title: Genome-wide identification and functional analysis of long noncoding RNAs involved in the response to graphene oxide.
abstract: Long noncoding RNAs (lncRNAs), which are defined as noncoding RNAs having at least 200 nucleotides, can potentially regulate various biological processes. However, the roles of lncRNAs in regulating cellular response to engineered nanomaterials (ENMs) are still unclear. Using Hiseq 2000 sequencing technique, we performed a genome-wide screen to identify lncRNAs involved in the control of toxicity of graphene oxide (GO) using in vivo Caenorhabditis elegans assay system. HiSeq 2000 sequencing, followed by quantitative analysis, identified only 34 dysregulated lncRNAs in GO exposed nematodes. Bioinformatics analysis implies the biological processes and signaling pathways mediated by candidate lncRNAs involved in the control of GO toxicity. A lncRNAs-miRNAs network possibly involved in the control of GO toxicity was further raised. Moreover, we identified the shared lncRNAs based on the molecular regulation basis for chemical surface modifications and/or genetic mutations in reducing GO toxicity. We further provide direct evidence that these shared lncRNAs, linc-37 and linc-14, were involved in the control of chemical surface modifications and genetic mutations in reducing GO toxicity. linc-37 binding to transcriptional factor FOXO/DAF-16 might be important for the control of GO toxicity. Our whole-genome identification and functional analysis of lncRNAs highlights the important roles of lncRNAs based molecular mechanisms for cellular responses to ENMs in organisms.
authors.affiliation: Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China.
authors.forename: Qiuli
authors.initials: Q
authors.lastname: Wu
authors.affiliation: Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China.
authors.forename: Xiaoxiao
authors.initials: X
authors.lastname: Han
authors.affiliation: Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China.
authors.forename: Yizhou
authors.initials: Y
authors.lastname: Zhuo
authors.affiliation: Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China.
authors.forename: Siting
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China.
authors.forename: Yunli
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China. Electronic address: dayongw@seu.edu.cn.
authors.forename: Dayong
authors.initials: D
authors.lastname: Wang
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000187:drug effects / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics; D005786:Gene Expression Regulation / Q000187:drug effects; D049751:Genome, Helminth / Q000187:drug effects; D006108:Graphite / Q000633:toxicity*; D009153:Mutagens / Q000633:toxicity*; D049329:Nanostructures / Q000633:toxicity*; D010087:Oxides / Q000633:toxicity*; D062085:RNA, Long Noncoding / Q000235:genetics*
chemical_list: D029742:Caenorhabditis elegans Proteins; D009153:Mutagens; D010087:Oxides; D062085:RNA, Long Noncoding; D006108:Graphite
keywords: Caenorhabditis elegans; Chemical modification; Genetic mutation; Graphene oxide; LncRNAs