate of thermal repositioning. Remarkably, Lys 3 Gln substitution mutations, which are used to mimic Lys acetylation, do not fully duplicate the effects of the H3-K115Ac or H3-K122Ac modifications. Our results are consistent with the conclusion that acetylation in the dyad interface reduces DNA-histone interaction(s), which may facilitate nucleosome repositioning and/or assembly/disassembly.All eukaryotic genomes are organized into strings of nucleosomes, where 147 bp of DNA are tightly wrapped around a histone protein octamer (1). Many biological processes are dependent on DNA-protein interactions. However, access to DNA-binding sites is often restricted by the nucleosome structure. Alterations in nucleosome structure, dynamics, and positioning have been hypothesized to play a gatekeeper role in regulating biological processes such as DNA replication, repair, and transcription (2).The post-translational modification (PTM) 3 of core histones (3) plays a central role in regulating the biological processing of eukaryotic genomes. Until recently, known histone PTMs were almost exclusively located on the unstructured histone tail regions, which extend from the structured core of the nucleosomes. PTMs in the histone tails can function to directly alter nucleosome (4 -6) and/or chromatin structure and stability (7,8) and function as protein-binding sites (9) in the "histone code" model (10).During the past 5 years over 30 additional histone PTMs were identified within structured regions of the nucleosome (11-13). Many of these modifications are buried within the nucleosome core and thus are not readily accessible for protein binding. Fifteen of these histone PTMs are located in the DNAhistone interface, where the histone octamer contacts the phosphate backbone of the wrapped DNA (14). Studies have suggested that only mild structural perturbations occur in coremodified nucleosomes, which implies that modifications buried beneath the DNA are unlikely to provide a protein-binding site (15). This has led to two additional models for the function of nucleosome core PTMs.Modifications such as Lys acetylation that reduce the positive charge of the histone octamer surface may reduce the bindi...

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“…Clearly, this represents a successful example for installing methyl group to the lysine residues in the N-terminal regions of the core histones. In addition to its use in studying H3K9 methylation, the NCL strategy was utilized to generate several other homogeneously modified histones, including H4 with K16 acetylation, 190 H4 with K5, 8 or 12 acetylations, 189 and H3 with S10 phosphorylation. 191 These examples illustrate that NCL is a robust tool to address the PTMs occurring on the Nterminal tails.…”

Section: Adding Methylation Marks To the Amino-termini Of Histones Usmentioning

confidence: 99%

“…This is especially challenging for histone synthesis or semisynthesis because almost no cysteine residues are present in histones (the only one is H3 Cys110). Use of auxiliary groups [201][202][203] or desulfurization after the ligation reaction 189,204,205 has been shown by several groups to expand NCL reactions beyond cysteine. In applying NCL for selective labeling of a recombinant protein, certain intrinsic properties of the protein target may be affected.…”

Section: Limitations Of Nclmentioning

confidence: 99%

Chemical and biochemical approaches in the study of histone methylation and demethylation

Luo

Wang

et al. 2010

Med. Res. Rev.

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Histone methylation represents one of the most critical epigenetic events in DNA function regulation in eukaryotic organisms. Classic molecular biology and genetics tools provide significant knowledge about mechanisms and physiological roles of histone methyltransferases and demethylases in various cellular processes. In addition to this stream line, development and application of chemistry and chemistry-related techniques are increasingly involved in biological study, and provide information otherwise difficulty to obtain by standard molecular biology methods. Herein, we review recent achievements and progress in developing and applying chemical and biochemical approaches in the study of histone methylation, including chromatin immunoprecipitation (ChIP), chemical ligation, mass spectrometry (MS), biochemical assays, and inhibitor development. These technological advances allow histone methylation to be studied from genome-wide level to molecular and atomic levels. With ChIP technology, information can be obtained about precise mapping of histone methylation patterns at specific promoters, genes or other genomic regions. MS is particularly useful in detecting and analyzing methylation marks in histone and nonhistone protein substrates. Chemical approaches that permit site-specific incorporation of methyl groups into histone proteins greatly facilitate the investigation of the biological impacts of methylation at individual modification sites. Discovery and design of selective organic inhibitors of histone methyltransferases and demethylases provide chemical probes to interrogate methylation-mediated cellular pathways. Overall, these chemistry-related technological advances have greatly improved our understanding of the biological functions of histone methylation in normal physiology and diseased states, and also are of great potential to translate basic epigenetics research into diagnostic and therapeutic application in the clinic.

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Facile synthesis of site-specifically acetylated and methylated histone proteins: Reagents for evaluation of the histone code hypothesis

Cited by 114 publications

References 31 publications

Nuclear ADP-Ribosylation Reactions in Mammalian Cells: Where Are We Today and Where Are We Going?

Nuclear ADP-Ribosylation Reactions in Mammalian Cells: Where Are We Today and Where Are We Going?

Acetylation of Histone H3 at the Nucleosome Dyad Alters DNA-Histone Binding

Chemical and biochemical approaches in the study of histone methylation and demethylation

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