NDLI: Identification of Target Genes Regulated by KSHV miRNAs in KSHV-Infected Lymphoma Cells

Content Provider	Springer Nature Link
Author	Quan, Liangliang Qiu, Tao Liang, Jiulong Li, Miao Zhang, Yu Tao, Kai
Copyright Year	2015
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.
Starting Page	875
Ending Page	880
Page Count	6
File Format	PDF
ISSN	12194956
Journal	Pathology & Oncology Research
Volume Number	21
Issue Number	4
e-ISSN	15322807
Language	English
Publisher	Springer Netherlands
Publisher Date	2015-02-04
Publisher Place	Dordrecht
Access Restriction	Subscribed
Subject Keyword	Kaposi’s sarcoma-associated herpesvirus Gene microRNAs Functional annotation Cancer Research Oncology Pathology Immunology Biomedicine general
Content Type	Text
Resource Type	Article
Subject	Cancer Research Pathology and Forensic Medicine Oncology

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