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Event: 2152

Key Event Title

A descriptive phrase which defines a discrete biological change that can be measured. More help

Epigenetic modification process

Short name
The KE short name should be a reasonable abbreviation of the KE title and is used in labelling this object throughout the AOP-Wiki. More help
Epigenetic modification process
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Biological Context

Structured terms, selected from a drop-down menu, are used to identify the level of biological organization for each KE. More help
Level of Biological Organization
Cellular

Cell term

The location/biological environment in which the event takes place.The biological context describes the location/biological environment in which the event takes place.  For molecular/cellular events this would include the cellular context (if known), organ context, and species/life stage/sex for which the event is relevant. For tissue/organ events cellular context is not applicable.  For individual/population events, the organ context is not applicable.  Further information on Event Components and Biological Context may be viewed on the attached pdf. More help

Organ term

The location/biological environment in which the event takes place.The biological context describes the location/biological environment in which the event takes place.  For molecular/cellular events this would include the cellular context (if known), organ context, and species/life stage/sex for which the event is relevant. For tissue/organ events cellular context is not applicable.  For individual/population events, the organ context is not applicable.  Further information on Event Components and Biological Context may be viewed on the attached pdf. More help

Key Event Components

The KE, as defined by a set structured ontology terms consisting of a biological process, object, and action with each term originating from one of 14 biological ontologies (Ives, et al., 2017; https://aopwiki.org/info_pages/2/info_linked_pages/7#List). Biological process describes dynamics of the underlying biological system (e.g., receptor signalling).Biological process describes dynamics of the underlying biological system (e.g., receptor signaling).  The biological object is the subject of the perturbation (e.g., a specific biological receptor that is activated or inhibited). Action represents the direction of perturbation of this system (generally increased or decreased; e.g., ‘decreased’ in the case of a receptor that is inhibited to indicate a decrease in the signaling by that receptor).  Note that when editing Event Components, clicking an existing Event Component from the Suggestions menu will autopopulate these fields, along with their source ID and description.  To clear any fields before submitting the event component, use the 'Clear process,' 'Clear object,' or 'Clear action' buttons.  If a desired term does not exist, a new term request may be made via Term Requests.  Event components may not be edited; to edit an event component, remove the existing event component and create a new one using the terms that you wish to add.  Further information on Event Components and Biological Context may be viewed on the attached pdf. More help

Key Event Overview

AOPs Including This Key Event

All of the AOPs that are linked to this KE will automatically be listed in this subsection. This table can be particularly useful for derivation of AOP networks including the KE.Clicking on the name of the AOP will bring you to the individual page for that AOP. More help
AOP Name Role of event in AOP Point of Contact Author Status OECD Status
Activation of uterine estrogen receptor-alfa, endometrial adenocarcinoma KeyEvent Barbara Viviani (send email) Under development: Not open for comment. Do not cite Under Review

Taxonomic Applicability

Latin or common names of a species or broader taxonomic grouping (e.g., class, order, family) that help to define the biological applicability domain of the KE.In many cases, individual species identified in these structured fields will be those for which the strongest evidence used in constructing the AOP was available in relation to this KE. More help
Term Scientific Term Evidence Link
mammals mammals NCBI

Life Stages

An indication of the the relevant life stage(s) for this KE. More help
Life stage Evidence
All life stages

Sex Applicability

An indication of the the relevant sex for this KE. More help
Term Evidence
Female

Key Event Description

A description of the biological state being observed or measured, the biological compartment in which it is measured, and its general role in the biology should be provided. More help

Epigenetic modifications are the processes that involve changes in gene expression without modifying the DNA sequence (Shaw, 2006).

The main processes are DNA methylation, histone modification, alterations of factors involved in nucleosomes assembly and remodeling, and gene regulation by non-coding RNAs (Rodríguez-Paredes & Esteller, 2011).

DNA methylation is the addition of methyl groups in a CpG dinucleotide by DNA methyltransferases (DNMTs), resulting in the regulation of the expression of that gene (Sharma et al., 2010). DNA methylation usually affects the gene promoter, leading to the inhibition of gene transcription (Lee et al., 2020). In mammals, the DNMT family includes five proteins: DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L (DNMT3-like) (Bestor, 2000).

The other important epigenetic process is histone modifications. Histones are proteins involved in DNA packaging into nucleosomes. The modifications on the tails of histones modify the chromatin formation, affecting gene accessibility (Greer & Shi, 2012). In particular, eukaryotic cells have 5 main families of histones, and histone H3 has an important role in the epigenetics (Shechter et al., 2007). Histones can undergo methylation, acetylation or phosphorylation (Ilango et al., 2020). Methylation of histones is carried out by histone methyltransferases and demethylation by histone demethylases. Based on the different lysine that is methylated, there could be the activation or the repression of transcription. For example, if lysine 4, 36 or 79 undergo methylation there will be as consequence the activation of transcription (Kouzarides, 2007), whereas lysines 9 or 27 methylation is linked to transcriptional repression (Raha et al., 2011). Furthermore, also the number of methyl groups is an important factor in the transcriptional effect. Lysine 9 di- and tri-methylation is associated with repression, whereas lysine 4 mono-methylation is associated with transcriptional activation (Lachner et al., 2001; Rosenfeld et al., 2009).

Modification of the acetylation status of histones is under the control of histone acetyltransferases (HATs) that carry out acetylation, which can be reverted by histone deacetylases (HDACs). Histone acetylation instead is usually associated to an increased transcription, due to the removal of positive charges and therefore the relaxion of the chromatin (euchromatin), whereas histone deacetylation is related to transcription repression, due to the formation of heterochromatin (Watson et al., 2014).

There is also emerging evidence of a crosstalk between methylated DNA regions and histone deacetylation (Lee et al., 2020). Indeed, histone deacetylases are part of a multiprotein transcription repression complex and they are associated to Sin3A and methyl-CpG binding proteins (MeCPs). MeCPs are able to bind to CpG islands which are methylated and to interact with Sin3A, that in turns interacts with histone deacetylases, leading to transcriptional repression (Bird & Wolffe, 1999, Cho et al., 2004; Song et al., 2013).

Finally, non-coding RNAs, like lncRNA, sncRNA, miRNA, siRNA and piRNA, are some of the main players in epigenetics (Rajagopal et al., 2020). They are RNA transcripts that will not be translated into proteins, but they modulate gene expression by inhibiting target mRNA transcripts or by favoring their degradation (Esteller, 2011). They are involved in the development of several diseases, including cancer (Esteller, 2011). Between them, lncRNAs are characterized by different actions, such as histone modification and transcriptional regulation (Jiang et al., 2020).

How It Is Measured or Detected

A description of the type(s) of measurements that can be employed to evaluate the KE and the relative level of scientific confidence in those measurements.These can range from citation of specific validated test guidelines, citation of specific methods published in the peer reviewed literature, or outlines of a general protocol or approach (e.g., a protein may be measured by ELISA). Do not provide detailed protocols. More help

Histone methylation

Histone methylation can be detected directly by measuring histone methyltransferase activity/inhibition on specific histones using commercially available kits or indirectly as detection of specific histone methylation levels by western blotting with antibodies raised against specific histone modifications.

DNA methylation (Urdinguio et al, 2009)

Site-specific DNA methylation

Bisulfite genomic sequencing of multiple clones is a DNA-methylation assay that entails initial modification of DNA by sodium bisulphite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent genomic sequencing. This assay constitutes one of the gold standards for DNA-methylation analysis, but is time consuming and expensive.

Methylation-specific PCR uses bisulfite modified DNA and subsequent amplification with primers that are specific for methylated versus unmethylated DNA. This method is fast and cheap, but is not quantitative and requires previous knowledge of the DNA-methylation pattern.

MethyLight is a high-throughput quantitative methylation assay that uses fluorescence-based real-time PCR technology. This technique also uses bisulfite modified DNA.

Pyrosequencing is a DNA-sequencing method in which light is emitted as a result of an enzymatic reaction each time a nucleotide is incorporated into the growing DNA chain.

Methylation-dependent DNA sequence variation, after sodium bisulphite treatment, is treated as a single nucleotide polymorphism.

Genome-wide DNA methylation

DNA-methylation arrays involve the modified DNA being hybridisied after bisulfite treatment to previously designed arrays and each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles printed in the platform. The arrays are imaged using a BeadArray Reader. This technique is reliable and automatised, but is limited to the CpG sites present in the array.

Methylated DNA immunoprecipitation (methyl-DIP) involves immunoprecipitation with anti-5- methylcytosine antibodies followed by hybridisation to genomic microarrays or ultrasequencing, allowing the identification of methyl-CpG rich sequences. This method allows wide coverage of the human genome, but is expensive and requires a caerful bioinformatic analysis.

Global DNA-methylation quantification

High-performance capillary electrophoresis (HPCE) provides reliable measure of the total 5- methylcytosine DNA content starting with small amounts of sample, but requires specialised machinery.

High performance liquid chromatography (HPLC) provides a reliable measure of the total 5- methylcytosine DNA content but requires important amounts of sample and specialised machinery.

In situ DNA-methylation imaging

Immunostaining with anti-5-methylcytosine antibodies requires the use of other markers to map the stained regions and has variability depending on the antibody badge.

miRNAs and LncRNA

A broad spectrum of methods is available in miRNAs lncRNA research, ranging from computational annotation of lncRNA genes to molecular and cellular analyses of the function of individual lncRNA. Description of these methods and methodological details are provided in a series of methods and protocols published in Methods in Molecular Biology by Humana Press (2006 and 2021)

In Vivo measurements of epigenetic biomarkers

Zebrafish has been proposed as a model for gene expression assessment of epigenetic biomarkers (Torres et al. 2021). In this model, morphological abnormalities and epigenetic changes were assessed at 80 hours-post fertilization, including DNA global methylation and gene expression of both DNA and histone epigenetic modifications

Domain of Applicability

A description of the scientific basis for the indicated domains of applicability and the WoE calls (if provided).  More help

Epigenetic modulation is widely involved in developmental processes, differentiation, and reprogramming of stem cells, as well as a variety of human diseases. Dysregulation of epigenetic control is involved in several pathologies (Feinberg, 2007). Large amount of data accumulated in cancer epigenetics where epigenetic alterations contribute to cancer initiation and progression (Jones and Baylin, 2007; Esteller, 2008)

References

List of the literature that was cited for this KE description. More help

Bestor TH. The DNA methyltransferases of mammals. Hum Mol Genet 2000; 9: 2395–402.

Bird, A. P., & Wolffe, A. P. (1999). Methylation-induced repression--belts, braces, and chromatin. Cell, 99(5), 451-454. https://doi.org/10.1016/s0092-8674(00)81532-9

Cho, K. S., Elizondo, L. I., & Boerkoel, C. F. (2004). Advances in chromatin remodeling and human disease. Current opinion in genetics & development, 14(3), 308-315. https://doi.org/10.1016/j.gde.2004.04.015

Esteller M. Epigenetics in cancer. N Engl J Med 2008; 358: 1148–59.

Esteller M. (2011). Non-coding RNAs in human disease. Nature reviews. Genetics, 12(12), 861-874. https://doi.org/10.1038/nrg3074

Feinberg AP. Phenotypic plasticity and the epigenetics of human disease. Nature 2007; 447: 433–40.

Greer, E. L., & Shi, Y. (2012). Histone methylation: a dynamic mark in health, disease and inheritance. Nature reviews. Genetics, 13(5), 343-357. https://doi.org/10.1038/nrg3173

Ilango, S., Paital, B., Jayachandran, P., Padma, P. R., & Nirmaladevi, R. (2020). Epigenetic alterations in cancer. Frontiers in bioscience (Landmark edition), 25(6), 1058-1109. https://doi.org/10.2741/4847

Jiang, W., Xia, J., Xie, S., Zou, R., Pan, S., Wang, Z. W., Assaraf, Y. G., & Zhu, X. (2020). Long non-coding RNAs as a determinant of cancer drug resistance: Towards the overcoming of chemoresistance via modulation of lncRNAs. Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy, 50, 100683. https://doi.org/10.1016/j.drup.2020.100683

Jones PA, Baylin SB. The epigenomics of cancer. Cell 2007; 128: 683–92.

Kouzarides T. (2007). Chromatin modifications and their function. Cell, 128(4), 693-705. https://doi.org/10.1016/j.cell.2007.02.005

Lachner, M., O'Carroll, D., Rea, S., Mechtler, K., & Jenuwein, T. (2001). Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature, 410(6824), 116-120. https://doi.org/10.1038/35065132

Lee, H. T., Oh, S., Ro, D. H., Yoo, H., & Kwon, Y. W. (2020). The Key Role of DNA Methylation and Histone Acetylation in Epigenetics of Atherosclerosis. Journal of lipid and atherosclerosis, 9(3), 419-434. https://doi.org/10.12997/jla.2020.9.3.419

Long Non-Coding RNAs, Methods and Protocols (2021). Eds. Lin Zhang, Xiaowen Hu, Humana New York, NY,  https://doi.org/10.1007/978-1-0716-1697-0

MicroRNA Protocols. Methods and Protocols (2006).  Ed. Shao-Yao Ying, Humana New York, NY, doi.org/10.1385/1597451231

Raha, P., Thomas, S., & Munster, P. N. (2011). Epigenetic modulation: a novel therapeutic target for overcoming hormonal therapy resistance. Epigenomics, 3(4), 451-470. https://doi.org/10.2217/epi.11.72

Rajagopal, T., Talluri, S., Akshaya, R. L., & Dunna, N. R. (2020). HOTAIR LncRNA: A novel oncogenic propellant in human cancer. Clinica chimica acta; international journal of clinical chemistry, 503, 1-18. https://doi.org/10.1016/j.cca.2019.12.028

Rodríguez-Paredes, M., & Esteller, M. (2011). Cancer epigenetics reaches mainstream oncology. Nature medicine, 17(3), 330-339. https://doi.org/10.1038/nm.2305

Rosenfeld, J. A., Wang, Z., Schones, D. E., Zhao, K., DeSalle, R., & Zhang, M. Q. (2009). Determination of enriched histone modifications in non-genic portions of the human genome. BMC genomics, 10, 143. https://doi.org/10.1186/1471-2164-10-143

Sharma, S., Kelly, T. K., & Jones, P. A. (2010). Epigenetics in cancer. Carcinogenesis, 31(1), 27-36. https://doi.org/10.1093/carcin/bgp220

Shaw R. (2006). The epigenetics of oral cancer. International journal of oral and maxillofacial surgery, 35(2), 101-108. https://doi.org/10.1016/j.ijom.2005.06.014

Shechter, D., Dormann, H. L., Allis, C. D., & Hake, S. B. (2007). Extraction, purification and analysis of histones. Nature protocols, 2(6), 1445-1457. https://doi.org/10.1038/nprot.2007.202

Song, C. X., Szulwach, K. E., Dai, Q., Fu, Y., Mao, S. Q., Lin, L., Street, C., Li, Y., Poidevin, M., Wu, H., Gao, J., Liu, P., Li, L., Xu, G. L., Jin, P., & He, C. (2013). Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell, 153(3), 678-691. https://doi.org/10.1016/j.cell.2013.04.001

Torres T, Ruivo R, Santos MM. Epigenetic biomarkers as tools for chemical hazard assessment: Gene expression profiling using the model Danio rerio. Sci Total Environ. 2021 Jun 15;773:144830. doi: 10.1016/j.scitotenv.2020.144830. Epub 2021 Jan 29. PMID: 33592472.

Urdinguio RG, Sanchez-Mut JV, Esteller M. Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies. Lancet Neurol 2009; 8: 1056–72

Watson, J.D., Baker, T.A., Gann, A., Levine, M., Losik, R. (2014). Molecular biology of the gene (Seventh ed.). Boston: Pearson/CSH Press. ISBN 978-0-321-76243-6.