Editing Epigenome (section)

== Types ==
{{main|Epigenetics}}
The main types of epigenetic changes include:<ref name = "Al_Aboud_2023">{{cite book | vauthors = Al Aboud NM, Tupper C, Jialal I | chapter = Genetics, Epigenetic Mechanism | date = August 2023 | title = StatPearls [Internet] | location = Treasure Island (FL) | publisher = StatPearls Publishing | pmid = 30422591 | chapter-url = https://www.ncbi.nlm.nih.gov/books/NBK532999/ }}</ref>

=== DNA methylation ===
{{main|DNA methylation}}

Addition of a methyl group to the DNA molecule, typically at [[cytosine]] bases. This modification generally leads to [[gene silencing]] by preventing the binding of [[transcription factor]]s and other proteins necessary for gene expression.<ref name = "Al_Aboud_2023" />

DNA functionally interacts with a variety of epigenetic marks, such as cytosine methylation, also known as [[5-Methylcytosine|5-methylcytosine]] (5mC). This epigenetic mark is widely conserved and plays major roles in the regulation of gene expression, in the silencing of [[Transposable element|transposable elements]] and [[Repeated sequence (DNA)|repeat sequences]].<ref name=":6">{{cite journal | vauthors = Taudt A, Colomé-Tatché M, Johannes F | title = Genetic sources of population epigenomic variation | journal = Nature Reviews. Genetics | volume = 17 | issue = 6 | pages = 319–332 | date = June 2016 | pmid = 27156976 | doi = 10.1038/nrg.2016.45 | s2cid = 336906 }}</ref>

Individuals differ with their epigenetic profile, for example the variance in [[CpG site|CpG]] methylation among individuals is about 42%. On the contrary, epigenetic profile (including methylation profile) of each individual is constant over the course of a year, reflecting the constancy of our [[phenotype]] and metabolic traits. Methylation profile, in particular, is quite stable in a 12-month period and appears to change more over decades.<ref name=":0">{{cite journal | vauthors = Tabassum R, Sivadas A, Agrawal V, Tian H, Arafat D, Gibson G | title = Omic personality: implications of stable transcript and methylation profiles for personalized medicine | journal = Genome Medicine | volume = 7 | issue = 1 | pages = 88 | date = August 2015 | pmid = 26391122 | pmc = 4578259 | doi = 10.1186/s13073-015-0209-4 | doi-access = free }}</ref>

==== Methylation sites ====
CoRSIVs are '''Co'''rrelated '''R'''egions of '''S'''ystemic '''I'''nterindividual '''V'''ariation in DNA methylation. They span only 0.1% of the human genome, so they are very rare; they can be inter-correlated over long genomic distances (>50 kbp). CoRSIVs are also associated with genes involved in a lot of human disorders, including tumors, mental disorders and cardiovascular diseases. It has been observed that disease-associated CpG sites are 37% enriched in CoRSIVs compared to control regions and 53% enriched in CoRSIVs relative to tDMRs (tissue specific Differentially Methylated Regions).<ref name=":2">{{cite journal | vauthors = Gunasekara CJ, Scott CA, Laritsky E, Baker MS, MacKay H, Duryea JD, Kessler NJ, Hellenthal G, Wood AC, Hodges KR, Gandhi M, Hair AB, Silver MJ, Moore SE, Prentice AM, Li Y, Chen R, Coarfa C, Waterland RA | title = A genomic atlas of systemic interindividual epigenetic variation in humans | journal = Genome Biology | volume = 20 | issue = 1 | pages = 105 | date = June 2019 | pmid = 31155008 | pmc = 6545702 | doi = 10.1186/s13059-019-1708-1 | doi-access = free }}</ref>

Most of the CoRSIVs are only 200 – 300 bp long and include 5–10 CpG dinucleotides, the largest span several kb and involve hundreds of CpGs. These regions tend to occur in clusters and the two genomic areas of high CoRSIV density are observed at the major histocompatibility ([[Major histocompatibility complex|MHC]]) locus on [[chromosome 6]] and at the pericentromeric region on the long arm of chromosome 20.<ref name=":2" />

CoRSIVs are enriched in [[Intergenic region|intergenic]] and quiescent regions (e.g. [[Subtelomere|subtelomeric]] regions) and contain many transposable elements, but few CpG islands (CGI) and transcription factor binding sites. CoRSIVs are under-represented in the proximity of genes, in [[Heterochromatin|heterochromatic]] regions, active [[Promoter (genetics)|promoters]], and [[Enhancer (genetics)|enhancers]]. They are also usually not present in highly conserved genomic regions.<ref name=":2" />

CoRSIVs can have a useful application: measurements of CoRSIV methylation in one tissue can provide some information about epigenetic regulation in other tissues, indeed we can predict the expression of associated genes because systemic epigenetic variants are generally consistent in all tissues and cell types.<ref>{{cite journal | vauthors = Waterland RA, Michels KB | title = Epigenetic epidemiology of the developmental origins hypothesis | journal = Annual Review of Nutrition | volume = 27 | issue = 1 | pages = 363–388 | date = 2007 | pmid = 17465856 | doi = 10.1146/annurev.nutr.27.061406.093705 }}</ref>

==== Factors affecting methylation pattern ====
Quantification of the heritable basis underlying population epigenomic variation is also important to delineate its cis- and trans-regulatory architecture. In particular, most studies state that inter-individual differences in DNA methylation are mainly determined by cis-regulatory sequence [[Polymorphism (biology)|polymorphisms]], probably involving mutations in TFBSs (Transcription Factor Binding Sites) with downstream consequences on local chromatin environment. The sparsity of [[trans-acting]] polymorphisms in humans suggests that such effects are highly deleterious. Indeed, trans-acting factors are expected to be caused by mutations in chromatin control genes or other highly pleiotropic regulators. If trans-acting variants do exist in human populations, they probably segregate as rare alleles or originate from somatic mutations and present with clinical phenotypes, as is the case in many cancers.<ref name=":6" />

==== Correlation between methylation and gene expression ====
DNA methylation (in particular in CpG regions) is able to affect gene expression: hypermethylated regions tend to be differentially expressed. In fact, people with a similar methylation profile tend to also have the same [[transcriptome]]. Moreover, one key observation from human methylation is that most functionally relevant changes in CpG methylation occur in regulatory elements, such as enhancers.

Anyway, differential expression concerns only a slight number of methylated genes: only one fifth of genes with CpG methylation shows variable expression according to their methylation state. It is important to notice that methylation is not the only factor affecting [[Regulation of gene expression|gene regulation]].<ref name=":0" />

==== Methylation in embryos ====
It was revealed by [[immunostaining]] experiments that in human preimplantation embryos there is a global DNA [[demethylation]] process. After [[fertilisation]], the [[DNA methylation]] level decreases sharply in the early [[Pronucleus|pronuclei]]. This is a consequence of active DNA demethylation at this stage. But global demethylation is not an irreversible process, in fact ''de novo'' methylation occurring from the early to mid-pronuclear stage and from the 4-cell to the 8-cell stage.<ref name=":3">{{cite journal | vauthors = Wen L, Tang F | title = Human Germline Cell Development: from the Perspective of Single-Cell Sequencing | language = English | journal = Molecular Cell | volume = 76 | issue = 2 | pages = 320–328 | date = October 2019 | pmid = 31563431 | doi = 10.1016/j.molcel.2019.08.025 | doi-access = free }}</ref>

The percentage of DNA methylation is different in [[oocyte]]s and in [[sperm]]: the mature oocyte has an intermediate level of DNA methylation (72%), instead the sperm has high level of DNA methylation (86%). Demethylation in paternal genome occurs quickly after fertilisation, whereas the maternal genome is quite resistant at the demethylation process at this stage. Maternal different methylated regions (DMRs) are more resistant to the preimplantation demethylation wave.<ref name=":3" />

CpG methylation is similar in [[germinal vesicle]] (GV) stage, intermediate [[metaphase I]] (MI) stage and mature [[metaphase II]] (MII) stage. Non-CpG methylation continues to accumulate in these stages.<ref name=":3" />

[[Chromatin]] accessibility in germline was evaluated by different approaches, like sc[[ATAC-seq]] and sciATAC-seq, scCOOL-seq, scNOMe-seq and sc[[DNase-Seq|DNase-seq]]. Stage-specific proximal and distal regions with accessible chromatin regions were identified. Global chromatin accessibility is found to gradually decrease from the [[zygote]] to the 8-cell stage and then increase. Parental allele-specific analysis shows that paternal genome becomes more open than the maternal genome from the late zygote stage to the 4-cell stage, which may reflect decondensation of the paternal genome with replacement of [[protamine]]s by [[histone]]s.<ref name=":3" />

==== Sequence-Dependent Allele-Specific Methylation ====
DNA methylation imbalances between homologous chromosomes show sequence-dependent behavior. Difference in the methylation state of neighboring cytosines on the same chromosome occurs due to the difference in DNA sequence between the chromosomes. Whole-genome [[bisulfite sequencing]] (WGBS) is used to explore sequence-dependent allele-specific methylation (SD-ASM) at a single-chromosome resolution level and comprehensive whole-genome coverage. The results of WGBS tested on 49 methylomes revealed CpG methylation imbalances exceeding 30% differences in 5% of the loci.<ref name="Onuchic_2018">{{cite journal | vauthors = Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A | title = Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci | journal = Science | location = New York, N.Y. | volume = 361 | issue = 6409 | pages = | date = September 2018 | pmid = 30139913 | pmc = 6198826 | doi = 10.1126/science.aar3146 }}</ref>

On the sites of gene regulatory loci bound by transcription factors the random switching between methylated and unmethylated states of DNA was observed. This is also referred as stochastic switching and it is linked to selective buffering of [[gene regulatory circuit]] against mutations and genetic diseases. Only rare genetic variants show the stochastic type of gene regulation.

The study made by ''Onuchic et al.'' was aimed to construct the maps of allelic imbalances in DNA methylation, gene transcription, and also of histone modifications. 36 cell and tissue types from 13 participant donors were used to examine 71 epigenomes. The results of WGBS tested on 49 methylomes revealed CpG methylation imbalances exceeding 30% differences in 5% of the loci. The stochastic switching occurred at thousands of heterozygous regulatory loci that were bound to transcription factors. The intermediate methylation state is referred to the relative frequencies between methylated and unmethylated epialleles. The epiallele frequency variations are correlated with the allele affinity for transcription factors.

The analysis of the study suggests that human epigenome in average covers approximately 200 adverse SD-ASM variants. The sensitivity of the genes with tissue-specific expression patterns gives the opportunity for the evolutionary innovation in gene regulation.<ref name="Onuchic_2018" />

Haplotype reconstruction strategy is used to trace chromatin chemical modifications (using ChIP-seq) in a variety of human tissues. Haplotype-resolved epigenomic maps can trace allelic biases in chromatin configuration. A substantial variation among different tissues and individuals is observed. This allows the deeper understanding of cis-regulatory relationships between genes and control sequences.<ref name=":4">{{cite journal | vauthors = Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B | title = Integrative analysis of haplotype-resolved epigenomes across human tissues | journal = Nature | volume = 518 | issue = 7539 | pages = 350–354 | date = February 2015 | pmid = 25693566 | pmc = 4449149 | doi = 10.1038/nature14217 | bibcode = 2015Natur.518..350L }}</ref>

=== Histone modification ===
{{main|Histone modification}}

Post-translational modifications of histone proteins, which include methylation, [[acetylation]], [[phosphorylation]], [[ubiquitination]], and [[sumoylation]]. These modifications can either activate or repress gene expression by altering chromatin structure and accessibility of the DNA to transcriptional machinery.

The epigenetic profiles of human tissues reveals the following distinct histone modifications in different functional areas:<ref name=":4" />
{| class="wikitable"
!Active Promoters
!Active Enhancers
!Transcribed Gene Bodies
!Silenced Regions
|-
|[[H3K4me3]]
|[[H3K4me1]]
|[[H3K36me3]]
|[[H3K27me3]]
|-
|[[H3K27ac]]
|[[H3K27ac]]
|
|[[H3K9me3]]
|}

==== Acetylation  ====
{{main|Histone acetylation}}
Histone acetylation neutralizes the positive charge on histones. This weakens the electrostatic attraction to negatively charged DNA and causes unwinding of DNA from histones, making the DNA more accessible to the transcriptional machinery and hence resulting in transcriptional activation.<ref name="Sterner_2000">{{cite journal | vauthors = Sterner DE, Berger SL | title = Acetylation of histones and transcription-related factors | journal = Microbiology and Molecular Biology Reviews | volume = 64 | issue = 2 | pages = 435–59 | date = June 2000 | pmid = 10839822 | pmc = 98999 | doi = 10.1128/MMBR.64.2.435-459.2000 }}</ref>

==== Methylation ====
{{main|Histone methylation}}
Can lead to activation or repression of gene expression depending on the specific amino acids that are methylated.

=== Non-coding RNA gene silencing ===
[[Non-coding RNA]] (ncRNA) gene silencing involves various types of non-coding RNAs, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and small interfering RNAs (siRNAs).  These RNA molecules can modulate gene expression by various mechanisms, including mRNA degradation, inhibition of translation, and chromatin remodeling.<ref name = "Al_Aboud_2023" />