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Review

Recent advances in histone modification and histone modifying enzyme assays

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Pages 27-36 | Received 22 Jul 2018, Accepted 10 Dec 2018, Published online: 19 Dec 2018

References

  • Peterson CL, Laniel M-A. Histones and histone modifications. Curr Biol. 2004;14:R546–R551.
  • Ma F, Zhang CY. Histone modifying enzymes: novel disease biomarkers and assay development. Expert Rev Mol Diagn. 2016;16:297–306.
  • Pestinger V, Wijeratne SS, Rodriguez-Melendez R, et al. Novel histone biotinylation marks are enriched in repeat regions and participate in repression of transcriptionally competent genes. J Nutr Biochem. 2011;22:328–333.
  • Doenecke D, Karlson P. Albrecht Kossel and the discovery of histones. Trends Biochem Sci. 1984;9:404–405.
  • Allfrey VG, Faulkner R, Mirsky AE. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA. 1964;51:786–794.
  • Strahl BD, Allis CD. The language of covalent histone modifications. Nature. 2000;403:41.
  • Chi P, Allis CD, Wang GG. Covalent histone modifications — miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer. 2010;10:457.
  • Verdin E, Ott M. 50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond. Nat Rev Mol Cell Biol. 2015;16:258–264.
  • Pedersen MT, Helin K. Histone demethylases in development and disease. Trends Cell Biol. 2010;20:662–671.
  • Rice JC, Allis CD. Histone methylation versus histone acetylation: new insights into epigenetic regulation. Curr Opin Cell Biol. 2001;13:263–273.
  • Masumoto H, Hawke D, Kobayashi R, et al. A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response. Nature. 2005;436:294–298.
  • O’Geen H, Ren C, Nicolet CM, et al. dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression. Nucleic Acids Res. 2017;45:9901–9916.
  • Dhar S, Gursoy-Yuzugullu O, Parasuram R, et al. The tale of a tail: histone H4 acetylation and the repair of DNA breaks. Philos Trans R Soc Lond B Biol Sci. 2017;372.
  • Tan M, Luo H, Lee S, et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell. 2011;146:1016–1028.
  • Olsen CA. Expansion of the lysine acylation landscape. Angew Chem Int. 2012;51:3755–3756.
  • Dai LZ, Peng C, Montellier E, et al. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat Chem Biol. 2014;10:365–U73.
  • Xiong X, Panchenko T, Yang S et al. Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2. Nat Chem Biol. 2016;12:1111–1118
  • Grunstein M. Histone acetylation in chromatin structure and transcription. Nature. 1997;389:349.
  • Fuchs J, Demidov D, Houben A, et al. Chromosomal histone modification patterns – from conservation to diversity. Trends Plant Sci. 2006;11:199–208.
  • Francis YI, Fa M, Ashraf H, et al. Dysregulation of histone acetylation in the APP/PS1 mouse model of Alzheimer’s disease. J Alzheimers Dis. 2009;18:131–139.
  • Miao F, Smith DD, Zhang L, et al. Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes. Diabetes. 2008;57:3189–3198.
  • Wang J, Weaver ICG, Gauthier-Fisher A, et al. CBP histone acetyltransferase activity regulates embryonic neural differentiation in the normal and Rubinstein-Taybi syndrome brain. Dev Cell. 2010;18:114–125.
  • Hanauer A, Young ID. Coffin-Lowry syndrome: clinical and molecular features. J Med Genet. 2002;39:705–713.
  • Bradbury CA, Khanim FL, Hayden R, et al. Histone deacetylases in acute myeloid leukaemia show a distinctive pattern of expression that changes selectively in response to deacetylase inhibitors. Leukemia. 2005;19:1751.
  • Zhang K, Dent SY. Histone modifying enzymes and cancer: going beyond histones. J Cell Biochem. 2005;96:1137–1148.
  • Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet. 2007;8:286.
  • Elsheikh SE, Green AR, Rakha EA, et al. Global histone modifications in breast cancer correlate with tumor phenotypes, prognostic factors, and patient outcome. Cancer Res. 2009;69:3802–3809.
  • Waldmann T, Schneider R. Targeting histone modifications—epigenetics in cancer. Curr Opin Cell Biol. 2013;25:184–189.
  • Seligson DB, Horvath S, McBrian MA, et al. Global levels of histone modifications predict prognosis in different cancers. Am J Pathol. 2009;174:1619–1628.
  • Redon CE, Nakamura AJ, Zhang Y-W, et al. Histone γH2AX and poly(ADP-Ribose) as clinical pharmacodynamic biomarkers. Clin Cancer Res. 2010;16:4532–4542.
  • Pfister S, Rea S, Taipale M, et al. The histone acetyltransferase hMOF is frequently downregulated in primary breast carcinoma and medulloblastoma and constitutes a biomarker for clinical outcome in medulloblastoma. Int J Cancer. 2008;122:1207–1213.
  • Ait-Si-Ali S, Ramirez S, Robin P, et al. A rapid and sensitive assay for histone acetyl-transferase activity. Nucleic Acids Res. 1998;26:3869–3870.
  • Dhayalan A, Dimitrova E, Rathert P, et al. A continuous protein methyltransferase (G9a) assay for enzyme activity measurement and inhibitor screening. J Biomol Screen. 2009;14:1129–1133.
  • Delcuve GP, Davie JR. Western blotting and immunochemical detection of histones electrophoretically resolved on acid-urea-Triton- and sodium dodecyl sulfate-polyacrylamide gels. Anal Biochem. 1992;200:339–341.
  • Waterborg JH, Harrington RE. Western blotting of histones from acid-urea-Triton-and sodium dodecyl sulfate-polyacrylamide gels. Anal Biochem. 1987;162:430–434.
  • Wen Q, Gu Y, Tang LJ, et al. Peptide-templated gold nanocluster beacon as a sensitive, label-free sensor for protein post-translational modification enzymes. Anal Chem. 2013;85:11681–11685.
  • Liu X, Xiang M, Tong Z, et al. Activatable fluorescence probe via self-immolative intramolecular cyclization for histone deacetylase imaging in live cells and tissues. Anal Chem. 2018;90:5534–5539.
  • Yitao H, Pei L, Yiting X, et al. Fluorescent nanosensor for probing histone acetyltransferase activity based on acetylation protection and magnetic graphitic nanocapsules. Small. 2015;11:877–885.
  • Liu Y, Perez L, Gill AD, et al. Site-selective sensing of histone methylation enzyme activity via an arrayed supramolecular tandem assay. J Am Chem Soc. 2017;139:10964–10967.
  • Chen L-Y, Wang C-W, Yuan Z, et al. Fluorescent gold nanoclusters: recent advances in sensing and imaging. Anal Chem. 2015;87:216–229.
  • Chen W-Y, Chen L-Y, Ou C-M, et al. Synthesis of fluorescent gold nanodot–liposome hybrids for detection of phospholipase c and its inhibitor. Anal Chem. 2013;85:8834–8840.
  • Liu J-M, Chen J-T, Yan X-P. Near infrared fluorescent trypsin stabilized gold nanoclusters as surface plasmon enhanced energy transfer biosensor and in vivo cancer imaging bioprobe. Anal Chem. 2013;85:3238–3245.
  • Zhang J, Sajid M, Na N, et al. The application of Au nanoclusters in the fluorescence imaging of human serum proteins after native PAGE: enhancing detection by low-temperature plasma treatment. Biosens Bioelectron. 2012;35:313–318.
  • Spellman D, McEvoy E, O’Cuinn G, et al. Proteinase and exopeptidase hydrolysis of whey protein: comparison of the TNBS, OPA and pH stat methods for quantification of degree of hydrolysis. Int Dairy J. 2003;13:447–453.
  • Holzmeister P, Acuna GP, Grohmann D, et al. Breaking the concentration limit of optical single-molecule detection. Chem Soc Rev. 2014;43:1014–1028.
  • Yoshiharu I, Toshio Y. Single molecule detection in life sciences. Single Mol. 2000;1:5–16.
  • Ma F, Liu W-J, Tang B, et al. A single quantum dot-based nanosensor for the signal-on detection of DNA methyltransferase. Chem Commun. 2017;53:6868–6871.
  • Ma F, Li Y, Tang B, et al. Fluorescent biosensors based on single-molecule counting. Acc Chem Res. 2016;49:1722–1730.
  • Ma F, Liu M, Wang ZY, et al. Multiplex detection of histone-modifying enzymes by total internal reflection fluorescence-based single-molecule detection. Chem Commun. 2016;52:1218–1221.
  • Johnsson A, Durand‐Dubief M, Xue‐Franzén Y, et al. HAT–HDAC interplay modulates global histone H3K14 acetylation in gene‐coding regions during stress. EMBO Rep. 2009;10:1009–1014.
  • Tachibana M, Matsumura Y, Fukuda M, et al. G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription. Embo J. 2008;27:2681–2690.
  • Ghale G, Ramalingam V, Urbach AR, et al. Determining protease substrate selectivity and inhibition by label-free supramolecular tandem enzyme assays. J Am Chem Soc. 2011;133:7528–7535.
  • Guo D-S, Yang J, Liu Y. Specifically monitoring butyrylcholinesterase by supramolecular tandem assay. Chem Eur J. 2013;19:8755–8759.
  • Hennig A, Bakirci H, Nau WM. Label-free continuous enzyme assays with macrocycle-fluorescent dye complexes. Nat Methods. 2007;4:629.
  • Mara F, Srikanth K, Ana R, et al. A fluorescence-based supramolecular tandem assay for monitoring lysine methyltransferase activity in homogeneous solution. Chem Eur J. 2012;18:3521–3528.
  • Jacopozzi P, Dalcanale E. Metal-induced self-assembly of cavitand-based cage molecules. Angew Chem Int Ed. 1997;36:613–615.
  • Xia Z, Rao J. Biosensing and imaging based on bioluminescence resonance energy transfer. Curr Opin Biotech. 2009;20:37–44.
  • Sapsford KE, Berti L, Medintz IL. Materials for fluorescence resonance energy transfer analysis: beyond traditional donor–acceptor combinations. Angew Chem Int Ed. 2006;45:4562–4589.
  • Sekar TV, Foygel K, Gelovani JG, et al. Genetically encoded molecular biosensors to image histone methylation in living animals. Anal Chem. 2015;87:892–899.
  • Simon Jeffrey A, Kingston Robert E. Occupying chromatin: polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying. Put Mol Cell. 2013;49:808–824.
  • Stewart MD, Li J, Wong J. Relationship between histone H3 lysine 9 methylation, transcription repression, and heterochromatin protein 1 recruitment. Mol Cell Biol. 2005;25:2525–2538.
  • O’Geen H, Echipare L, Farnham PJ. Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol Biol. 2011;791:265–286.
  • Park PJ. ChIP–seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009;10:669.
  • Yoshida W, Kezuka A, Abe K, et al. Detection of histone modification by chromatin immunoprecipitation combined zinc finger luciferase-based bioluminescence resonance energy transfer assay. Anal Chem. 2013;85:6485–6490.
  • Sinha AK. Colorimetric assay of catalase. Anal Biochem. 1972;47:389–394.
  • Medley CD, Smith JE, Tang Z, et al. Gold nanoparticle-based colorimetric assay for the direct detection of cancerous cells. Anal Chem. 2008;80:1067–1072.
  • Kolusheva S, Boyer L, Jelinek R. A colorimetric assay for rapid screening of antimicrobial peptides. Nat Biotechnol. 2000;18:225.
  • Li H, Rothberg L. Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc Natl Acad Sci USA. 2004;101:14036–14039.
  • Zhao W, Brook MA, Li Y. Design of gold nanoparticle-based colorimetric biosensing assays. ChemBioChem. 2008;9:2363–2371.
  • Ge C, Yu L, Fang Z, et al. An enhanced strip biosensor for rapid and sensitive detection of histone methylation. Anal Chem. 2013;85:9343–9349.
  • Wang J. Electrochemical detection for microscale analytical systems: a review. Talanta. 2002;56:223–231.
  • Xu D, Xu D, Yu X, et al. Label-free electrochemical detection for aptamer-based array electrodes. Anal Chem. 2005;77:5107–5113.
  • Xiao Y, Qu X, Plaxco KW, et al. Label-free electrochemical detection of DNA in blood serum via target-induced resolution of an electrode-bound dna pseudoknot. J Am Chem Soc. 2007;129:11896–11897.
  • Hu Y, Chen S, Han Y, et al. Unique electrocatalytic activity of a nucleic acid-mimicking coordination polymer for the sensitive detection of coenzyme A and histone acetyltransferase activity. Chem Commun. 2015;51:17611–17614.
  • Kneipp K, Wang Y, Kneipp H, et al. Single molecule detection using surface-enhanced Raman scattering (SERS). Phys Rev Lett. 1997;78:1667–1670.
  • Wang Y, Deng X, Liu J, et al. Surface enhanced Raman scattering based sensitive detection of histone demethylase activity using a formaldehyde-selective reactive probe. Chem Commun. 2013;49:8489–8491.
  • Bontempi N, Biavardi E, Bordiga D, et al. Probing lysine mono-methylation in histone H3 tail peptides with an abiotic receptor coupled to a non-plasmonic resonator. Nanoscale. 2017;9:8639–8646.
  • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422:198–207.
  • Tang H, Tian B, Brasier AR, et al. Measurement of histone methylation dynamics by one-carbon metabolic isotope labeling and high-energy collisional dissociation methylation signature ion detection. Sci Rep. 2016;6:31537.
  • Peterson AC, Russell JD, Bailey DJ, et al. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteomics. 2012;11:1475–1488.
  • Thomas SN, Chen L, Liu Y, et al. Targeted proteomic analyses of histone H4 acetylation changes associated with homologous-recombination-deficient high-grade serous ovarian carcinomas. J Proteome Res. 2017;16:3704–3710.
  • Hyun S, Lee KH, Han A, et al. An RNA aptamer that selectively recognizes symmetric dimethylation of arginine 8 in the histone H3 n-terminal peptide. Nucleic Acid Ther. 2011;21:157–163.
  • Shao N, Zhang K, Chen Y, et al. Preparation and characterization of DNA aptamer based spin column for enrichment and separation of histones. Chem Commun. 2012;48:6684–6686.
  • Ramos E, Moreno M, Martín ME, et al. In vitro selection of leishmania infantum H3-binding ssdna aptamers. Oligonucleotides. 2010;20:207–213.
  • Lin L, Fu Q, Williams BAR, et al. Recognition imaging of acetylated chromatin using a dna aptamer. Biophys J. 2009;97:1804–1807.
  • Lin L, Hom D, Lindsay SM, et al. In vitro selection of histone H4 Aptamers for recognition imaging microscopy. J Am Chem Soc. 2007;129:14568–14569.
  • Williams BAR, Lin L, Lindsay SM, et al. Evolution of a histone H4-K16 acetyl-specific dna aptamer. J Am Chem Soc. 2009;131:6330–6331.
  • Ma F, Liu M, Tang B, et al. Sensitive quantification of microRNAs by isothermal helicase-dependent amplification. Anal Chem. 2017;89:6182–6187.
  • Lizardi PM, Huang X, Zhu Z, et al. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet. 1998;19:225.
  • Notomi T, Okayama H, Masubuchi H, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28:e63–e.
  • Van Ness J, Van Ness LK, Galas DJ. Isothermal reactions for the amplification of oligonucleotides. Proc Natl Acad Sci USA. 2003;100:4504–4509.
  • Chinen AB, Guan CM, Ferrer JR, et al. Nanoparticle probes for the detection of cancer biomarkers, cells, and tissues by fluorescence. Chem Rev. 2015;115:10530–10574.
  • Zhou J, Yang Y, Zhang C-Y. Toward biocompatible semiconductor quantum dots: from biosynthesis and bioconjugation to biomedical application. Chem Rev. 2015;115:11669–11717.
  • Ma F, Li -C-C, Zhang C-Y. Development of quantum dot-based biosensors: principles and applications. J Mater Chem B. 2018;6:6173–6190.

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