title: Identification of up-regulated and down-regulated cis-natural antisense             transcripts in the human B lymphoblastic cell line IM-9 after X-ray irradiation.
abstract: Ionizing radiation (IR) causes DNA injury and induces multiple signal mechanisms, including the regulation of DNA repair, the cell cycle and gene expression through the activation of p53-related pathways. Cis-natural antisense transcripts (cis-NATs), which are transcribed from the DNA strand opposite to that for mRNA of the gene, are recognized as important regulators of gene expression in eukaryotic cells, but the effects on cis-NAT expression by IR are unknown to date. Therefore, we investigated the effects of X-ray irradiation on cis-NAT expression together with mRNA expression using a human B lymphoblast cell line (IM-9), a custom-microarray and strand-specific RT-qPCR. Eighteen, 33 and 106 mRNAs were demonstrated to be differentially expressed in IM-9 cells after 1, 2 and 4 Gy irradiation, respectively, as compared to 0 Gy by microarray analysis (fold change, FC >2.0). On the other hand, 10, 22 and 43 NATs were demonstrated to be differentially expressed in IM-9 cells after 1, 2 and 4 Gy irradiation, respectively, as compared to 0 Gy by microarray analysis (FC >2.0). Among these mRNAs/NATs, the IR dose-dependent up-regulation of mRNAs and cis-NATs of MDM2 and CDKN1A were confirmed by strand-specific RT-qPCR. Additionally, the cis-NATs of MDM2 were indicated to be localized in the cytoplasm, while cis-NATs of CDKN1A were located in the nucleus and cytoplasm. In conclusion, the radiation-responsive cis-NATs in conjunction with mRNAs were identified for the first time in the present study. It is possible that these cis-NATs regulate the gene expression in a post-transcriptional fashion. The IR dose-dependent up- and down-regulation of these mRNAs/cis-NATs may be a marker for ionizing radiation.
authors.affiliation: Department of Biomedical Sciences, Division of Medical Life Sciences, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori 036-8564, Japan. mchiba32@cc.hirosaki-u.ac.jp
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Chiba
authors.forename: Tomisato
authors.initials: T
authors.lastname: Miura
authors.forename: Kosuke
authors.initials: K
authors.lastname: Kasai
authors.forename: Satoru
authors.initials: S
authors.lastname: Monzen
authors.forename: Ikuo
authors.initials: I
authors.lastname: Kashiwakura
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yasue
authors.forename: Toshiya
authors.initials: T
authors.lastname: Nakamura
mesh_terms: D045744:Cell Line, Tumor; D050759:Cyclin-Dependent Kinase Inhibitor p21 / Q000096:biosynthesis; D015536:Down-Regulation / Q000528:radiation effects*; D015973:Gene Expression Regulation, Leukemic / Q000528:radiation effects*; D006801:Humans; D015452:Precursor B-Cell Lymphoblastic Leukemia-Lymphoma / Q000378:metabolism*; D051736:Proto-Oncogene Proteins c-mdm2 / Q000096:biosynthesis; D016372:RNA, Antisense / Q000096:biosynthesis*; D012333:RNA, Messenger / Q000096:biosynthesis; D012334:RNA, Neoplasm / Q000096:biosynthesis*; D014158:Transcription, Genetic / Q000528:radiation effects*; D015854:Up-Regulation / Q000528:radiation effects*; D014965:X-Rays / Q000009:adverse effects
chemical_list: C493956:CDKN1A protein, human; D050759:Cyclin-Dependent Kinase Inhibitor p21; D016372:RNA, Antisense; D012333:RNA, Messenger; D012334:RNA, Neoplasm; C497206:MDM2 protein, human; D051736:Proto-Oncogene Proteins c-mdm2