Editing Nucleosome (section)

===ATP-dependent nucleosome remodeling===
A number of distinct reactions are associated with the term [[ATP-dependent chromatin remodeling]]. Remodeling enzymes have been shown to slide nucleosomes along DNA,<ref name="pmid10466730">{{cite journal | vauthors = Whitehouse I, Flaus A, Cairns BR, White MF, Workman JL, Owen-Hughes T | title = Nucleosome mobilization catalysed by the yeast SWI/SNF complex | journal = Nature | volume = 400 | issue = 6746 | pages = 784–787 | date = August 1999 | pmid = 10466730 | doi = 10.1038/23506 | s2cid = 2841873 | bibcode = 1999Natur.400..784W }}</ref> disrupt histone-DNA contacts to the extent of destabilizing the H2A/H2B dimer<ref name="pmid12620227">{{cite journal | vauthors = Kassabov SR, Zhang B, Persinger J, Bartholomew B | title = SWI/SNF unwraps, slides, and rewraps the nucleosome | journal = Molecular Cell | volume = 11 | issue = 2 | pages = 391–403 | date = February 2003 | pmid = 12620227 | doi = 10.1016/S1097-2765(03)00039-X | doi-access = free }}</ref><ref name="pmid14690611">{{cite journal | vauthors = Bruno M, Flaus A, Stockdale C, Rencurel C, Ferreira H, Owen-Hughes T | title = Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities | journal = Molecular Cell | volume = 12 | issue = 6 | pages = 1599–1606 | date = December 2003 | pmid = 14690611 | pmc = 3428624 | doi = 10.1016/S1097-2765(03)00499-4 }}</ref> and to generate negative superhelical torsion in DNA and chromatin.<ref name="pmid11163188">{{cite journal | vauthors = Havas K, Flaus A, Phelan M, Kingston R, Wade PA, Lilley DM, Owen-Hughes T | title = Generation of superhelical torsion by ATP-dependent chromatin remodeling activities | journal = Cell | volume = 103 | issue = 7 | pages = 1133–1142 | date = December 2000 | pmid = 11163188 | doi = 10.1016/S0092-8674(00)00215-4 | s2cid = 7911590 | doi-access = free }}</ref> Recently, the Swr1 remodeling enzyme has been shown to introduce the variant histone H2A.Z into nucleosomes.<ref name="pmid14645854">{{cite journal | vauthors = Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C | title = ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex | journal = Science | volume = 303 | issue = 5656 | pages = 343–348 | date = January 2004 | pmid = 14645854 | doi = 10.1126/science.1090701 | s2cid = 9881829 | bibcode = 2004Sci...303..343M | url = https://zenodo.org/record/1230842 | doi-access = free }}</ref> At present, it is not clear if all of these represent distinct reactions or merely alternative outcomes of a common mechanism. What is shared between all, and indeed the hallmark of ATP-dependent chromatin remodeling, is that they all result in altered DNA accessibility.

Studies looking at gene activation ''in vivo''<ref name="pmid14675539">{{cite journal | vauthors = Métivier R, Penot G, Hübner MR, Reid G, Brand H, Kos M, Gannon F | title = Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter | journal = Cell | volume = 115 | issue = 6 | pages = 751–763 | date = December 2003 | pmid = 14675539 | doi = 10.1016/S0092-8674(03)00934-6 | s2cid = 145525 | doi-access = free }}</ref> and, more astonishingly, remodeling ''in vitro''<ref name="pmid15099516">{{cite journal | vauthors = Nagaich AK, Walker DA, Wolford R, Hager GL | title = Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling | journal = Molecular Cell | volume = 14 | issue = 2 | pages = 163–174 | date = April 2004 | pmid = 15099516 | doi = 10.1016/S1097-2765(04)00178-9 | doi-access = free }}</ref> have revealed that chromatin remodeling events and transcription-factor binding are cyclical and periodic in nature. While the consequences of this for the reaction mechanism of chromatin remodeling are not known, the dynamic nature of the system may allow it to respond faster to external stimuli. A recent study indicates that nucleosome positions change significantly during mouse embryonic stem cell development, and these changes are related to binding of developmental transcription factors.<ref>{{cite journal | vauthors = Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Höfer T, Rippe K | title = Genome-wide nucleosome positioning during embryonic stem cell development | journal = Nature Structural & Molecular Biology | volume = 19 | issue = 11 | pages = 1185–1192 | date = November 2012 | pmid = 23085715 | doi = 10.1038/nsmb.2419 | s2cid = 34509771 }}</ref>