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The long noncoding RNA SPRIGHTLY acts as an intra-nuclear organizing hub for pre-mRNA molecules.

ABSTRACT: We report the application of domain-specific chromatin isolation by RNA purification (dChIRP) to identify RNA binding partners of long coding RNA, SPRIGHTLY. We demonstrate by SHAPE-Seq and dChIRP that SPRIGHTLY RNA secondary structure has a core pseudo-knotted domain. This lncRNA interacts with the intronic regions of six pre-mRNAs: SOX5, SMYD3, SND1, MEOX2, DCTN6, and RASAL2, all of which have cancer related functions. Hemizygous knockout of SPRIGHTLY by CRISPR/Cas9 in melanoma cells significantly decreases SPRIGHTLY lncRNA levels, simultaneously decreases the levels of its interacting pre-mRNA molecules, decreases anchorage-independent growth rate of cells, and the rate of in vivo tumor growth in mouse xenografts. These results provide the first demonstration of a lncRNA’s 3-dimensional coordinating role in facilitating cancer-related gene expression in human melanomas.

ORGANISM(S): Homo sapiens

PROVIDER: GSE95597 | GEO | 2017/06/09

SECONDARY ACCESSION(S): PRJNA377614

REPOSITORIES: GEO

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Project description:SET (Su) and MYND (myeloid-Nervy-DEAF-1) domain-containing protein (SMYD) is a methyltransferase family, including five members of which SMYD1, SMYD2, SMYD3 and SMYD4, has been found to play critical roles in human carcinogenesis. It has been demonstrated that the altered expression of SMYD3 is associated with the progression of several solid tumors, including bladder cancer, glioma, gastric cancer, prostate cancer and colorectal cancer. Several trials have explored the effects of SMYD3 overexpression on proliferation, viability, cancer cells migration and invasion. The series of elegant experiments suggested that SMYD3 could serve as a potential biomarker for clinically aggressive disease and an attractive therapeutic target. In our previous study (PMID: 26980013), we found SMYD3 expression is frequently upregulated in human esophageal squamous cell carcinoma (ESCC) clinical tissues, correlating with overall survival of ESCC patients. RNAi-mediated knockdown of SMYD3 suppressed ESCC cell proliferation, migration and invasion in vitro, and inhibited local tumor invasion in vivo. To identify genes and biological pathways associated with SMYD3 functions and mechanism, SMYD3 was knockdowned bypGLV3/H1/GFP/+Puro Vector in ESCC cell line KYSE150 with an empty plasmid as a control, these two cells were applied for mRNA expression profile analyses to find the differentially expressed genes using GeneChipÂ® PrimeViewâ¢ Human Gene Expression Array. shRNA sequences targeting SMYD3 was ligated into the pGLV3/H1/GFP/+Puro Vector and transfected into ESCC cell line KYSE150 with an empty plasmid as a control. The mRNA expression profiles of SMYD3 knockdown was analyzed by GeneChipÂ®Â PrimeViewâ¢Â HumanÂ Gene Expression Array (Affymetrix,Â USA). The knockdown of SMYD3 was confirmed by QRT-PCR and Western blot. Total RNAs from SMYD3 knockdown cells and control cells were extracted for GeneChipÂ® PrimeViewâ¢ Human Gene Expression Array.

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The long noncoding RNA SPRIGHTLY acts as an intra-nuclear organizing hub for pre-mRNA molecules.

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