A Method for Genetically Installing Site-Specific Acetylation in Recombinant Histones Defines the Effects of H3 K56 Acetylation

Neumann, Heinz; Hancock, Susan M.; Buning, Ruth; Routh, Andrew; Chapman, Lynda; Somers, Joanna; Owen-Hughes, Tom; Noort, John van; Rhodes, Daniela; Chin, Jason W.

doi:10.1016/j.molcel.2009.07.027

Cited by 467 publications

(549 citation statements)

References 56 publications

(71 reference statements)

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“…We then asked whether a recombinant nucleosome in which the only posttranslational modification is the acetylation of H3 at K56 promotes binding to recombinant Oct4 in vitro. Nucleosomes in which only H3K56 or H3K9 is acetylated were prepared as described (27,28). Using the in vitro binding assay, we found that acetylation of H3K56 promotes the binding of Oct4 to nucleosomes much more strongly than to the unmodified nucleosomes or to nucleosomes containing H3K9ac (Fig.…”

Section: H3k56ac Presence Is Correlated With That Of Key Transcriptionalmentioning

confidence: 97%

“…1F). Thus, acetylation of H3K56 not only decreases nucleosome stability (29), increases unwrapping of nucleosomal DNA ends, and may affect histonehistone interactions (27,30), but H3K56ac may also free H3K56 sufficiently from local nucleosomal constraints to enable H3K56ac recognition by Oct4. Taken together, our data indicate that H3K56ac interacts with Oct4 in vivo in mouse ESCs and directly in vitro.…”

Section: H3k56ac Presence Is Correlated With That Of Key Transcriptionalmentioning

confidence: 99%

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Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency

Tan

Xue

Song

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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The presence of acetylated histone H3K56 (H3K56ac) in human ES cells (ESCs) correlates positively with the binding of Nanog, Sox2, and Oct4 (NSO) transcription factors at their target gene promoters. However, the function of H3K56ac there has been unclear. We now report that Oct4 interacts with H3K56ac in mouse ESC nuclear extracts and that perturbing H3K56 acetylation decreases Oct4-H3 binding. This interaction is likely to be direct because it can be recapitulated in vitro in an H3K56ac-dependent manner and is functionally important because H3K56ac combines with NSO factors in chromatin immunoprecipitation sequencing to mark the regions associated with pluripotency better than NSO alone. Moreover, reducing H3K56ac by short hairpin Asf1a decreases expression of pluripotency-related markers and increases expression of differentiation-related ones. Therefore, our data suggest that H3K56ac plays a central role in binding to Oct4 to promote the pluripotency of ESCs.

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Section: H3k56ac Presence Is Correlated With That Of Key Transcriptionalmentioning

confidence: 97%

Section: H3k56ac Presence Is Correlated With That Of Key Transcriptionalmentioning

confidence: 99%

Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency

Tan

Xue

Song

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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show abstract

“…Meanwhile, numerous acetylated proteins have been produced using this method. Chin and colleagues investigated the impact of acetylation of histone H3 at lysine 56 on the stability of nucleosomes [45]. This modification had been observed on the nascent protein and implicated in the modulation of chromatin structure during DNA replication and repair.…”

Section: Lysine Acetylationmentioning

confidence: 99%

Rewiring translation – Genetic code expansion and its applications

Neumann

2012

FEBS Letters

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a b s t r a c tWith few minor variations, the genetic code is universal to all forms of life on our planet. It is difficult to imagine that one day organisms might exist that use an entirely different code to translate the information of their genome. Recent developments in the field of synthetic biology, however, have opened the gate to their creation. The genetic code of several organisms has been expanded by the heterologous expression of evolved aminoacyl-tRNA synthetase/tRNA CUA pairs that mediate the incorporation of unnatural amino acids in response to amber codons. These UAAs introduce exciting new features into proteins, such as spectroscopic probes, UV-inducible crosslinkers, and functional groups for bioorthogonal conjugations or posttranslational modifications. Orthogonal ribosomes provide a parallel translational machinery in Escherichia coli that has lost its evolutionary constraints. Evolved variants of these ribosomes translate amber or quadruplet codons with massively enhanced efficiency. Here, I review these recent developments emphasizing their tremendous potential to facilitate biochemical and cell biological studies.

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“…187,206 This strategy evolves an orthogonal pyrrolysyl-tRNA synthetase/ tRNA CUA pair that specifically recognizes N ε -tert-butyloxycarbonyl-N ε -methyl-L-lysine and directs its incorporation into recombinant proteins such as histone H3. N ε -methyl-Llysine was not used directly in the protein synthesis because the pyrrolysyl-tRNA synthetase did not accept methyl-lysine as a substrate.…”

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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A Method for Genetically Installing Site-Specific Acetylation in Recombinant Histones Defines the Effects of H3 K56 Acetylation

Cited by 467 publications

References 56 publications

Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency

Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency

Rewiring translation – Genetic code expansion and its applications

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

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