Epigenetics and Noncoding RNA – Principles and Clinical Impact

Abstract

Genetics studies the inheritance of genetic information encoded by the base pair sequence and its variants. Sequence variants can have severe consequences as seen in genetically inherited diseases (e. g. osteogenesis Imperfecta, hypophosphatasia). On the other hand, epigenetics deals with inherited and dynamically reversible modifications of chromatin without changing the base pair sequence, resulting in a change in phenotype without a change in genotype. These modifications primarily exert their effects by influencing gene expression. Initially, the definition of epigenetics exclusively comprised inherited changes that persist across several generations without changes in the DNA sequence. This definition has been extended to include also dynamic and partially reversible changes that occur more short-term. These gene modulatory effects introduce new levels of complexity and are crucial determinants of cell fate and organismal development. With its length of approximately two meters, human DNA has to be compacted to fit into the nuclei and fulfill its functions. DNA is wrapped around histone octamers into so-called nucleosomes. DNA, histones, and other DNA-associated proteins together form what is called chromatin. DNA packaging is achieved by variable degrees of chromatin condensation depending on cell type and context. Epigenetic transcriptional regulation modifies the affinity and accessibility of cis-regulatory elements (CREs) for transcription factors and the basic transcriptional machinery and governs interaction between CREs. CREs include promoters, enhancers, silencers, and insulators and are potent modulators of gene expression impacting core cell biological processes such as proliferation and differentiation. Chromatin looping and remodeling by differential covalent modifications of DNA (e. g., methylation or hydroxylation) and histone tails (e. g., acetylation or methylation) elicit fundamental changes in CRE accessibility, thus impacting gene expression. Chromatin looping depends on a specialized machinery including cohesins. Chromatin modifications are mediated by specific enzymes like DNA methylases (DNMTs), histone-modifying enzymes, like histone methyl- and acetyltransferases (KMTs, HATs/KATs), and histone demethylases and deacetylases (KDMs, HDACs). It becomes increasingly evident that epigenetic (dys)regulation plays a decisive role in physiology and pathophysiology, impacting many age-related diseases like cancer and degenerative pathologies (e. g., osteoporosis, Alzheimer’s, or Parkinson’s) in a significant fashion. Recently, small-molecule inhibitors of chromatin-modifying enzymes (e. g., vorinostat) have been identified and successfully introduced in therapy. Significant progress in high-throughput sequencing technologies and big data analysis has broadened our understanding of noncoding (nc) RNAs and DNA sequence regions in (post-)transcriptional regulation and disease development. Among ncRNAs that play vital roles in gene expression are micro- (miRs) and long noncoding RNAs (lncRNAs; e. g., XIST or HOTAIR). By interacting with the coding genome, these RNAs modulate important genetic programs. Interfering RNAs can, for example, enhance the post-transcriptional degradation of transcripts, altering their translation, or assist in the recruitment of chromatin-modifying enzymes to regulate transcription. They can also be packaged into extracellular vesicles as cargo and thus deliver critical information to the microenvironment or even systemically to distant tissues. Therefore, ncRNAs represent a novel playground for therapeutical investigations and supplement epigenetic mechanisms of gene regulation while being subject to epigenetic regulation themselves. Last but not least, dysregulated ncRNAs can also propagate disease. Until recently, the detection of epigenetic phenomena necessitated invasive diagnostic interventions. However, with the arrival of so-called “liquid biopsies” an analysis of circulating cell-free DNA fragments (cfDNA) and RNAs as well as vesicle-packed RNAs through minimal invasively drawn blood samples can be obtained. Such “fragmentomics” and RNAomics approaches on peripheral blood will ultimately serve as diagnostic tools for personalized clinical interventions.

Zusammenfassung

Die Genetik befasst sich mit der Erforschung der Vererbung und mit Varianten der Basenpaarfolge innerhalb unseres Genoms. Sequenzvarianten können schwerwiegende Folgen für den Organismus haben, wie man sie bei genetisch vererbten Krankheiten sieht wie z. B. Osteogenesis Imperfecta-oder Hypophosphatasie. Die Epigenetik hingegen befasst sich mit der Erforschung von teilweise vererbten und dynamischen Modifikationen des Chromatins, die über Veränderungen der Genexpression ohne eine Veränderung der zugrundeliegenden DNA-Sequenz zu einer Veränderung des Phänotyps führen können. Ursprünglich umfasste die Definition der Epigenetik ausschließlich vererbte Veränderungen, die über mehrere Generationen bestehen bleiben. Diese Definition wurde erweitert und umfasst nun auch dynamische und teilweise reversible Veränderungen, die eher kurzfristig auftreten. Was auf den ersten Blick wie eine Einführung von Unschärfe erscheint, führt neue Ebenen der Komplexität epigenetischer Phänomene ein und ähnelt viel mehr der Dynamik von Veränderungen in einem individuellen Leben eines Organismus. Die menschliche DNA, mit ihrer Länge von etwa 2 m, ist je nach Zelltyp und Zellkontext variabel verpackt. Die DNA-Verpackung wird erreicht, indem die DNA periodisch um Histon-Oktamere zu sogenannten Nukleosomen (147 bp/Nukleosom) gewickelt wird. DNA, Histone und andere DNA-assoziierte Proteine bilden zusammen das so genannte Chromatin. Epigenetische Regulation modifiziert die Affinität und Zugänglichkeit von cis-regulatorischen Elementen (CREs) für Transkriptionsfaktoren und die grundlegende Transkriptionsmaschinerie. CREs umfassen Promotoren, Enhancer, Silencer und Insulatoren und sind mächtige Modulatoren der Genexpression, die zentrale zellbiologische Prozesse wie Proliferation und Differenzierung beeinflussen. Chromatin-Remodelierung, differentielle chemische Modifikationen der DNA (z. B. Methylierung oder Hydroxylierung) und der Histonschwänze (z. B. Acetylierung oder Methylierung) bewirken fundamentale Veränderungen in der Zugänglichkeit von CREs und beeinflussen so die Chromatinstruktur und die Genexpression. Diese Modifikationen werden durch spezifische Enzyme wie DNA-Methyltransferasen (DNMTs), histonmodifizierende Enzyme wie Histon-Methyl- und -Acetyltransferasen (KMTs, HATs/KATs) und Histon-Deacetylasen und -Demethylasen (KDMs, HDACs) katalysiert. Es wird immer deutlicher, dass epigenetische (Dys-)Regulation eine wichtige Rolle in der Physiologie und Pathophysiologie spielt und die Entwicklung von Krankheiten in erheblichem Maße beeinflusst, darunter viele altersbedingte Krankheiten wie Krebs und degenerative Pathologien (z. B. Osteoporose, Alzheimer oder Parkinson). In jüngster Zeit wurden niedermolekulare Inhibitoren von chromatinmodifizierenden Enzymen (z. B. Voronistat) identifiziert und erfolgreich zur Behandlung von Krankheiten eingesetzt. Große Fortschritte in der RNA-Sequenzierungstechnologie mit hohem Durchsatz und der Big-Data-Analyse haben unser Verständnis von nicht-kodierender RNA und DNA-Sequenzregionen in der Transkriptionsregulation und Krankheitsentwicklung erweitert und vertieft. Zu den nichtcodierenden RNAs, die eine wichtige Rolle bei der Genexpression spielen, gehören micro- (miRs) und lange nichtcodierende RNAs (lncRNAs; z. B. XIST oder HOTAIR). Durch Interferenz mit dem kodierenden Transkriptom modulieren solche RNAs wichtige genetische Programme. Interferierende RNAs können z. B. den Abbau von kodierenden Transkripten verstärken und so deren Translation verändern oder bei der Rekrutierung von chromatinmodifizierenden Enzymen zur Regulierung der Transkription helfen. Sie können auch als Fracht in extrazelluläre Vesikel verpackt werden und so wichtige Informationen an die Mikroumgebung oder sogar systemisch an entfernte Gewebe liefern. In diesem Sinne stellt die RNA-Welt ein neues Feld möglicher therapeutischer Interventionen dar. Nichtkodierende RNAs ergänzen somit epigenetische Mechanismen der Genregulation, auch wenn sie nicht primär als epigenetische Mechanismen angesehen werden. Sie fügen der Genexpression ohne Mutation eine weitere Komplexitätsebene hinzu und unterliegen selbst epigenetischen Veränderungen. Nicht zuletzt können dysregulierte nichtkodierende RNAs auch Krankheiten fördern. Bis vor kurzem erforderte der Nachweis von epigenetischen Phänomenen invasive diagnostische Eingriffe. Mit dem Aufkommen sogenannter „Liquid Biopsies“ ist jedoch eine Analyse zirkulierender zellfreier DNA-Fragmente (cfDNA) und RNAs sowie vesikulärer RNAs durch minimal-invasiv entnommene Blutproben möglich. Solche „Fragmentomics“- und RNAomics-Ansätze aus peripherem Blut werden in Zukunft immer mehr verfeinert und dienen letztlich als diagnostisches Werkzeug für personalisierte klinische Interventionen.

Key words

Epigenetics - noncoding RNAs - Bone biology

Schlüsselwörter

Epigenetik - nichtkodierende RNAs - Knochenbiologie

Publication History

Received: 10 June 2021

Accepted: 11 June 2021

Article published online:
17 September 2021

• References

• 1 Lander ES, Linton LM, Birren B. et al. Initial sequencing and analysis of the human genome. Nature 2001; 409: 860-921. DOI: 10.1038/35057062.
• 2 Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489: 57-74. DOI: 10.1038/nature11247.
• 3 Neph S, Vierstra J, Stergachis AB. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012; 489: 83-90. DOI: 10.1038/nature11212.
• 4 Richard Boland C. Non-coding RNA: It’s Not Junk. Dig Dis Sci 2017; 62: 1107-1109. DOI: 10.1007/s10620-017-4506-1.
• 5 Thurman RE, Rynes E, Humbert R. et al. The accessible chromatin landscape of the human genome. Nature 2012; 489: 75-82. DOI: 10.1038/nature11232.
• 6 Gregorova J, Vychytilova-Faltejskova P, Sevcikova S. Epigenetic Regulation of MicroRNA Clusters and Families during Tumor Development. Cancers (Basel) 2021; 13: 1333. DOI: 10.3390/cancers13061333.
• 7 Boivin V, Deschamps-Francoeur G, Couture S. et al. Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes. RNA 2018; 24: 950-965. DOI: 10.1261/rna.064493.117.
• 8 Boivin V, Deschamps-Francoeur G, Scott MS. Protein coding genes as hosts for noncoding RNA expression. Semin Cell Dev Biol 2018; 75: 3-12. DOI: 10.1016/j.semcdb.2017.08.016.
• 9 Lo YMD, Han DSC, Jiang P. et al. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science 2021; 372. DOI: 10.1126/science.aaw3616.
• 10 Cramer P. Organization and regulation of gene transcription. Nature 2019; 573: 45-54. DOI: 10.1038/s41586-019-1517-4.
• 11 Kyrchanova O, Georgiev P. Mechanisms of Enhancer-Promoter Interactions in Higher Eukaryotes. Int J Mol Sci 2021; 22: 671. DOI: 10.3390/ijms22020671.
• 12 Davidson IF, Bauer B, Goetz D. et al. DNA loop extrusion by human cohesin. Science 2019; 366: 1338-1345 DOI: 10.1126/science.aaz3418.
• 13 de Wit E, Vos ES, Holwerda SJ. et al. CTCF Binding Polarity Determines Chromatin Looping. Mol Cell 2015; 60: 676-684. DOI: 10.1016/j.molcel.2015.09.023.
• 14 Kempfer R, Pombo A. Methods for mapping 3D chromosome architecture. Nat Rev Genet 2020; 21: 207-226 DOI: 10.1038/s41576-019-0195-2.
• 15 McArthur E, Capra JA. Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. Am J Hum Genet 2021; 108: 269-283. DOI: 10.1016/j.ajhg.2021.01.001.
• 16 Spielmann M, Lupianez DG, Mundlos S. Structural variation in the 3D genome. Nat Rev Genet 2018; 19: 453-467. DOI: 10.1038/s41576-018-0007-0.
• 17 Takayama N, Murison A, Takayanagi SI. et al. The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization. Cell Stem Cell 2021; 28: 488-501, e410. DOI: 10.1016/j.stem.2020.11.001.
• 18 Park SY, Kim JS. A short guide to histone deacetylases including recent progress on class II enzymes. Exp Mol Med 2020; 52: 204-212. DOI: 10.1038/s12276-020-0382-4.
• 19 Olins DE, Olins AL. Chromatin history: our view from the bridge. Nat Rev Mol Cell Biol 2003; 4: 809-814. DOI: 10.1038/nrm1225.
• 20 Rando OJ, Ahmad K. Rules and regulation in the primary structure of chromatin. Curr Opin Cell Biol 2007; 19: 250-256 DOI: 10.1016/j.ceb.2007.04.006.
• 21 Deichmann U. Chromatin: Its history, current research, and the seminal researchers and their philosophy. Perspect Biol Med 2015; 58: 143-164 DOI: 10.1353/pbm.2015.0024.
• 22 Duc C, Thiriet C. Replication-Coupled Chromatin Remodeling: An Overview of Disassembly and Assembly of Chromatin during Replication. Int J Mol Sci 2021; 22: 1113. DOI: 10.3390/ijms22031113.
• 23 Berger SL, Kouzarides T, Shiekhattar R. et al. An operational definition of epigenetics. Genes Dev 2009; 23: 781-783. DOI: 10.1101/gad.1787609.
• 24 Bird A. Perceptions of epigenetics. Nature 2007; 447: 396-398 DOI: 10.1038/nature05913.
• 25 Zhao Y, Chen Y, Jin M. et al. The crosstalk between m(6)A RNA methylation and other epigenetic regulators: a novel perspective in epigenetic remodeling. Theranostics 2021; 11: 4549-4566 DOI: 10.7150/thno.54967.
• 26 Khodadadi E, Fahmideh L, Khodadadi E. et al. Current Advances in DNA Methylation Analysis Methods. Biomed Res Int 2021; 2021: 8827516. DOI: 10.1155/2021/8827516.
• 27 de Lima Camillo LP, Quinlan RBA. A ride through the epigenetic landscape: aging reversal by reprogramming. Geroscience. 2021 DOI: 10.1007/s11357-021-00358-6
• 28 Pouikli A, Tessarz P. Epigenetic alterations in stem cell ageing-a promising target for age-reversing interventions? Brief Funct Genomics. 2021 DOI: 10.1093/bfgp/elab010
• 29 van Mierlo G, Vermeulen M. Chromatin proteomics to study epigenetics – challenges and opportunities. Mol Cell Proteomics. 2021 20. 100056 DOI: 10.1074/mcp.R120.002208
• 30 Feng S, Jacobsen SE, Reik W. Epigenetic reprogramming in plant and animal development. Science 2010; 330: 622-627. DOI: 10.1126/science.1190614.
• 31 Sun L, Fu X, Ma G. et al. Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate Transitions. Front Cell Dev Biol 2021; 9: 637309. DOI: 10.3389/fcell.2021.637309.
• 32 Greenberg MVC. Get Out and Stay Out: New Insights Into DNA Methylation Reprogramming in Mammals. Front Cell Dev Biol 2020; 8: 629068. DOI: 10.3389/fcell.2020.629068.
• 33 Kribelbauer JF, Loker RE, Feng S. et al. Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins. Mol Cell 2020; 78: 152-167 e111. DOI: 10.1016/j.molcel.2020.01.027.
• 34 Singer BD. A Practical Guide to the Measurement and Analysis of DNA Methylation. Am J Respir Cell Mol Biol 2019; 61: 417-428 DOI: 10.1165/rcmb.2019-0150TR.
• 35 Heyn H, Li N, Ferreira HJ. et al. Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A 2012; 109: 10522-10527. DOI: 10.1073/pnas.1120658109.
• 36 Horvath S, Raj K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat Rev Genet 2018; 19: 371-384. DOI: 10.1038/s41576-018-0004-3.
• 37 Gorgoulis V, Adams PD, Alimonti A. et al. Cellular Senescence: Defining a Path Forward. Cell 2019; 179: 813-827. DOI: 10.1016/j.cell.2019.10.005.
• 38 Cruickshanks HA, McBryan T, Nelson DM. et al. Senescent cells harbour features of the cancer epigenome. Nat Cell Biol 2013; 15: 1495-1506. DOI: 10.1038/ncb2879.
• 39 Beck D, Ben Maamar M, Skinner MK. Integration of sperm ncRNA-directed DNA methylation and DNA methylation-directed histone retention in epigenetic transgenerational inheritance. Epigenetics Chromatin 2021; 14: 6. DOI: 10.1186/s13072-020-00378-0.
• 40 Gomathi K, Akshaya N, Srinaath N. et al. Histone acetyl transferases and their epigenetic impact on bone remodeling. Int J Biol Macromol 2021; 170: 326-335. DOI: 10.1016/j.ijbiomac.2020.12.173.
• 41 Ali I, Conrad RJ, Verdin E. et al. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118: 1216-1252. DOI: 10.1021/acs.chemrev.7b00181.
• 42 Xia C, Tao Y, Li M. et al. Protein acetylation and deacetylation: An important regulatory modification in gene transcription (Review). Exp Ther Med 2020; 20: 2923-2940. DOI: 10.3892/etm.2020.9073.
• 43 Wiesel-Motiuk N, Assaraf YG. The key roles of the lysine acetyltransferases KAT6A and KAT6B in physiology and pathology. Drug Resist Updat 2020; 53: 100729 DOI: 10.1016/j.drup.2020.100729.
• 44 Huang M, Huang J, Zheng Y. et al. Histone acetyltransferase inhibitors: An overview in synthesis, structure-activity relationship and molecular mechanism. Eur J Med Chem 2019; 178: 259-286 DOI: 10.1016/j.ejmech.2019.05.078.
• 45 Peng X, Liao G, Sun P. et al. An Overview of HDAC Inhibitors and their Synthetic Routes. Curr Top Med Chem 2019; 19: 1005-1040. DOI: 10.2174/1568026619666190227221507.
• 46 Yao Z, Chen Y, Cao W. et al. Chromatin-modifying drugs and metabolites in cell fate control. Cell Prolif 2020; 53: e12898. DOI: 10.1111/cpr.12898.
• 47 Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res 2011; 21: 381-395. DOI: 10.1038/cr.2011.22.
• 48 Li K, Wang Z. Histone crotonylation-centric gene regulation. Epigenetics Chromatin 2021; 14: 10. DOI: 10.1186/s13072-021-00385-9.
• 49 Sikder S, Kaypee S, Kundu TK. Regulation of epigenetic state by non-histone chromatin proteins and transcription factors: Implications in disease. J Biosci 2020; 45: 15.
• 50 Magana-Acosta M, Valadez-Graham V. Chromatin Remodelers in the 3D Nuclear Compartment. Front Genet 2020; 11: 600615. DOI: 10.3389/fgene.2020.600615.
• 51 Kumar S, Gonzalez EA, Rameshwar P. et al. Non-Coding RNAs as Mediators of Epigenetic Changes in Malignancies. Cancers (Basel) 2020; 12: 3657. DOI: 10.3390/cancers12123657.
• 52 Schoenfelder S, Fraser P. Long-range enhancer-promoter contacts in gene expression control. Nat Rev Genet 2019; 20: 437-455. DOI: 10.1038/s41576-019-0128-0.
• 53 van Steensel B, Furlong EEM. The role of transcription in shaping the spatial organization of the genome. Nat Rev Mol Cell Biol 2019; 20: 327-337. DOI: 10.1038/s41580-019-0114-6.
• 54 Rowley MJ, Corces VG. Organizational principles of 3D genome architecture. Nat Rev Genet 2018; 19: 789-800. DOI: 10.1038/s41576-018-0060-8.
• 55 Belokopytova P, Fishman V. Predicting Genome Architecture: Challenges and Solutions. Front Genet 2020; 11: 617202 DOI: 10.3389/fgene.2020.617202.
• 56 Nurminen V, Seuter S, Carlberg C. Primary Vitamin D Target Genes of Human Monocytes. Front Physiol 2019; 10: 194. DOI: 10.3389/fphys.2019.00194.
• 57 Duchaine TF, Fabian MR. Mechanistic Insights into MicroRNA-Mediated Gene Silencing. Cold Spring Harb Perspect Biol 2019; 11: a032771. DOI: 10.1101/cshperspect.a032771.
• 58 Engreitz JM, Ollikainen N, Guttman M. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol 2016; 17: 756-770. DOI: 10.1038/nrm.2016.126.
• 59 Kim DH, Saetrom P, Snove O. et al. MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci U S A 2008; 105: 16230-16235. DOI: 10.1073/pnas.0808830105.
• 60 Hensley AP, McAlinden A. The role of microRNAs in bone development. Bone 2021; 143: 115760. DOI: 10.1016/j.bone.2020.115760.
• 61 Muraca M, Cappariello A. The Role of Extracellular Vesicles (EVs) in the Epigenetic Regulation of Bone Metabolism and Osteoporosis. Int J Mol Sci 2020; 21: 8682 DOI: 10.3390/ijms21228682.
• 62 Hammond SM. An overview of microRNAs. Adv Drug Deliv Rev 2015; 87: 3-14. DOI: 10.1016/j.addr.2015.05.001.
• 63 Saul D, Kosinsky RL. Epigenetics of Aging and Aging-Associated Diseases. Int J Mol Sci 2021; 22: 401 DOI: 10.3390/ijms22010401.
• 64 Kinser HE, Pincus Z. MicroRNAs as modulators of longevity and the aging process. Hum Genet 2020; 139: 291-308. DOI: 10.1007/s00439-019-02046-0.
• 65 Chuang JC, Jones PA. Epigenetics and microRNAs. Pediatr Res 2007; 61: 24R-29R. DOI: 10.1203/pdr.0b013e3180457684.
• 66 Amiri A, Barreto GE, Sathyapalan T. et al. siRNA Therapeutics: Future Promise for Neurodegenerative Diseases. Curr Neuropharmacol. 2021 DOI: 10.2174/1570159X19666210402104054
• 67 Fitzgerald K, White S, Borodovsky A. et al. A Highly Durable RNAi Therapeutic Inhibitor of PCSK9. N Engl J Med 2017; 376: 41-51. DOI: 10.1056/NEJMoa1609243.
• 68 Zhang MM, Bahal R, Rasmussen TP. et al. The growth of siRNA-based therapeutics: Updated clinical studies. Biochem Pharmacol. 2021 DOI: 10.1016/j.bcp.2021.114432
• 69 Hu B, Zhong L, Weng Y. et al. Therapeutic siRNA: state of the art. Signal Transduct Target Ther 2020; 5: 101. DOI: 10.1038/s41392-020-0207-x.
• 70 Zhou Z, Hossain MS, Liu D. Involvement of the long noncoding RNA H19 in osteogenic differentiation and bone regeneration. Stem Cell Res Ther 2021; 12: 74 DOI: 10.1186/s13287-021-02149-4.
• 71 Song W, Xie J, Li J. et al. The Emerging Roles of Long Noncoding RNAs in Bone Homeostasis and Their Potential Application in Bone-Related Diseases. DNA Cell Biol 2020; 39: 926-937 DOI: 10.1089/dna.2020.5391.
• 72 Yu L, Xia K, Cen X. et al. DNA methylation of noncoding RNAs: new insights into osteogenesis and common bone diseases. Stem Cell Res Ther 2020; 11: 109. DOI: 10.1186/s13287-020-01625-7.