Skip to main content

Advertisement

SpringerLink
Log in

Regulation of epigenetic state by non-histone chromatin proteins and transcription factors: Implications in disease

  • Review
  • Published:
Journal of Biosciences Aims and scope Submit manuscript

Abstract

Besides the fundamental components of the chromatin, DNA and octameric histone, the non-histone chromatin proteins and non-coding RNA play a critical role in the organization of functional chromatin domains. The non-histone chromatin proteins therefore regulate the transcriptional outcome in both physiological and pathophysiological state as well. They also help to maintain the epigenetic state of the genome indirectly. Several transcription factors and histone interacting factors also contribute in the maintenance of the epigenetic states, especially acetylation by the induction of autoacetylation ability of p300/CBP. Alterations of KAT activity have been found to be causally related to disease manifestation, and thus could be potential therapeutic target.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3

Similar content being viewed by others

References

  • Agresti A and Bianchi ME 2003 HMGB proteins and gene expression. Curr. Opin. Genet. Dev. 13 170–178

    CAS  PubMed  Google Scholar 

  • Aranda S, Mas G and Di Croce L 2015 Regulation of gene transcription by Polycomb proteins. Sci. Adv. 1 1–16

    Google Scholar 

  • Arensman MD, Telesca D, Lay AR, et al. 2014 The CREB-binding protein inhibitor ICG-001 suppresses pancreatic cancer growth. Mol. Cancer Ther. 13 2303–2314

    CAS  PubMed  PubMed Central  Google Scholar 

  • Arif M, Vedamurthy BM, Choudhari R, et al. 2010 Nitric oxide-mediated histone hyperacetylation in oral cancer: target for a water-soluble HAT inhibitor, CTK7A. Chem. Biol. 17 903–913

    CAS  PubMed  Google Scholar 

  • Babu D and Fullwood MJ 2015 3D genome organization in health and disease: Emerging opportunities in cancer translational medicine. Nucleus 6 382–393

    CAS  PubMed  PubMed Central  Google Scholar 

  • Baell JB, Laever D, Hermans S, et al. 2018 Inhibitors of histone acetyltransferases KAT6A/B induce senescence and arrest tumour growth. Nature 560 253–257

    CAS  PubMed  Google Scholar 

  • Balasubramanyam K, Varier RA, Altaf M, et al. 2004 Curcumin, a novel p300/CREB-binding protein-specific inhibitor of Acetyltransferase, represses the Acetylation of histone/nonhistone proteins and histone acetyltransferase-dependent chromatin transcription. J. Biol. Chem. 279 51163–51171

    CAS  PubMed  Google Scholar 

  • Balasubramanyam K, Altaf M, Varier RA, et al. 2004 Polyisoprenylated benzophenone, garcinol, a natural histone acetyltransferase inhibitor, represses chromatin transcription and alters global gene expression. J. Biol. Chem. 279 33716–33726

    CAS  PubMed  Google Scholar 

  • Balasubramanyam K, Swaminathan V, Ranganathan A and Kundu TK 2003 Small molecule modulators of histone acetyltransferase p300. J. Biol. Chem. 278 19134–19140

    CAS  PubMed  Google Scholar 

  • Bannister AJ and Kouzarides T 2011 Regulation of chromatin by histone modifications. Cell Res. 21 381–395

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bannister AJ and Kouzarides T 2005 Reversing histone methylation. Nature 436 1103–1106

    CAS  PubMed  Google Scholar 

  • Bannister AJ, Zegerman P, Partridge JF, et al. 2001 Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410 120–124

    CAS  PubMed  Google Scholar 

  • Barski A, Cuddapah S, Cui K, et al. 2007 High-resolution profiling of histone methylations in the human genome. Cell 129 823–837

    CAS  PubMed  Google Scholar 

  • Bártová E, Kreǰcí J, Harničarová A, Galiová G and Kozubek S 2008 Histone modifications and nuclear architecture: A review. J. Histochem. Cytochem. 56 711–721

    PubMed  PubMed Central  Google Scholar 

  • Batta K and Kundu TK 2007 Activation of p53 function by human transcriptional coactivator pc4: role of protein-protein interaction, DNA bending, and posttranslational modifications. Mol. Cell. Biol. 27 7603–7614

    CAS  PubMed  PubMed Central  Google Scholar 

  • Behjati S, Tarpey P, Presneau N,et al. 2013 Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone. Nat. Genet. 45 1479–1482

    CAS  PubMed  Google Scholar 

  • Berger SL 2007 The complex language of chromatin regulation during transcription. Nature 447 407–412

    CAS  PubMed  Google Scholar 

  • Berson A, Nativio R, Berger SL and Bonini NM 2018 epigenetic regulation in neurodegenerative diseases. Trends Neurosci. 41 587–598

    CAS  PubMed  PubMed Central  Google Scholar 

  • Black JC, Mosley A, Kitada T, Washburn M and Carey M 2008 The SIRT2 deacetylase regulates autoacetylation of p300. Mol. Cell 32 449–455

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bonev B and Cavalli G 2016 Organization and function of the 3D genome. Nat. Rev. Genet. 17 661–678

    CAS  PubMed  Google Scholar 

  • Bose DA and Berger SL 2017 eRNA binding produces tailored CBP activity profiles to regulate gene expression. RNA Biol. 14 1655–1659

    PubMed  PubMed Central  Google Scholar 

  • Bose DA, Donahue G, Reinberg D, et al. 2017 RNA Binding to CBP stimulates histone acetylation and transcription. Cell 168 135–149.e22

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bowers EM, Yan G, Mukherjee C, et al. 2010 Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem. Biol. 17 471–482

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cancer Genome Atlas Research Network, Ley T, Miller C, et al. 2013 Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med. 368 2059–2074

  • Caridi PC, Delabaere L, Zapotoczny G and Chiolo I 2017 And yet, it moves: nuclear and chromatin dynamics of a heterochromatic double-strand break. Philos. Trans. R. Soc. B Biol. Sci. 372 20160291

  • Ceschin DG, Walia M, Wenk S, et al. 2011 Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin. Genes Dev. 25 1132–1146

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chan K-M, Fang D, Gan H, et al. 2013 The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression. Genes Dev. 27 985–990

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chatterjee S, Mizar P, Cassel R, et al. 2013 A novel activator of CBP/p300 acetyltransferases promotes neurogenesis and extends memory duration in adult mice. J. Neurosci. 33 10698–10712

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chatterjee S,Cassel R, Schneider-Anthony A, et al. 2018 Reinstating plasticity and memory in a tauopathy mouse model with an acetyltransferase activator. EMBO Mol. Med. 10 e8587

    PubMed  PubMed Central  Google Scholar 

  • Das C, Hizume K, Batta K, et al. 2006 Transcriptional Coactivator PC4, a chromatin-associated protein, induces chromatin condensation. Mol. Cell. Biol. 26 8303–8315

    CAS  PubMed  PubMed Central  Google Scholar 

  • Das C, Gadad SS and Kundu TK 2010 Human positive coactivator 4 controls heterochromatinization and silencing of neural gene expression by interacting with REST/NRSF and CoREST. J. Mol. Biol. 397 1–12

    CAS  PubMed  Google Scholar 

  • Ea V, Baudement MO, Lesne A and Forné T 2015 Contribution of topological domains and loop formation to 3D chromatin organization. Genes (Basel). 6 734–750

    CAS  PubMed  PubMed Central  Google Scholar 

  • Eberharter A and Becker PB 2002 Histone acetylation: A switch between repressive and permissive chromatin. Second in review on chromatin dynamics. EMBO Rep. 3 224–229

    CAS  PubMed  PubMed Central  Google Scholar 

  • Eissenberg JC and Elgin SC 2000 The HP1 protein family: Getting a grip on chromatin. Curr. Opin. Genet. Dev. 10 204–210

    CAS  PubMed  Google Scholar 

  • Elsheikh SE, Green A, Rakha E, et al. 2009 Global histone modifications in breast cancer correlate with tumor phenotypes, prognostic factors, and patient outcome. Cancer Res. 69 3802–3809

    CAS  PubMed  Google Scholar 

  • Emami KH, Nguyen Cu, Ma H, et al. 2004 A small molecule inhibitor of beta-catenin/CREB-binding protein transcription [corrected]. Proc. Natl. Acad. Sci. U. S. A. 101 12682–12687

    CAS  PubMed  PubMed Central  Google Scholar 

  • Erkina TY, Zou Y, Freeling S, Vorobyev VI and Erkine AM 2009 Functional interplay between chromatin remodeling complexes RSC, SWI/SNF and ISWI in regulation of yeast heat shock genes. Nucleic Acids Res. 38 1441–1449

    PubMed  PubMed Central  Google Scholar 

  • Falk H, Connor T, Yang H, et al. 2011 An efficient high-throughput screening method for MYST family acetyltransferases, a new class of epigenetic drug targets. J. Biomol. Screen. 16 1196–1205

    CAS  PubMed  Google Scholar 

  • Fischle W, Wang Y and Allis CD 2003 Histone and chromatin cross-talk. Curr. Opin. Cell Biol. 15 172–183

    CAS  PubMed  Google Scholar 

  • Flavahan WA, Gaskell E and Bernstein BE 2017 Epigenetic plasticity and the hallmarks of cancer. Science (80-.) 357, eaal2380

  • Fraga MF, Ballestar E, Villar-Garea A, et al. 2005 Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat. Genet. 37 391–400

    CAS  PubMed  Google Scholar 

  • Galande S, Purbey PK, Notani D and Kumar PP 2007 The third dimension of gene regulation: organization of dynamic chromatin loopscape by SATB1. Curr. Opin. Genet. Dev. 17 408–414. https://doi.org/10.1016/j.gde.2007.08.003

    Article  CAS  PubMed  Google Scholar 

  • Gang EJ, Hsieh Y, Pham J, et al. 2014 Small-molecule inhibition of CBP/catenin interactions eliminates drug-resistant clones in acute lymphoblastic leukemia. Oncogene 33 2169–2178

    CAS  PubMed  Google Scholar 

  • Garcia-Carpizo V, Ruiz-Llorente S, Sarmentero J, et al. 2018 CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation. Epigenetics Chromatin 11 30

    PubMed  PubMed Central  Google Scholar 

  • Ge H and Roeder RG 1994 Purification, cloning, and characterization of a human coactivator, PC4, that mediates transcriptional activation of class II genes. Cell 78 513–523

    CAS  PubMed  Google Scholar 

  • Gerlitz G 2010 HMGNs, DNA repair and cancer. Biochim. Biophys. Acta - Gene Regul. Mech. 1799 80–85

    CAS  Google Scholar 

  • Gjoneska E, Pfenning AR, Mathys H, et al. 2015 Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease. Nature 518 365–369

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gonzalez-Sandoval A and Gasser SM 2016 On TADs and LADs: Spatial control over gene expression. Trends Genet. 32 485–495

    CAS  PubMed  Google Scholar 

  • Hamamori Y, Sartorelli V, Ogryzko Vet al. 1999 Regulation of Histone Acetyltransferases p300 and PCAF by the bHLH Protein Twist and Adenoviral Oncoprotein E1A. Cell 96 405–413

  • Han L, Pandian G, Chandran A, et al. 1999 A synthetic DNA-binding domain guides distinct chromatin-modifying small molecules to activate an identical gene network. Angew. Chemie Int. Ed. 54 8700–8703 2015

    CAS  Google Scholar 

  • Hansson ML, Popko-Ścibor AE, Just Ribeiro M Saint, et al. 2009 The transcriptional coactivator MAML1 regulates p300 autoacetylation and HAT activity. Nucleic Acids Res. 37 2996–3006

  • Hay DA, Fedorov O, Martin S, et al. 2014 Discovery and optimization of small-molecule ligands for the CBP/p300 Bromodomains. J. Am. Chem. Soc. 136 9308–9319

    CAS  PubMed  PubMed Central  Google Scholar 

  • Holland KA 2002 Chromosomes: nonhistone proteins. Encycl. Life Sci. 1–9 https://doi.org/10.1038/npg.els.0001158

  • Hutson TH, Kathe C, Palmisano I, et al. 2019 Cbp-dependent histone acetylation mediates axon regeneration induced by environmental enrichment in rodent spinal cord injury models. Sci. Transl. Med. 11 eaaw2064

  • Ignacio Martín-Subero J 2011 How epigenomics brings phenotype into being. Pediatr Endocrinol. Rev. 9 506–510

    Google Scholar 

  • Jiang H, Poirier MA, Liang Y, et al. 2006 Depletion of CBP is directly linked with cellular toxicity caused by mutant huntingtin. Neurobiol. Dis. 23 543–551

    CAS  PubMed  Google Scholar 

  • Kaypee S, Sudarshan D, Shanmugam M, et al. 2016 Aberrant lysine acetylation in tumorigenesis: Implications in the development of therapeutics. Pharmacol. Ther. 162 98–119

    CAS  PubMed  Google Scholar 

  • Kaypee S, Sahadevan SA, Patil S, et al. 2018a Mutant and wild-type tumor suppressor p53 Induces p300 autoacetylation. iScience 4 260–272

  • Kaypee S, Sahadevan SA, Sudarshan D, et al. 2018b Oligomers of human histone chaperone NPM1 alter p300/KAT3B folding to induce autoacetylation. Biochim. Biophys. Acta Gen. Subj. 1862 1729–1741

    CAS  PubMed  Google Scholar 

  • Kaypee S, Sahadevan SA, Patil S, et al. 2018c The wild-type and gain-of-function mutant p53 enhance p300 autoacetylation through conformational switching. bioRxiv 194704

  • Kontopoulos E, Parvin JD and Feany MB 2006 α-synuclein acts in the nucleus to inhibit histone acetylation and promote neurotoxicity. Hum. Mol. Genet. 15 3012–3023

    CAS  PubMed  Google Scholar 

  • Kretzschmar M, Kaiser K, Lottspeich F and Meisterernst M 1994 A novel mediator of class II gene transcription with homology to viral immediate-early transcriptional regulators. Cell 78 525–534

    CAS  PubMed  Google Scholar 

  • Krishnakumar R and Kraus WL 2010 PARP-1 regulates chromatin structure and transcription through a KDM5B-dependent pathway. Mol. Cell 39 736–749

    CAS  PubMed  PubMed Central  Google Scholar 

  • Krouwels IM, Wiesmeijer K, Abraham TE, et al. 2005 A glue for heterochromatin maintenance: stable SUV39H1 binding to heterochromatin is reinforced by the SET domain. J. Cell Biol. 170 537–549

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kuang X, Zhu J, Peng Z, Wang J and Chen Z 2016 Transducin (Beta)-Like 1 X-Linked receptor 1 correlates with clinical prognosis and epithelial–mesenchymal transition in hepatocellular carcinoma. Dig. Dis. Sci. 61 489–500

    CAS  PubMed  Google Scholar 

  • Lachner M, O’Carroll D, Rea S, Mechtler K and Jenuwein T 2001 Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410 116–120

    CAS  PubMed  Google Scholar 

  • Larson AG, Elnatan D, Keenen M, et al. 2017 Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 547 236–240

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lasko LM, Jakob CG, Edalji RP, et al. 2017 Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours. Nature 550 128–132

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lau OD, Kundu TK, Soccio RE, et al. 2000 HATs off: selective synthetic inhibitors of the histone acetyltransferases p300 and PCAF. Mol. Cell 5 589–595

    CAS  PubMed  Google Scholar 

  • Lewis PW, Muller MM, Koletsky MS, et al. 2013 Inhibition of PRC2 Activity by a gain-of-function H3 mutation found in pediatric glioblastoma. Science 340 857–861

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li G and Reinberg D 2011 Chromatin higher-order structures and gene regulation. Curr. Opin. Genet. Dev. 21 175–186

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lieberman-Aiden E, van Berkum N, Williams L, et al. 2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326 289–293

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu B, Cheng J, Zhang, X, et al. 2010 Global histone modification patterns as prognostic markers to classify glioma patients. Cancer Epidemiol. Biomarkers Prev. 19 2888–2896

    CAS  PubMed  Google Scholar 

  • Luijsterburg MS, Dinant C, Lans H et.al. 2009 Heterochromatin protein 1 is recruited to various types of DNA damage. J. Cell Biol. 185 577–586

    CAS  PubMed  PubMed Central  Google Scholar 

  • Martire S, Gogate AA, Whitmill A, et al. 2019 Phosphorylation of histone H3.3 at serine 31 promotes p300 activity and enhancer acetylation. Nat. Genet. 51 941–946

    CAS  PubMed  PubMed Central  Google Scholar 

  • Meisterernst M, Roy AL, Lieu HM and Roeder RG 1991 Activation of class II gene transcription by regulatory factors is potentiated by a novel activity. Cell 66 981–993

    CAS  PubMed  Google Scholar 

  • Moustakim M, Clark P, Trulli L, et al. 2017 Discovery of a PCAF Bromodomain chemical probe. Angew. Chem. Int. Ed. Engl. 56 827–831

    CAS  PubMed  Google Scholar 

  • Nacev BA, Feng L, Bagert JD, et al. 2019 The expanding landscape of ‘oncohistone’ mutations in human cancers. Nature 567 473–478

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nagaraj AB, Joseph P, Kovalenko O, et al. 2015 Critical role of Wnt/β-catenin signaling in driving epithelial ovarian cancer platinum resistance. Oncotarget 6 23720–23734

    PubMed  PubMed Central  Google Scholar 

  • Nakayama J -i, Rice JC, Strahl BD, Allis CD and Grewal SI 2001 Role of histone H3 Lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292 110–113

  • Nebbioso A, Tambaro FP, Dell’Aversana C and Altucci L 2018 Cancer epigenetics: Moving forward. PLOS Genet. 14, e1007362

    PubMed  Google Scholar 

  • Ngo L, Brown T and Zheng YG 2019 Bisubstrate inhibitors to target histone acetyltransferase 1. Chem. Biol. Drug Des. 93 865–873

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nucifora FC, Sasaki M, Peters MF, et al. 2001 Interference by huntingtin and atrophin-1 with cbp-mediated transcription leading to cellular toxicity. Science 291 2423–2428

    CAS  PubMed  Google Scholar 

  • Ordog T, Syed SA, Hayashi Y and Asuzu DT 2012 Epigenetics and chromatin dynamics: A review and a paradigm for functional disorders. Neurogastroenterol. Motil. 24 1054–1068

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ortega E, Rengachari S, Ibrahim Z, et al. 2018 Transcription factor dimerization activates the p300 acetyltransferase. Nature 562 538–544

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pastore A, Gaiti F, Lu S, et al. 2019 Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nat. Commun. 10 1874

    PubMed  PubMed Central  Google Scholar 

  • Pavan Kumar P, Bischof O, Purbey P, et al. 2007 Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat. Cell Biol. 9 45–56

    CAS  PubMed  Google Scholar 

  • Pegg N, Brooks N, Worthington J, et al. 2017 Characterisation of CCS1477: A novel small molecule inhibitor of p300/CBP for the treatment of castration resistant prostate cancer. J. Clin. Oncol. 35 11590–11590

    Google Scholar 

  • Peleg S, Feller C, Ladurner AG and Imhof A 2016 The metabolic impact on histone acetylation and transcription in ageing. Trends Biochem. Sci. 41 700–711

    CAS  PubMed  Google Scholar 

  • Rao SS P, Huntley MH, Durand NC, et al. 2014 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159 1665–1680

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rodriguez H, Rafehi H, Bhave M and El-Osta A 2017 Metabolism and chromatin dynamics in health and disease. Mol. Aspects Med. 54 1–15

    CAS  PubMed  Google Scholar 

  • Romero FA, Murray J, Lai KW, et al. 2017 GNE-781, A highly advanced potent and selective bromodomain inhibitor of cyclic adenosine monophosphate response element binding protein, binding protein (CBP). J. Med. Chem. 60 9162–9183

    CAS  PubMed  Google Scholar 

  • Rubinstein JH and Taybi H 1963 Broad thumbs and toes and facial abnormalities. A possible mental retardation syndrome. Am. J. Dis. Child. 105 588–608

  • Sbardella G, Castellano S, Vicidomini C, et al. 2008 Identification of long chain alkylidenemalonates as novel small molecule modulators of histone acetyltransferases. Bioorg. Med. Chem. Lett. 18 2788–2792

    CAS  PubMed  Google Scholar 

  • Schwartzentruber J, Korshunov A, Liu X, et al. 2012 Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 482 226–231

    CAS  PubMed  Google Scholar 

  • Seligson DB, Horvath S, Shi T, et al. 2005 Global histone modification patterns predict risk of prostate cancer recurrence. Nature 435 1262–1266

    CAS  PubMed  Google Scholar 

  • Selvi BR, Jagadeesan D, Suma BS, et al. 2008 Intrinsically fluorescent carbon nanospheres as a nuclear targeting vector: delivery of membrane-impermeable molecule to modulate gene expression in vivo. Nano Lett. 8 3182–3188

    CAS  PubMed  Google Scholar 

  • Sen N, Hara M, Kornberg MD, et al. 2008 Nitric oxide-induced nuclear GAPDH activates p300/CBP and mediates apoptosis. Nat. Cell Biol. 10 866–873

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shandilya J, Swaminathan V, Gadad SS, et al. 2009 Acetylated NPM1 localizes in the nucleoplasm and regulates transcriptional activation of genes implicated in oral cancer manifestation. Mol. Cell. Biol. 29 5115–5127

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shrimp JH, Sorum AW, Garlick JM, et al. 2016 Characterizing the covalent targets of a small molecule inhibitor of the lysine acetyltransferase P300. ACS Med. Chem. Lett. 7 151–155

    CAS  PubMed  Google Scholar 

  • Sikder S, Kumari S, Mustafi P, et al. 2019 Non-histone human chromatin protein PC4 is critical for genomic integrity and negatively regulates autophagy. FEBS J. 286 4422–4442

    CAS  PubMed  Google Scholar 

  • Steffan JS, Bodai L, Pallos J, et al. 2001 Histone deacetylase inhibitors arrest polyglutamine-dependent neurodegeneration in Drosophila. Nature 413 739–743

    CAS  PubMed  Google Scholar 

  • Strom AR, Emelyanov AV, Mir M, et al. 2017 Phase separation drives heterochromatin domain formation. Nature 547 241–245

    CAS  PubMed  PubMed Central  Google Scholar 

  • Struhl K 1998 Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12 599–606

    CAS  PubMed  Google Scholar 

  • Talbert PB and Henikoff S 2010 Histone variants ancient wrap artists of the epigenome. Nat. Rev. Mol. Cell Biol. 11 264–275

    CAS  PubMed  Google Scholar 

  • Talbert PB and Henikoff S 2017 Histone variants on the move: Substrates for chromatin dynamics. Nat. Rev. Mol. Cell Biol. 18 115–126

    CAS  PubMed  Google Scholar 

  • Thomas B and Beal MF 2011 Molecular insights into Parkinson’s disease. F1000 Med. Rep. 3 7

  • Thompson PR, Wang D, Wang L, et al. 2004 Regulation of the p300 HAT domain via a novel activation loop. Nat. Struct. Mol. Biol. 11 308–315

    CAS  PubMed  Google Scholar 

  • Tie F, Banerjee R, Fu C et.al. 2016 Polycomb inhibits histone acetylation by CBP by binding directly to its catalytic domain. Proc. Natl. Acad. Sci. USA 113 E744–E753

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tzika E, Dreker T and Imhof A 2018 Epigenitics and metabolism in health and disease. Front. Genet. 9 https://doi.org/10.3389/fgene.2018.00361

  • Vecellio M, Spallotta F, Nanni S, et al. 2014 The histone acetylase activator pentadecylidenemalonate 1b rescues proliferation and differentiation in the human cardiac mesenchymal cells of type 2 diabetic patients. Diabetes 63 2132–2147

    CAS  PubMed  Google Scholar 

  • Venkatesh S and Workman JL 2015 Histone exchange, chromatin structure and the regulation of transcription. Nat. Rev. Mol. Cell Biol. 16 178–189

    CAS  PubMed  Google Scholar 

  • Wang S, Su JH, Beliveau BJet al. 2016 Spatial organization of chromatin domains and compartments in single chromosomes. Science 353 598–602

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Wang L and Gong Z 2019 regulation of acetylation in high mobility group protein B1 cytosol translocation. DNA Cell Biol. 38 491–499

    CAS  PubMed  Google Scholar 

  • Wapenaar H and Dekker FJ 2016 Histone acetyltransferases: challenges in targeting bi-substrate enzymes. Clin. Epigenetics 8 59

    PubMed  PubMed Central  Google Scholar 

  • Wei W, Coelho CM, Li X.et al. 2012 p300/CBP-associated factor selectively regulates the extinction of conditioned fear. J. Neurosci. 32 11930–11941

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wright RHG, Fernandez-Fuentes N, Oliva B and Beato M 2016 Insight into the machinery that oils chromatin dynamics. Nucleus 7 532–539

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu G, Broniscer A, McEachron TA, et al. 2012 Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat. Genet. 44 251–253

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu J, Xie N, Wu Z, Zhang Y and Zheng YG 2009 Bisubstrate inhibitors of the MYST HATs Esa1 and Tip60. Bioorg. Med. Chem. 17 1381–1386

    CAS  PubMed  Google Scholar 

  • Yao TP, Oh SP, Fuchs M, et al. 1998 Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300. Cell 93 361–372

    CAS  PubMed  Google Scholar 

  • Yasui D, Miyano M, Cai S, et al. 2002 SATB1 targets chromatin remodelling to regulate genes over long distances. Nature 1181 641–645

    Google Scholar 

Download references

Acknowledgements

We acknowledge JNCASR. TKK is a recipient of Sir J. C. Bose National Fellowship. SS and SK were CSIR and UGC Senior Research Fellows, respectively.

Author information

Authors and Affiliations

  1. Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560 064, India

    Sweta Sikder, Stephanie Kaypee & Tapas K Kundu

Authors
  1. Sweta Sikder
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stephanie Kaypee
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tapas K Kundu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tapas K Kundu.

Additional information

This article is part of the Topical Collection: Chromatin Biology and Epigenetics.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sikder, S., Kaypee, S. & Kundu, T.K. Regulation of epigenetic state by non-histone chromatin proteins and transcription factors: Implications in disease. J Biosci 45, 15 (2020). https://doi.org/10.1007/s12038-019-9974-3

Download citation

  • Published:

  • DOI: https://doi.org/10.1007/s12038-019-9974-3

Keywords

Search

Navigation