Editing Nucleosome (section)

===Dynamic nucleosome remodelling across the Yeast genome===
Studies in 2007 have catalogued nucleosome positions in yeast and shown that nucleosomes are depleted in [[Promoter (biology)|promoter]] regions and [[Origin of replication|origins of replication]].<ref name="pmid17392789">{{cite journal | vauthors = Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF | title = Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome | journal = Nature | volume = 446 | issue = 7135 | pages = 572–576 | date = March 2007 | pmid = 17392789 | doi = 10.1038/nature05632 | s2cid = 4416890 | bibcode = 2007Natur.446..572A }}</ref><ref name="pmid17320508">{{cite journal | vauthors = Li B, Carey M, Workman JL | title = The role of chromatin during transcription | journal = Cell | volume = 128 | issue = 4 | pages = 707–719 | date = February 2007 | pmid = 17320508 | doi = 10.1016/j.cell.2007.01.015 | s2cid = 1773333 | doi-access = free }}</ref><ref name="pmid18075583">{{cite journal | vauthors = Whitehouse I, Rando OJ, Delrow J, Tsukiyama T | title = Chromatin remodelling at promoters suppresses antisense transcription | journal = Nature | volume = 450 | issue = 7172 | pages = 1031–1035 | date = December 2007 | pmid = 18075583 | doi = 10.1038/nature06391 | s2cid = 4305576 | bibcode = 2007Natur.450.1031W }}</ref>
About 80% of the yeast genome appears to be covered by nucleosomes<ref name="pmid17873876">{{cite journal | vauthors = Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C | title = A high-resolution atlas of nucleosome occupancy in yeast | journal = Nature Genetics | volume = 39 | issue = 10 | pages = 1235–1244 | date = October 2007 | pmid = 17873876 | doi = 10.1038/ng2117 | s2cid = 12816925 }}</ref> and the pattern of nucleosome positioning clearly relates to DNA regions that regulate [[Transcription (genetics)|transcription]], regions that are transcribed and regions that initiate DNA replication.<ref name="pmid20351051">{{cite journal | vauthors = Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM | title = Conserved nucleosome positioning defines replication origins | journal = Genes & Development | volume = 24 | issue = 8 | pages = 748–753 | date = April 2010 | pmid = 20351051 | pmc = 2854390 | doi = 10.1101/gad.1913210 }}</ref> Most recently, a new study examined ''dynamic changes'' in nucleosome repositioning during a global transcriptional reprogramming event to elucidate the effects on nucleosome displacement during genome-wide transcriptional changes in yeast (''[[Saccharomyces cerevisiae]]'').<ref name="pmid18351804">{{cite journal | vauthors = Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR | title = Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation | journal = PLOS Biology | volume = 6 | issue = 3 | pages = e65 | date = March 2008 | pmid = 18351804 | pmc = 2267817 | doi = 10.1371/journal.pbio.0060065 | doi-access = free }}</ref> The results suggested that nucleosomes that were localized to promoter regions are displaced in response to stress (like [[heat shock]]). In addition, the removal of nucleosomes usually corresponded to transcriptional activation and the replacement of nucleosomes usually corresponded to transcriptional repression, presumably because [[transcription factor]] binding sites became more or less accessible, respectively. In general, only one or two nucleosomes were repositioned at the promoter to effect these transcriptional changes. However, even in chromosomal regions that were not associated with transcriptional changes, nucleosome repositioning was observed, suggesting that the covering and uncovering of transcriptional DNA does not necessarily produce a transcriptional event. After transcription, the rDNA region has to protected from any damage, it suggested HMGB proteins play a major role in protecting the nucleosome free region.<ref>{{cite journal | vauthors = Murugesapillai D, McCauley MJ, Huo R, Nelson Holte MH, Stepanyants A, Maher LJ, Israeloff NE, Williams MC | display-authors = 6 | title = DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin | journal = Nucleic Acids Research | volume = 42 | issue = 14 | pages = 8996–9004 | date = August 2014 | pmid = 25063301 | pmc = 4132745 | doi = 10.1093/nar/gku635 }}</ref><ref>{{cite journal | vauthors = Murugesapillai D, McCauley MJ, Maher LJ, Williams MC | title = Single-molecule studies of high-mobility group B architectural DNA bending proteins | journal = Biophysical Reviews | volume = 9 | issue = 1 | pages = 17–40 | date = February 2017 | pmid = 28303166 | pmc = 5331113 | doi = 10.1007/s12551-016-0236-4 }}</ref>