Identification and interrogation of combinatorial histone modifications

Karch, Kelly R.; DeNizio, Jamie E.; Black, Ben E.; Garcia, Benjamin A.

doi:10.3389/fgene.2013.00264

Cited by 68 publications

(60 citation statements)

References 114 publications

(149 reference statements)

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“…Histone modifications are a major type of epigenetics which consist of acetylation, phosphorylation and methylation [67]. Recently, Johnson et al documented a wide range of histone modifications occurring in hypoxia, they have showed a direct interaction of modified histones with promoter regions of hypoxia responsive genes [68].…”

Section: Epigenetics/hif-1a Network Signaling Pathwaymentioning

confidence: 99%

Hypoxia-inducible factor-1alpha in hepatic fibrosis: A promising therapeutic target

et al. 2015

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Section: Epigenetics/hif-1a Network Signaling Pathwaymentioning

confidence: 99%

Hypoxia-inducible factor-1alpha in hepatic fibrosis: A promising therapeutic target

et al. 2015

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“…Top-down and middle-down proteomics are not high throughput and are best carried out on either purified proteins or protein mixtures of low complexity. Classic examples of studies using top-down, middle-down, but also bottomup proteomics on proteins with different PTMs involve histones (Karch et al, 2013) and the p53 tumor suppression protein (DeHart et al, 2014).…”

Section: Proteins With Multiple Ptms Combinatorial Ptms and Cross Tmentioning

confidence: 99%

Update: Post-translational protein modifications in plant metabolism

2015

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ORCID ID: 0000-0001-9536-0487 (K.J.v.W.).Posttranslational modifications (PTMs) of proteins greatly expand proteome diversity, increase functionality, and allow for rapid responses, all at relatively low costs for the cell. PTMs play key roles in plants through their impact on signaling, gene expression, protein stability and interactions, and enzyme kinetics. Following a brief discussion of the experimental and bioinformatics challenges of PTM identification, localization, and quantification (occupancy), a concise overview is provided of the major PTMs and their (potential) functional consequences in plants, with emphasis on plant metabolism. Classic examples that illustrate the regulation of plant metabolic enzymes and pathways by PTMs and their cross talk are summarized. Recent large-scale proteomics studies mapped many PTMs to a wide range of metabolic functions. Unraveling of the PTM code, i.e. a predictive understanding of the (combinatorial) consequences of PTMs, is needed to convert this growing wealth of data into an understanding of plant metabolic regulation.The primary amino acid sequence of proteins is defined by the translated mRNA, often followed by Nor C-terminal cleavages for preprocessing, maturation, and/or activation. Proteins can undergo further reversible or irreversible posttranslational modifications (PTMs) of specific amino acid residues. Proteins are directly responsible for the production of plant metabolites because they act as enzymes or as regulators of enzymes. Ultimately, most proteins in a plant cell can affect plant metabolism (e.g. through effects on plant gene expression, cell fate and development, structural support, transport, etc.). Many metabolic enzymes and their regulators undergo a variety of PTMs, possibly resulting in changes in oligomeric state, stabilization/degradation, and (de)activation (Huber and Hardin, 2004), and PTMs can facilitate the optimization of metabolic flux. However, the direct in vivo consequence of a PTM on a metabolic enzyme or pathway is frequently not very clear, in part because it requires measurements of input and output of the reactions, including flux through the enzyme or pathway. This Update will start out with a short overview on the major PTMs observed for each amino acid residue (Table I), followed by a brief discussion of techniques for the characterization of protein PTMs, including determination of the localization within proteins (i.e. the specific residues) and occupancy. Challenges in dealing with multiple PTMs per protein and cross talk between PTMs will be briefly outlined. We then describe the major physiological PTMs observed in plants as well as PTMs that are nonenzymatically induced during sample preparation (Table II). Finally, this Update is completed with a number of well-studied, classical examples of the regulation of plant metabolism by PTMs, in particular for enzymes in primary metabolism (Calvin cycle, glycolysis, and respiration) and the C4 shuttle accommodating photosynthesis in C4 plants (Table III). As will be ev...

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“…This effort has led to the characterization of the asymmetric existence of H3K27me3 and H3K4me3 within a nucleosome at bivalent promoters of embryonic stem (ES) cells (Voigt et al 2012). Middle-down and top-down MS technologies are powerful tools for the identification of combinatorial histone PTM patterns at the single histone peptide level when paired with state-of-the-art sample fractionation and fragmentation methods (Karch et al 2013). In recent years, these efforts have led to the identification of hundreds of histone PTM patterns.…”

Section: Ways To Explore Histone Modification Patterns and Their Readoutmentioning

confidence: 99%

“…Such functional diversity linked to a single histone mark raises issues related to recruitment specificity and the existence of more context-dependent mechanisms for epigenetic message decoding. In fact, accumulating evidence demonstrates that histone modifications exist as a pattern or signature across functionally distinct chromatin domains (Han and Garcia 2013;Karch et al 2013). Correspondingly, hundreds of histone "reader" modules have been characterized to recognize histone PTMs in a site-and type-specific manner (Musselman et al 2012a;Patel and Wang 2013;Taverna et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Histone Recognition by Tandem Modules and Modulation by Multiple PTMs

Zhao

Patel

2015

Histone Recognition

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Histone post-translational modifications (PTMs) are considered to constitute a layer of epigenetic information, which helps to organize the genome of eukaryotic cells at the chromatin level and directs the establishment and maintenance of particular cellular traits. Recent progress suggests that the "ON" or "OFF" states of chromatin are not simply determined by the readout of a single histone or epigenetic mark. In fact, histone modifications often exist in pairs or as a pattern to mediate particular downstream events. In accordance, the "reader" modules that usually recognize histone marks in a type-and site-specific way are often linked in tandem within one protein or coexist within a complex, suggesting the involvement of multivalent mechanisms for the decoding of histone modification patterns. Here, we summarize recent advances in histone recognition by tandem modules and its modulation by multiple PTMs from a structural perspective with implications on biological outcome. The molecular recognition events discussed here illustrate how chromatin regulators make use of paired or integrated "reader" modules to translate particular histone PTM signatures into specific biological outcomes.

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Identification and interrogation of combinatorial histone modifications

Cited by 68 publications

References 114 publications

Hypoxia-inducible factor-1alpha in hepatic fibrosis: A promising therapeutic target

Hypoxia-inducible factor-1alpha in hepatic fibrosis: A promising therapeutic target

Update: Post-translational protein modifications in plant metabolism

Histone Recognition by Tandem Modules and Modulation by Multiple PTMs

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