title: Identification of Target Genes Regulated by KSHV miRNAs in KSHV-Infected Lymphoma Cells.
abstract: This study aimed to identify target genes regulated by KSHV miRNAs in KSHV-infected lymphoma cells. Original Ago HITS-CLIP data of BC-3 and BCBL-1 cell lines were downloaded from SRA database in NCBI, including mRNA and miRNA samples. The raw mRNA reads were mapped into human reference genome hg19 via TopHat for read alignment. PCR duplicates were removed via the SAM tool and the peaks of reads were analyzed via Cufflinks. For miRNA data, the raw data were mapped to the mature miRNA sequences based on miRBase via Bowtie. Peak intersection was computed by using intersectBed in BEDtools. Then, the mature miRNA seeds were identified and then were aligned with 3' UTR merged peaks. The regulationships of miRNAs and their corresponding genes were analyzed based on the signal of RNA-induced silencing complex. Totally, 7 KSHV-related genes regulated by KSHV miRNAs were identified, including IPO5, EDA, NT5C3, WSB1, KCNS1, PRAM1 and MTRNR2L6. Among them, EDA, MTRNR2L6 and IPO5 were regulated by multiple KSHV miRNAs, such as kshv-miR-K12-1-5p, kshv-miR-K12-4-3p and kshv-miR-K12-3-5p, respectively. Furthermore, expression of kshv-miR-K12-1-5p and kshv-miR-K12-3-5p in BCBL-1 cell line were lower than that in BC-3 cell line, conversely, expression of kshv-miR-K12-4-3p in BCBL-1 cell line were higher than that in BC-3 cell line. In conclusion, potential target genes regulated by KSHV miRNAs in KSHV-infected lymphoma cells might play key roles in the nosogenesis of this disease. These findings might provide the basis for deep understanding of KSHV-infected tumors and further molecular experiments.
authors: Department of Plastic Surgery, General Hospital of Shenyang Military Area Command, PLA, No. 83 Wenhua Road, Shenhe District, Shenyang, 110016, Liaoning Province, China.
authors: Liangliang
authors: L
authors: Quan
authors: Tao
authors: T
authors: Qiu
authors: Jiulong
authors: J
authors: Liang
authors: Miao
authors: M
authors: Li
authors: Yu
authors: Y
authors: Zhang
authors: Kai
authors: K
authors: Tao
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D015720:5'-Nucleotidase / Q000235:genetics / Q000378:metabolism; D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism; D053331:Ectodysplasins / Q000235:genetics / Q000378:metabolism; D006023:Glycoproteins / Q000235:genetics / Q000378:metabolism; D019288:Herpesvirus 8, Human / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins; D047908:Intracellular Signaling Peptides and Proteins; D008223:Lymphoma / Q000235:genetics / Q000378:metabolism* / Q000821:virology; D035683:MicroRNAs / Q000235:genetics*; D024642:Potassium Channels, Voltage-Gated / Q000235:genetics / Q000378:metabolism; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics*; D012334:RNA, Neoplasm / Q000235:genetics / Q000378:metabolism*; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D012514:Sarcoma, Kaposi / Q000235:genetics / Q000378:metabolism* / Q000821:virology; D014407:Tumor Cells, Cultured; D028961:beta Karyopherins / Q000235:genetics / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D048868:Adaptor Proteins, Signal Transducing; C506018:EDA protein, human; D053331:Ectodysplasins; D006023:Glycoproteins; C107940:IPO5 protein, human; D036341:Intercellular Signaling Peptides and Proteins; D047908:Intracellular Signaling Peptides and Proteins; C503456:KCNS1 protein, human; C000607374:MTRNR2L1 protein, human; D035683:MicroRNAs; C430907:PRAM1 protein, human; D024642:Potassium Channels, Voltage-Gated; D011506:Proteins; D012333:RNA, Messenger; D012334:RNA, Neoplasm; D012367:RNA, Viral; C120287:WSB1 protein, human; D028961:beta Karyopherins; D015720:5'-Nucleotidase; C412794:NT5C3A protein, human
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