Transcriptomic analysis of gastric cancer cells in response to stable over-expression of SNORA37

Small nucleolar RNAs (snoRNAs) are a highly conserved category of non-coding RNAs that play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of snoRNAs in regulating gastric cancer progression remain to be determined. We identify that as an ELAVL1-generated 129-nt H/ACA box snoRNA derived from host gene methyl-CpG binding domain protein 2 (MBD2), SNORA37 is a driver of gastric cancer progression. To investigate the mechanisms underlying the functions of SNORA37, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human gastric cancer MKN-45 cells in response to stable over-expression of SNORA37. The results showed that stable over-expression of SNORA37 led to 1521 alternative splicing events in MKN-45 cells. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to SNORA37 over-expression in human gastric cancer cells, and these findings will help us understand the pathogenesis of cancer progression. Total RNA of cells stably transfected with empty vector or SNORA37 was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an llumina Novaseg 6000 platform were performed by Wuhan SeqHealth Technology Co., Ltd. (Wuhan, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value less than 0.05.