title: Identification of intermediate-size non-coding RNAs involved in the UV-induced DNA damage response in C. elegans.
abstract: BACKGROUND
  A network of DNA damage response (DDR) mechanisms functions coordinately to maintain genome integrity and prevent disease. The Nucleotide Excision Repair (NER) pathway is known to function in the response to UV-induced DNA damage. Although numbers of coding genes and miRNAs have been identified and reported to participate in UV-induced DNA damage response (UV-DDR), the precise role of non-coding RNAs (ncRNAs) in UV-DDR remains largely unknown.
  
  
  RESULTS
  We used high-throughput RNA-sequencing (RNA-Seq) to discover intermediate-size (70-500 nt) ncRNAs (is-ncRNAs) in C. elegans, using the strains of L4 larvae of wild-type (N2), UV-irradiated (N2/UV100) and NER-deficient mutant (xpa-1), and 450 novel non-coding transcripts were initially identified. A customized microarray assay was then applied to examine the expression profiles of both novel transcripts and known is-ncRNAs, and 57 UV-DDR-related is-ncRNA candidates showed expression variations at different levels between UV irradiated strains and non- irradiated strains. The top ranked is-ncRNA candidates with expression differences were further validated by qRT-PCR analysis, of them, 8 novel is-ncRNAs were significantly up-regulated after UV irradiation. Knockdown of two novel is-ncRNAs, ncRNA317 and ncRNA415, by RNA interference, resulted in higher UV sensitivity and significantly decreased expression of NER-related genes in C. elegans.
  
  
  CONCLUSIONS
  The discovery of above two novel is-ncRNAs in this study indicated the functional roles of is-ncRNAs in the regulation of UV-DDR network, and aided our understanding of the significance of ncRNA involvement in the UV-induced DNA damage response.
authors.affiliation: Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Aqian
authors.initials: A
authors.lastname: Li
authors.forename: Guifeng
authors.initials: G
authors.lastname: Wei
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Wang
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhou
authors.forename: Xian-en
authors.initials: XE
authors.lastname: Zhang
authors.forename: Lijun
authors.initials: L
authors.lastname: Bi
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000528:radiation effects; D004249:DNA Damage; D004260:DNA Repair / Q000235:genetics; D005786:Gene Expression Regulation / Q000528:radiation effects; D055785:Gene Knockdown Techniques; D056426:Genetic Loci; D059014:High-Throughput Nucleotide Sequencing; D007814:Larva / Q000235:genetics / Q000528:radiation effects; D020411:Oligonucleotide Array Sequence Analysis; D018510:RNA, Helminth / Q000235:genetics* / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014466:Ultraviolet Rays
chemical_list: D018510:RNA, Helminth; D022661:RNA, Untranslated