title: Nucleosome-free DNA regions differentially affect distant communication in chromatin.
abstract: Communication between distantly spaced genomic regions is one of the key features of gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter communication (EPC); however, the role of chromatin structure and dynamics in this process remains poorly understood. Here we show that nucleosome spacing and the presence of nucleosome-free DNA regions can modulate chromatin structure/dynamics and, in turn, affect the rate of EPC in vitro and in silico. Increasing the length of internucleosomal linker DNA from 25 to 60 bp results in more efficient EPC. The presence of longer nucleosome-free DNA regions can positively or negatively affect the rate of EPC, depending upon the length and location of the DNA region within the chromatin fiber. Thus the presence of histone-free DNA regions can differentially affect the efficiency of EPC, suggesting that gene regulation over a distance could be modulated by changes in the length of internucleosomal DNA spacers.
authors.affiliation: Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.|Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA.
authors.forename: Ekaterina V
authors.initials: EV
authors.lastname: Nizovtseva
authors.affiliation: Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Clauvelin
authors.affiliation: Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA.
authors.forename: Stefjord
authors.initials: S
authors.lastname: Todolli
authors.affiliation: Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA.
authors.forename: Yury S
authors.initials: YS
authors.lastname: Polikanov
authors.affiliation: Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.|Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA.|Biology Faculty, Moscow State University, Moscow 119991, Russia.
authors.forename: Olga I
authors.initials: OI
authors.lastname: Kulaeva
authors.affiliation: Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Wengrzynek
authors.affiliation: Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA.
authors.forename: Wilma K
authors.initials: WK
authors.lastname: Olson
authors.affiliation: Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.|Laboratory of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Vasily M
authors.initials: VM
authors.lastname: Studitsky
mesh_terms: D000818:Animals; D002645:Chickens; D002843:Chromatin / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D004247:DNA