In Vitro and in Vivo nucleosome positioning on the ovine beta-lactoglobulin gene are related - PubMed (original) (raw)
. 2006 Aug 11;361(2):216-30.
doi: 10.1016/j.jmb.2006.06.039. Epub 2006 Jul 3.
Affiliations
- PMID: 16859709
- DOI: 10.1016/j.jmb.2006.06.039
In Vitro and in Vivo nucleosome positioning on the ovine beta-lactoglobulin gene are related
Marieta Gencheva et al. J Mol Biol. 2006.
Abstract
Although positioned nucleosomes are known to play a direct, localised role in regulating access to DNA sequence, they also have the potential, through their long-range distribution, to affect the detailed structure of the higher-order chromatin fibre. To investigate this possibility, we firstly mapped, in vitro, the sequence-dependent positions that the core histone octamer adopts when reconstituted onto DNA containing the ovine beta-lactoglobulin gene. These positioning sites are discussed in terms of their relative affinity for the histone octamer, their locations with respect to the gene sequence and their periodic distribution throughout the gene region. Secondly, we mapped, in vivo, the sites that nucleosomes occupy on the same sequence in liver nuclei, where the gene is transcriptionally inactive. Although the sequence is largely packaged into regularly spaced nucleosomes, reflecting a fibre of uniform higher-order structure, this organisation is disrupted by a number of unusual chromatin structures in a region stretching from the second to the third introns of the gene. A comparison of the in vitro and in vivo nucleosome positioning data shows that they are qualitatively and quantitatively related, suggesting that the structure of the higher-order chromatin fibre containing the beta-lactoglobulin gene is determined, in part, by the long-range organisation of the non-coding sequences within which the gene is embedded.
Similar articles
- In silico approaches reveal the potential for DNA sequence-dependent histone octamer affinity to influence chromatin structure in vivo.
Fraser RM, Allan J, Simmen MW. Fraser RM, et al. J Mol Biol. 2006 Dec 8;364(4):582-98. doi: 10.1016/j.jmb.2006.08.092. Epub 2006 Sep 7. J Mol Biol. 2006. PMID: 17027853 - Nucleosome positioning on chicken and human globin gene promoters in vitro. Novel mapping techniques.
Yenidunya A, Davey C, Clark D, Felsenfeld G, Allan J. Yenidunya A, et al. J Mol Biol. 1994 Apr 8;237(4):401-14. doi: 10.1006/jmbi.1994.1243. J Mol Biol. 1994. PMID: 8151701 - New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning.
Lowary PT, Widom J. Lowary PT, et al. J Mol Biol. 1998 Feb 13;276(1):19-42. doi: 10.1006/jmbi.1997.1494. J Mol Biol. 1998. PMID: 9514715 - DNA recognition and nucleosome organization.
Travers A, Drew H. Travers A, et al. Biopolymers. 1997;44(4):423-33. doi: 10.1002/(SICI)1097-0282(1997)44:4<423::AID-BIP6>3.0.CO;2-M. Biopolymers. 1997. PMID: 9782778 Review. - Nucleosome positioning and gene regulation.
Lu Q, Wallrath LL, Elgin SC. Lu Q, et al. J Cell Biochem. 1994 May;55(1):83-92. doi: 10.1002/jcb.240550110. J Cell Biochem. 1994. PMID: 8083303 Review.
Cited by
- Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution.
Barbier J, Vaillant C, Volff JN, Brunet FG, Audit B. Barbier J, et al. Genes (Basel). 2021 Jun 1;12(6):851. doi: 10.3390/genes12060851. Genes (Basel). 2021. PMID: 34205881 Free PMC article. Review. - CpG domains downstream of TSSs promote high levels of gene expression.
Krinner S, Heitzer AP, Diermeier SD, Obermeier I, Längst G, Wagner R. Krinner S, et al. Nucleic Acids Res. 2014 Apr;42(6):3551-64. doi: 10.1093/nar/gkt1358. Epub 2014 Jan 9. Nucleic Acids Res. 2014. PMID: 24413563 Free PMC article. - The grammar of transcriptional regulation.
Weingarten-Gabbay S, Segal E. Weingarten-Gabbay S, et al. Hum Genet. 2014 Jun;133(6):701-11. doi: 10.1007/s00439-013-1413-1. Epub 2014 Jan 5. Hum Genet. 2014. PMID: 24390306 Free PMC article. Review. - A comparison of in vitro nucleosome positioning mapped with chicken, frog and a variety of yeast core histones.
Allan J, Fraser RM, Owen-Hughes T, Docherty K, Singh V. Allan J, et al. J Mol Biol. 2013 Nov 15;425(22):4206-22. doi: 10.1016/j.jmb.2013.07.019. Epub 2013 Jul 18. J Mol Biol. 2013. PMID: 23871836 Free PMC article. - Micrococcal nuclease does not substantially bias nucleosome mapping.
Allan J, Fraser RM, Owen-Hughes T, Keszenman-Pereyra D. Allan J, et al. J Mol Biol. 2012 Mar 30;417(3):152-64. doi: 10.1016/j.jmb.2012.01.043. Epub 2012 Jan 30. J Mol Biol. 2012. PMID: 22310051 Free PMC article.