title: Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin.
abstract: The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impact of these nucleosomes on the mutational and transcriptional landscape, and driven by evolutionary selection.
authors.affiliation: Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.|Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Xiong
authors.affiliation: Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.|Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
authors.forename: Shan
authors.initials: S
authors.lastname: Gao
authors.affiliation: Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Wen
authors.initials: W
authors.lastname: Dui
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Wentao
authors.initials: W
authors.lastname: Yang
authors.affiliation: Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Pharmacology and Molecular Sciences and The Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Sean D
authors.initials: SD
authors.lastname: Taverna
authors.affiliation: Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada.
authors.forename: Ronald E
authors.initials: RE
authors.lastname: Pearlman
authors.affiliation: Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada.
authors.forename: Wendy
authors.initials: W
authors.lastname: Ashlock
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China miaowei@ihb.ac.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Miao
authors.affiliation: Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA yifan@med.umich.edu.
authors.forename: Yifan
authors.initials: Y
authors.lastname: Liu
mesh_terms: D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D004257:DNA Polymerase II / Q000235:genetics / Q000378:metabolism; D048648:Macronucleus / Q000235:genetics* / Q000378:metabolism; D008836:Micrococcal Nuclease / Q000235:genetics / Q000378:metabolism; D048631:Micronucleus, Germline / Q000235:genetics; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D022821:RNA Splice Sites; D016808:Tetrahymena thermophila / Q000235:genetics*; D024363:Transcription Initiation Site
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D022821:RNA Splice Sites; D004257:DNA Polymerase II; D008836:Micrococcal Nuclease