Editing DNA (section)

=== Base modifications and DNA packaging ===
{{further|DNA methylation|Chromatin remodeling}}
<div class="thumb tright" style="background:#f9f9f9; border:1px solid #ccc; margin:0.5em;">
{| border="0" cellpadding="2" cellspacing="0" style="width:300px; font-size:85%; border:1px solid #ccc; margin:0.3em;"
|-
|[[File:Cytosin.svg|75px]]
|[[File:5-Methylcytosine.svg|95px]]
|[[File:Thymin.svg|97px]]
|-
|align=center|[[cytosine]]
|align=center|[[5-Methylcytosine|5-methylcytosine]]
|align=center|[[thymine]]
|}
<div style="border: none; width:300px;font-size: 90%;"><div class="thumbcaption">Structure of cytosine with and without the 5-methyl group. [[Deamination]] converts 5-methylcytosine into thymine.</div></div></div>
The expression of genes is influenced by how the DNA is packaged in chromosomes, in a structure called [[chromatin]]. Base modifications can be involved in packaging, with regions that have low or no gene expression usually containing high levels of [[methylation]] of [[cytosine]] bases. DNA packaging and its influence on gene expression can also occur by covalent modifications of the [[histone]] protein core around which DNA is wrapped in the chromatin structure or else by remodeling carried out by chromatin remodeling complexes (see [[Chromatin remodeling]]). There is, further, [[Crosstalk (biology)|crosstalk]] between DNA methylation and histone modification, so they can coordinately affect chromatin and gene expression.<ref>{{cite journal | vauthors = Hu Q, Rosenfeld MG | title = Epigenetic regulation of human embryonic stem cells | journal = Frontiers in Genetics | volume = 3 | pages = 238 | year = 2012 | pmid = 23133442 | pmc = 3488762 | doi = 10.3389/fgene.2012.00238 | doi-access = free }}</ref>

For one example, cytosine methylation produces [[5-Methylcytosine|5-methylcytosine]], which is important for [[X-inactivation]] of chromosomes.<ref>{{cite journal | vauthors = Klose RJ, Bird AP | title = Genomic DNA methylation: the mark and its mediators | journal = Trends in Biochemical Sciences | volume = 31 | issue = 2 | pages = 89–97 | date = February 2006 | pmid = 16403636 | doi = 10.1016/j.tibs.2005.12.008 }}</ref> The average level of methylation varies between organisms—the worm ''[[Caenorhabditis elegans]]'' lacks cytosine methylation, while [[vertebrate]]s have higher levels, with up to 1% of their DNA containing 5-methylcytosine.<ref>{{cite journal | vauthors = Bird A | title = DNA methylation patterns and epigenetic memory | journal = Genes & Development | volume = 16 | issue = 1 | pages = 6–21 | date = January 2002 | pmid = 11782440 | doi = 10.1101/gad.947102 | doi-access = free }}</ref> Despite the importance of 5-methylcytosine, it can [[deamination|deaminate]] to leave a thymine base, so methylated cytosines are particularly prone to [[mutation]]s.<ref>{{cite book | vauthors = Walsh CP, Xu GL | title = DNA Methylation: Basic Mechanisms | chapter = Cytosine methylation and DNA repair | volume = 301 | pages = 283–315 | year = 2006 | pmid = 16570853 | doi = 10.1007/3-540-31390-7_11 | isbn = 3-540-29114-8 | series = Current Topics in Microbiology and Immunology }}</ref> Other base modifications include adenine methylation in bacteria, the presence of [[5-hydroxymethylcytosine]] in the [[brain]],<ref>{{cite journal | vauthors = Kriaucionis S, Heintz N | title = The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain | journal = Science | volume = 324 | issue = 5929 | pages = 929–30 | date = May 2009 | pmid = 19372393 | pmc = 3263819 | doi = 10.1126/science.1169786 | bibcode = 2009Sci...324..929K }}</ref> and the [[glycosylation]] of uracil to produce the "J-base" in [[Kinetoplastida|kinetoplastids]].<ref>{{cite journal | vauthors = Ratel D, Ravanat JL, Berger F, Wion D | title = N6-methyladenine: the other methylated base of DNA | journal = BioEssays | volume = 28 | issue = 3 | pages = 309–15 | date = March 2006 | pmid = 16479578 | pmc = 2754416 | doi = 10.1002/bies.20342 }}</ref><ref>{{cite journal | vauthors = Gommers-Ampt JH, Van Leeuwen F, de Beer AL, Vliegenthart JF, Dizdaroglu M, Kowalak JA, Crain PF, Borst P | s2cid = 24801094 | title = beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei | journal = Cell | volume = 75 | issue = 6 | pages = 1129–36 | date = December 1993 | pmid = 8261512 | doi = 10.1016/0092-8674(93)90322-H | hdl = 1874/5219 | hdl-access = free }}</ref>