title: Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo.
abstract: Increased use of nanomaterials in industry, medicine, and consumer products has raised concerns over their toxicity. To ensure safe use of nanomaterials, understanding their biological effects at the molecular level is crucial. In particular, the regulatory mechanisms responsible for the cascade of genes activated by nanomaterial exposure are not well-characterized. To this end, we profiled the genome-wide usage of gene transcription start sites and linked active enhancer regions in lungs of C57BL/6 mice 24 h after intratracheal instillation of a single dose of the multiwalled carbon nanotube (MWCNT) Mitsui-7. Our results revealed a massive gene regulatory response, where expression of key inflammatory genes (e.g., Csf3, Il24, and Fgf23) was increased >100-fold 24 h after Mitsui-7 exposure. Many of the Mitsui-7-responsive transcription start sites were alternative transcription start sites for known genes, and the number of alternative transcription start sites used in a given gene was correlated with overall Mitsui-7 response. Strikingly, genes that were up-regulated after Mitsui-7 exposure only through their main annotated transcription start site were linked to inflammatory and defense responses, while genes up-regulated only through alternative transcription start sites were functionally heterogeneous and not inflammation-associated. Furthermore, we identified almost 12 000 active enhancers, many of which were Mitsui-7-responsive, and we identified similarly responding putative target genes. Overall, our study provides the location and activity of Mitsui-7-induced enhancers and transcription start sites, providing a useful resource for targeted experiments elucidating the biological effects of nanomaterials and the identification of biomarkers for early detection of MWCNT-induced inflammation.
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.|Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Jette
authors.initials: J
authors.lastname: Bornholdt
authors.affiliation: National Research Centre for the Working Environment , 2100 Copenhagen, Denmark.
authors.forename: Anne Thoustrup
authors.initials: AT
authors.lastname: Saber
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.|Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Berit
authors.initials: B
authors.lastname: Lilje
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.|Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Mette
authors.initials: M
authors.lastname: Boyd
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.|Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Mette
authors.initials: M
authors.lastname: Jørgensen
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.|Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Yun
authors.initials: Y
authors.lastname: Chen
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.|Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Morana
authors.initials: M
authors.lastname: Vitezic
authors.affiliation: National Research Centre for the Working Environment , 2100 Copenhagen, Denmark.
authors.forename: Nicklas Raun
authors.initials: NR
authors.lastname: Jacobsen
authors.affiliation: National Research Centre for the Working Environment , 2100 Copenhagen, Denmark.
authors.forename: Sarah Søs
authors.identifier: 0000-0001-7456-0017
authors.initials: SS
authors.lastname: Poulsen
authors.affiliation: National Research Centre for the Working Environment , 2100 Copenhagen, Denmark.
authors.forename: Trine
authors.initials: T
authors.lastname: Berthing
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Simon
authors.initials: S
authors.lastname: Bressendorff
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.|Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Vitting-Seerup
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Robin
authors.initials: R
authors.lastname: Andersson
authors.affiliation: National Research Centre for the Working Environment , 2100 Copenhagen, Denmark.
authors.forename: Karin Sørig
authors.initials: KS
authors.lastname: Hougaard
authors.affiliation: Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada.
authors.forename: Carole L
authors.initials: CL
authors.lastname: Yauk
authors.affiliation: Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada.
authors.forename: Sabina
authors.initials: S
authors.lastname: Halappanavar
authors.affiliation: National Research Centre for the Working Environment , 2100 Copenhagen, Denmark.|Department of Public Health, University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Håkan
authors.initials: H
authors.lastname: Wallin
authors.affiliation: National Research Centre for the Working Environment , 2100 Copenhagen, Denmark.|Department of Micro and Nanotechnology, Technical University of Denmark , 2800 Kongens Lyngby, Denmark.
authors.forename: Ulla
authors.initials: U
authors.lastname: Vogel
authors.affiliation: The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark.|Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark.
authors.forename: Albin
authors.identifier: 0000-0002-7109-7378
authors.initials: A
authors.lastname: Sandelin
mesh_terms: D000818:Animals; D000089703:Fibroblast Growth Factor-23; D007249:Inflammation / Q000235:genetics / Q000378:metabolism*; D000069555:Injection, Intratympanic; D008168:Lung / Q000187:drug effects* / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D037742:Nanotubes, Carbon / Q000737:chemistry / Q000633:toxicity*; D024363:Transcription Initiation Site / Q000187:drug effects
chemical_list: C000717428:Fgf23 protein, mouse; D037742:Nanotubes, Carbon; D000089703:Fibroblast Growth Factor-23
keywords: CAGE; MWCNT-7; Mitsui-7; TSS; enhancer; inflammation; multiwalled carbon nanotubes