Editing Epigenetics (section)

===Techniques used to study epigenetics===
Epigenetic research uses a wide range of [[molecular biology|molecular biological]] techniques to further understanding of epigenetic phenomena. These techniques include [[chromatin immunoprecipitation]] (together with its large-scale variants [[ChIP-on-chip]] and [[ChIP-Seq]]), [[fluorescent in situ hybridization]], methylation-sensitive [[restriction enzymes]], DNA adenine methyltransferase identification ([[DamID]]) and [[bisulfite sequencing]].<ref name="verma">{{cite journal | vauthors = Verma M, Rogers S, Divi RL, Schully SD, Nelson S, Joseph Su L, Ross SA, Pilch S, Winn DM, Khoury MJ | title = Epigenetic research in cancer epidemiology: trends, opportunities, and challenges | journal = Cancer Epidemiology, Biomarkers & Prevention | volume = 23 | issue = 2 | pages = 223–33 | date = February 2014 | pmid = 24326628 | pmc = 3925982 | doi = 10.1158/1055-9965.EPI-13-0573 }}</ref> Furthermore, the use of [[bioinformatics]] methods has a role in [[computational epigenetics]].<ref name=verma/>

====Chromatin Immunoprecipitation====
Chromatin Immunoprecipitation (ChIP) has helped bridge the gap between DNA and epigenetic interactions.<ref name="Abcam">{{Cite web|title=Studying epigenetics using ChIP|url=https://www.abcam.com/epigenetics/studying-epigenetics-using-chip | work = Abcam }}</ref> With the use of ChIP, researchers are able to make findings in regards to gene regulation, transcription mechanisms, and chromatin structure.<ref name="Abcam" />

====Fluorescent ''in situ'' hybridization====
Fluorescent ''in situ'' hybridization (FISH) is very important to understand epigenetic mechanisms.<ref name="Chaumeil_2008">{{cite book | vauthors = Chaumeil J, Augui S, Chow JC, Heard E | chapter = Combined Immunofluorescence, RNA Fluorescent in Situ Hybridization, and DNA Fluorescent in Situ Hybridization to Study Chromatin Changes, Transcriptional Activity, Nuclear Organization, and X-Chromosome Inactivation | title = The Nucleus | series = Methods in Molecular Biology | location = Clifton, N.J. | publisher = Springer | volume = 463 | pages = 297–308 | date = 2008 | pmid = 18951174 | doi = 10.1007/978-1-59745-406-3_18 | isbn = 978-1-58829-977-2 | chapter-url = }}</ref> FISH can be used to find the location of genes on chromosomes, as well as finding noncoding RNAs.<ref name="Chaumeil_2008" /><ref name="O'Connor_2008">{{Cite journal | vauthors = O'Connor C | title = Fluorescence in situ hybridization (FISH). | journal = Nature Education | date = 2008 | volume = 1 | issue = 1 | page = 171 |url= https://www.nature.com/scitable/topicpage/fluorescence-in-situ-hybridization-fish-327/ }}</ref> FISH is predominantly used for detecting chromosomal abnormalities in humans.<ref name="O'Connor_2008" />

====Methylation-sensitive restriction enzymes====
Methylation sensitive restriction enzymes paired with PCR is a way to evaluate methylation in DNA - specifically the CpG sites.<ref name="Hashimoto_2007">{{cite journal | vauthors = Hashimoto K, Kokubun S, Itoi E, Roach HI | title = Improved quantification of DNA methylation using methylation-sensitive restriction enzymes and real-time PCR | journal = Epigenetics | volume = 2 | issue = 2 | pages = 86–91 | year = 2007 | pmid = 17965602 | doi = 10.4161/epi.2.2.4203 | s2cid = 26728480 | doi-access = free }}</ref> If DNA is methylated, the restriction enzymes will not cleave the strand.<ref name="Hashimoto_2007" /> Contrarily, if the DNA is not methylated, the enzymes will cleave the strand and it will be amplified by PCR.<ref name="Hashimoto_2007" />

====Bisulfite sequencing====
Bisulfite sequencing is another way to evaluate DNA methylation. Cytosine will be changed to uracil from being treated with sodium bisulfite, whereas methylated cytosines will not be affected.<ref name="Hashimoto_2007" /><ref name="Li-Byarlay et al 2020">{{cite journal | vauthors = Li-Byarlay H, Boncristiani H, Howell G, Herman J, Clark L, Strand MK, Tarpy D, Rueppell O | title = Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection | journal = Frontiers in Genetics | volume = 11 | pages = 566320 | date = 24 September 2020 | pmid = 33101388 | pmc = 7546774 | doi = 10.3389/fgene.2020.566320 | doi-access = free }}</ref><ref name="ReferenceC">{{cite journal | vauthors = Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KC, Elsik CG, Wickline SA, Jacobsen SE, Ma J, Robinson GE | title = RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 110 | issue = 31 | pages = 12750–12755 | date = July 2013 | pmid = 23852726 | pmc = 3732956 | doi = 10.1073/pnas.1310735110 | doi-access = free | bibcode = 2013PNAS..11012750L }}</ref>

====Nanopore sequencing====
Certain sequencing methods, such as [[nanopore sequencing]], allow sequencing of native DNA. Native (=unamplified) DNA retains the epigenetic modifications which would otherwise be lost during the amplification step. Nanopore basecaller models can distinguish between the signals obtained for epigenetically modified bases and unaltered based and provide an epigenetic profile in addition to the sequencing result.<ref>{{cite journal | vauthors = Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W | title = Detecting DNA cytosine methylation using nanopore sequencing | journal = Nature Methods | volume = 14 | issue = 4 | pages = 407–410 | date = April 2017 | pmid = 28218898 | doi = 10.1038/nmeth.4184 | s2cid = 16152628 }}</ref>