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The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules

Lee, Bongyong and Sahoo, Anupama and Marchica, John and Holzhauser, Erwin and Chen, Xiaoli and Li, Jian-Liang and Seki, Tatsuya and Govindarajan, Subramaniam Shyamala and Markey, Fatu Badiane and Batish, Mona and Lokhande, Sonali J. and Zhang, Shaojie and Ray, Animesh and Perera, Ranjan J. (2017) The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules. Science Advances, 3 (5). Art. No. e1602505. ISSN 2375-2548. PMCID PMC5415337.

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Molecular mechanisms by which long noncoding RNA (lncRNA) molecules may influence cancerous condition are poorly understood. The aberrant expression of SPRIGHTLY lncRNA, encoded within the drosophila gene homolog Sprouty-4 intron, is correlated with a variety of cancers, including human melanomas. We demonstrate by SHAPE-seq and dChIRP that SPRIGHTLY RNA secondary structure has a core pseudoknotted 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 (clustered regularly interspaced short palindromic repeats)/Cas9 in melanoma cells significantly decreases SPRIGHTLY lncRNA levels, simultaneously decreases the levels of its interacting pre-mRNA molecules, and 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 an lncRNA’s three-dimensional coordinating role in facilitating cancer-related gene expression in human melanomas.

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Additional Information:© 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. Distributed under a Creative Commons Attribution Noncommercial License 4.0 (CC BY-NC). Submitted 14 October 2016; Accepted 3 March 2017; Published 3 May 2017. We thank Sanford Burnham Prebys Medical Discovery Institute Analytical Genomics Core Facility for deep sequencing, Bioinformatics Core for data analysis support, Histology Core, and Microscope Facility for immunohistochemistry studies, and D. McFadden (Sanford Burnham Prebys Medical Discovery Institute) for formatting the manuscript. This work was supported by NIH grants CA165184 and NCI 5P30CA030199 and Florida Department of Health, Bankhead-Coley Cancer Research Program 5BC08 to R.J.P. and NIH grant DP5 OD012160 to M.B. A.R. is funded by the U.S. Department of Defense (CDMRP #LC150653). Author contributions: B.L., A.R., and R.J.P. incepted the idea, planned the experiment, analyzed data, and wrote the manuscript. A.S. provided support in mouse xenograft studies. E.H., X.C., J.-L.L., S.J.L., T.S., and S.Z. were involved in dChIRP data analysis, SHAPE-seq data analysis, and building of SPRIGHTLY-interacting networks and pathways. J.M. and S.S.G. provided support in generating RNA-seq and SHAPE-seq data. F.B.M. conducted the RNA-FISH experiment. M.B. conducted the RNA-FISH experiment and data analysis. The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors. We do not have any materials obtained through a material transfer agreement. Cell lines and mice were purchased. Data are archived (GSE95597).
Funding AgencyGrant Number
NIHNCI 5P30CA030199
Florida Department of HealthUNSPECIFIED
Bankhead-Coley Cancer Research Program5BC08
NIHDP5 OD012160
Department of DefenseLC150653
Subject Keywords:long noncoding RNA; melanoma; gene regulation; pre-mRNA
Issue or Number:5
PubMed Central ID:PMC5415337
Record Number:CaltechAUTHORS:20170503-130329482
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Official Citation:B. Lee, A. Sahoo, J. Marchica, E. Holzhauser, X. Chen, J.-L. Li, T. Seki, S. S. Govindarajan, F. B. Markey, M. Batish, S. J. Lokhande, S. Zhang, A. Ray, R. J. Perera, The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules. Sci. Adv. 3, e1602505 (2017)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:77160
Deposited By: Tony Diaz
Deposited On:03 May 2017 20:55
Last Modified:03 Oct 2019 17:54

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