Editing Epigenetics (section)

====Repair of oxidative DNA damage can alter epigenetic markers====
In the steady state (with endogenous damages occurring and being repaired), there are about 2,400 oxidatively damaged guanines that form [[8-oxo-2'-deoxyguanosine]] (8-OHdG) in the average mammalian cell DNA.<ref name="pmid21163908">{{cite journal |vauthors=Swenberg JA, Lu K, Moeller BC, Gao L, Upton PB, Nakamura J, Starr TB |title=Endogenous versus exogenous DNA adducts: their role in carcinogenesis, epidemiology, and risk assessment |journal=Toxicol Sci |volume=120 |issue= Suppl 1|pages=S130–45 |date=March 2011 |pmid=21163908 |pmc=3043087 |doi=10.1093/toxsci/kfq371 |url=}}</ref> 8-OHdG constitutes about 5% of the oxidative damages commonly present in DNA.<ref name=Hamilton>{{cite journal |vauthors=Hamilton ML, Guo Z, Fuller CD, Van Remmen H, Ward WF, Austad SN, Troyer DA, Thompson I, Richardson A |title=A reliable assessment of 8-oxo-2-deoxyguanosine levels in nuclear and mitochondrial DNA using the sodium iodide method to isolate DNA |journal=Nucleic Acids Res |volume=29 |issue=10 |pages=2117–26 |date=May 2001 |pmid=11353081 |pmc=55450 |doi=10.1093/nar/29.10.2117 |url=}}</ref> The oxidized guanines do not occur randomly among all guanines in DNA. There is a sequence preference for the guanine at a [[DNA methylation|methylated]] [[CpG site]] (a cytosine followed by guanine along its [[Directionality (molecular biology)|5' → 3' direction]] and where the cytosine is methylated (5-mCpG)).<ref name="pmid24571128">{{cite journal |vauthors=Ming X, Matter B, Song M, Veliath E, Shanley R, Jones R, Tretyakova N |title=Mapping structurally defined guanine oxidation products along DNA duplexes: influence of local sequence context and endogenous cytosine methylation |journal=J Am Chem Soc |volume=136 |issue=11 |pages=4223–35 |date=March 2014 |pmid=24571128 |pmc=3985951 |doi=10.1021/ja411636j |bibcode=2014JAChS.136.4223M |url=}}</ref> A 5-mCpG site has the lowest ionization potential for guanine oxidation.{{citation needed|date=March 2023}}

[[File:Initiation of DNA demethylation at a CpG site.svg|thumb|Initiation of [[DNA demethylation]] at a [[CpG site]]. In adult somatic cells DNA methylation typically occurs in the context of CpG dinucleotides ([[CpG sites]]), forming [[5-methylcytosine]]-pG, or 5mCpG. Reactive oxygen species (ROS) may attack guanine at the dinucleotide site, forming [[8-oxo-2'-deoxyguanosine|8-hydroxy-2'-deoxyguanosine]] (8-OHdG), and resulting in a 5mCp-8-OHdG dinucleotide site. The [[base excision repair]] enzyme [[oxoguanine glycosylase|OGG1]] targets 8-OHdG and binds to the lesion without immediate excision. OGG1, present at a 5mCp-8-OHdG site recruits [[Tet methylcytosine dioxygenase 1|TET1]] and TET1 oxidizes the 5mC adjacent to the 8-OHdG. This initiates demethylation of 5mC.<ref name=Zhou>{{cite journal |vauthors=Zhou X, Zhuang Z, Wang W, He L, Wu H, Cao Y, Pan F, Zhao J, Hu Z, Sekhar C, Guo Z |title=OGG1 is essential in oxidative stress-induced DNA demethylation |journal=Cell Signal |volume=28 |issue=9 |pages=1163–1171 |date=September 2016 |pmid=27251462 |doi=10.1016/j.cellsig.2016.05.021 |url=}}</ref>]]

Oxidized guanine has mispairing potential and is mutagenic.<ref name="pmid31993111">{{cite journal |vauthors=Poetsch AR |title=The genomics of oxidative DNA damage, repair, and resulting mutagenesis |journal=Comput Struct Biotechnol J |volume=18 |issue= |pages=207–219 |date=2020 |pmid=31993111 |pmc=6974700 |doi=10.1016/j.csbj.2019.12.013 |url=}}</ref> [[Oxoguanine glycosylase]] (OGG1) is the primary enzyme responsible for the excision of the oxidized guanine during DNA repair. OGG1 finds and binds to an 8-OHdG within a few seconds.<ref name="pmid33171795">{{cite journal |vauthors=D'Augustin O, Huet S, Campalans A, Radicella JP |title=Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome? |journal=Int J Mol Sci |volume=21 |issue=21 |date=November 2020 |page=8360 |pmid=33171795 |pmc=7664663 |doi=10.3390/ijms21218360 |url=|doi-access=free }}</ref> However, OGG1 does not immediately excise 8-OHdG. In HeLa cells half maximum removal of 8-OHdG occurs in 30 minutes,<ref name="pmid15365186">{{cite journal |vauthors=Lan L, Nakajima S, Oohata Y, Takao M, Okano S, Masutani M, Wilson SH, Yasui A |title=In situ analysis of repair processes for oxidative DNA damage in mammalian cells |journal=Proc Natl Acad Sci U S A |volume=101 |issue=38 |pages=13738–43 |date=September 2004 |pmid=15365186 |pmc=518826 |doi=10.1073/pnas.0406048101 |bibcode=2004PNAS..10113738L |url=|doi-access=free }}</ref> and in irradiated mice, the 8-OHdGs induced in the mouse liver are removed with a half-life of 11 minutes.<ref name=Hamilton />

When OGG1 is present at an oxidized guanine within a methylated [[CpG site]] it recruits [[TET enzymes|TET1]] to the 8-OHdG lesion (see Figure). This allows TET1 to demethylate an adjacent methylated cytosine. Demethylation of cytosine is an epigenetic alteration.{{citation needed|date=March 2023}}

As an example, when human mammary epithelial cells were treated with H<sub>2</sub>O<sub>2</sub> for six hours, 8-OHdG increased about 3.5-fold in DNA and this caused about 80% demethylation of the 5-methylcytosines in the genome.<ref name=Zhou /> Demethylation of CpGs in a gene promoter by [[TET enzymes|TET enzyme]] activity increases transcription of the gene into messenger RNA.<ref name="pmid24108092">{{cite journal |vauthors=Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK |title=Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins |journal=Nat. Biotechnol. |volume=31 |issue=12 |pages=1137–42 |date=December 2013 |pmid=24108092 |pmc=3858462 |doi=10.1038/nbt.2726 }}</ref> In cells treated with H<sub>2</sub>O<sub>2</sub>, one particular gene was examined, [[Beta-secretase 1|''BACE1'']].<ref name=Zhou /> The methylation level of the ''BACE1'' [[CpG site#CpG islands|CpG island]] was reduced (an epigenetic alteration) and this allowed about 6.5 fold increase of expression of ''BACE1'' messenger RNA.{{citation needed|date=March 2023}}

While six-hour incubation with H<sub>2</sub>O<sub>2</sub> causes considerable demethylation of 5-mCpG sites, shorter times of H<sub>2</sub>O<sub>2</sub> incubation appear to promote other epigenetic alterations. Treatment of cells with H<sub>2</sub>O<sub>2</sub> for 30 minutes causes the mismatch repair protein heterodimer MSH2-MSH6 to recruit DNA methyltransferase 1 ([[DNMT1]]) to sites of some kinds of oxidative DNA damage.<ref name="pmid26186941">{{cite journal |vauthors=Ding N, Bonham EM, Hannon BE, Amick TR, Baylin SB, O'Hagan HM |title=Mismatch repair proteins recruit DNA methyltransferase 1 to sites of oxidative DNA damage |journal=J Mol Cell Biol |volume=8 |issue=3 |pages=244–54 |date=June 2016 |pmid=26186941 |pmc=4937888 |doi=10.1093/jmcb/mjv050 |url=}}</ref> This could cause increased methylation of cytosines (epigenetic alterations) at these locations.

Jiang et al.<ref name=Jiang>{{cite journal |vauthors=Jiang Z, Lai Y, Beaver JM, Tsegay PS, Zhao ML, Horton JK, Zamora M, Rein HL, Miralles F, Shaver M, Hutcheson JD, Agoulnik I, Wilson SH, Liu Y |title=Oxidative DNA Damage Modulates DNA Methylation Pattern in Human Breast Cancer 1 (BRCA1) Gene via the Crosstalk between DNA Polymerase β and a de novo DNA Methyltransferase |journal=Cells |volume=9 |issue=1 |date=January 2020 |page=225 |pmid=31963223 |pmc=7016758 |doi=10.3390/cells9010225 |url=|doi-access=free }}</ref> treated [[HEK 293 cells]] with agents causing oxidative DNA damage, ([[potassium bromate]] (KBrO3) or [[potassium chromate]] (K2CrO4)). [[Base excision repair]] (BER) of oxidative damage occurred with the DNA repair enzyme [[DNA polymerase|polymerase beta]] localizing to oxidized guanines. Polymerase beta is the main human polymerase in short-patch BER of oxidative DNA damage. Jiang et al.<ref name=Jiang /> also found that polymerase beta recruited the [[DNA methyltransferase]] protein DNMT3b to BER repair sites. They then evaluated the methylation pattern at the single nucleotide level in a small region of DNA including the [[promoter (genetics)|promoter]] region and the early transcription region of the [[BRCA1]] gene. Oxidative DNA damage from bromate modulated the DNA methylation pattern (caused epigenetic alterations) at CpG sites within the region of DNA studied. In untreated cells, CpGs located at −189, −134, −29, −19, +16, and +19 of the BRCA1 gene had methylated cytosines (where numbering is from the [[messenger RNA]] transcription start site, and negative numbers indicate nucleotides in the upstream [[Promoter (genetics)|promoter]] region). Bromate treatment-induced oxidation resulted in the loss of cytosine methylation at −189, −134, +16 and +19 while also leading to the formation of new methylation at the CpGs located at −80, −55, −21 and +8 after DNA repair was allowed.