Editing DNA methylation (section)

==DNA methylation marks==
[[DNA methylation marks]] – genomic regions with specific methylation patterns in a specific biological state such as tissue, cell type, individual – are regarded as possible functional regions involved in gene transcriptional regulation. Although various human cell types may have the same genome, these cells have different methylomes. The systematic identification and characterization of methylation marks across cell types are crucial to understanding the complex regulatory network for cell fate determination. Hongbo Liu et al. proposed an entropy-based framework termed SMART to integrate the whole genome bisulfite sequencing methylomes across 42 human tissues/cells and identified 757,887 genome segments.<ref>{{cite journal | vauthors = Liu H, Liu X, Zhang S, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J, Wu Q, Zhang Y | display-authors = 6 | title = Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes | journal = Nucleic Acids Research | volume = 44 | issue = 1 | pages = 75–94 | date = January 2016 | pmid = 26635396 | pmc = 4705665 | doi = 10.1093/nar/gkv1332 }}</ref> Nearly 75% of the segments showed uniform methylation across all cell types. From the remaining 25% of the segments, they identified cell type-specific hypo/hypermethylation marks that were specifically hypo/hypermethylated in a minority of cell types using a statistical approach and presented an atlas of the human methylation marks. Further analysis revealed that the cell type-specific hypomethylation marks were enriched through [[H3K27ac]] and transcription factor binding sites in a cell type-specific manner. In particular, they observed that the cell type-specific hypomethylation marks are associated with the cell type-specific super-enhancers that drive the expression of cell identity genes. This framework provides a complementary, functional annotation of the human genome and helps to elucidate the critical features and functions of cell type-specific hypomethylation.{{cn|date=March 2024}}

The entropy-based Specific Methylation Analysis and Report Tool, termed "SMART", which focuses on integrating a large number of DNA methylomes for the de novo identification of cell type-specific methylation marks. The latest version of SMART is focused on three main functions including de novo identification of differentially methylated regions (DMRs) by genome segmentation, identification of DMRs from predefined regions of interest, and identification of differentially methylated CpG sites.<ref>{{cite web|url=http://fame.edbc.org/smart/|title= SMART 2: A Comprehensive Analysis Tool for Bisulfite Sequencing Data |website= fame.edbc.org | vauthors = Hongbo L |date = 2016}}</ref>

=== In identification and detection of body fluids ===
DNA methylation allows for several tissues to be analyzed in one assay as well as for small amounts of body fluid to be identified with the use of extracted DNA. Usually, the two approaches of DNA methylation are either methylated-sensitive restriction enzymes or treatment with sodium bisulphite.<ref>{{cite journal | vauthors = Sijen T | title = Molecular approaches for forensic cell type identification: On mRNA, miRNA, DNA methylation and microbial markers | journal = Forensic Science International. Genetics | volume = 18 | pages = 21–32 | date = September 2015 | pmid = 25488609 | doi = 10.1016/j.fsigen.2014.11.015 }}</ref> Methylated sensitive restriction enzymes work by cleaving specific CpG, cytosine and guanine separated by only one phosphate group, recognition sites when the CpG is methylated. In contrast, unmethylated cytosines are transformed to uracil and in the process, methylated cytosines remain methylated. In particular, methylation profiles can provide insight on when or how body fluids were left at crime scenes, identify the kind of body fluid, and approximate age, gender, and phenotypic characteristics of perpetrators.<ref name=":4">{{cite journal | vauthors = Kader F, Ghai M | title = DNA methylation and application in forensic sciences | journal = Forensic Science International | volume = 249 | pages = 255–265 | date = April 2015 | pmid = 25732744 | doi = 10.1016/j.forsciint.2015.01.037 }}</ref> Research indicates various markers that can be used for DNA methylation. Deciding which marker to use for an assay is one of the first steps of the identification of body fluids. In general, markers are selected by examining prior research conducted. Identification markers that are chosen should give a positive result for one type of cell. One portion of the chromosome that is an area of focus when conducting DNA methylation are tissue-specific differentially methylated regions, T-DMRs. The degree of methylation for the T-DMRs ranges depending on the body fluid.<ref name=":4" /> A research team developed a marker system that is two-fold. The first marker is methylated only in the target fluid while the second is methylated in the rest of the fluids.<ref name=":3" /> For instance, if venous blood marker A is un-methylated and venous blood marker B is methylated in a fluid, it indicates the presence of only venous blood. In contrast, if venous blood marker A is methylated and venous blood marker B is un-methylated in some fluid, then that indicates venous blood is in a mixture of fluids. Some examples for DNA methylation markers are Mens1(menstrual blood), Spei1(saliva), and Sperm2(seminal fluid).

DNA methylation provides a relatively good means of sensitivity when identifying and detecting body fluids. In one study, only ten nanograms of a sample was necessary to ascertain successful results.<ref>{{cite journal | vauthors = Silva DS, Antunes J, Balamurugan K, Duncan G, Alho CS, McCord B | title = Developmental validation studies of epigenetic DNA methylation markers for the detection of blood, semen and saliva samples | journal = Forensic Science International. Genetics | volume = 23 | pages = 55–63 | date = July 2016 | pmid = 27010659 | doi = 10.1016/j.fsigen.2016.01.017 | hdl-access = free | hdl = 10923/23633 | s2cid = 7438775 }}</ref> DNA methylation provides a good discernment of mixed samples since it involves markers that give "on or off" signals. DNA methylation is not impervious to external conditions. Even under degraded conditions using the DNA methylation techniques, the markers are stable enough that there are still noticeable differences between degraded samples and control samples. Specifically, in one study, it was found that there were not any noticeable changes in methylation patterns over an extensive period of time.<ref name=":4" />

The detection of DNA methylation in cell-free DNA and other body fluids has recently become one of the main approaches to [[Liquid biopsy]].<ref>{{cite journal | vauthors = Dor Y, Cedar H | title = Principles of DNA methylation and their implications for biology and medicine | journal = Lancet | volume = 392 | issue = 10149 | pages = 777–786 | date = September 2018 | pmid = 30100054 | doi = 10.1016/S0140-6736(18)31268-6 | s2cid = 51965986 }}</ref> In particular, the identification of tissue-specific and disease-specific patterns allows for non-invasive detection and monitoring of diseases such as cancer.<ref>{{cite journal | vauthors = Liu MC, Oxnard GR, Klein EA, Swanton C, Seiden MV | title = Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA | journal = Annals of Oncology | volume = 31 | issue = 6 | pages = 745–759 | date = June 2020 | pmid = 33506766 | pmc = 8274402 | doi = 10.1016/j.annonc.2020.02.011 }}</ref> If compared to strictly genomic approaches to liquid biopsy, DNA methylation profiling offers a larger number of differentially methylated CpG sites and differentially methylated regions (DMRSs), potentially enhancing its sensitivity. Signal deconvolution algorithms based on DNA methylation have been successfully applied to cell-free DNA and can nominate the tissue of origin of cancers of unknown primary, allograft rejection, and resistance to hormone therapy.<ref>{{cite journal | vauthors = Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, Samet Y, Maoz M, Druid H, Arner P, Fu KY, Kiss E, Spalding KL, Landesberg G, Zick A, Grinshpun A, Shapiro AM, Grompe M, Wittenberg AD, Glaser B, Shemer R, Kaplan T, Dor Y | display-authors = 6 | title = Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease | journal = Nature Communications | volume = 9 | issue = 1 | pages = 5068 | date = November 2018 | pmid = 30498206 | pmc = 6265251 | doi = 10.1038/s41467-018-07466-6 | bibcode = 2018NatCo...9.5068M }}</ref>