Identification and Initial Functional Characterization of a Human Vascular Cell-Enriched Long Noncoding RNA

Bell, R. D., Long, X., Lin, M., Bergmann, J. H., Nanda, V., Cowan, S. L., Zhou, Q., Han, Y., Spector, D. L., Zheng, D., Miano, J. M. (2014) Identification and Initial Functional Characterization of a Human Vascular Cell-Enriched Long Noncoding RNA. Arteriosclerosis, thrombosis, and vascular biology, 34 (6). pp. 1249-1259. ISSN 1079-5642

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URL: http://www.ncbi.nlm.nih.gov/pubmed/24578380
DOI: 10.1161/atvbaha.114.303240

Abstract

OBJECTIVE: Long noncoding RNAs (lncRNAs) represent a rapidly growing class of RNA genes with functions related primarily to transcriptional and post-transcriptional control of gene expression. There is a paucity of information about lncRNA expression and function in human vascular cells. Thus, we set out to identify novel lncRNA genes in human vascular smooth muscle cells and to gain insight into their role in the control of smooth muscle cell phenotypes. APPROACH AND RESULTS: RNA sequencing of human coronary artery smooth muscle cells revealed 31 unannotated lncRNAs, including a vascular cell-enriched lncRNA (smooth muscle and endothelial cell-enriched migration/differentiation-associated long noncoding RNA [SENCR]). Strand-specific reverse transcription polymerase chain reaction (PCR) and rapid amplification of cDNA ends indicate that SENCR is transcribed antisense from the 5' end of the FLI1 gene and exists as 2 splice variants. RNA fluorescence in situ hybridization and biochemical fractionation studies demonstrate SENCR is a cytoplasmic lncRNA. Consistent with this observation, knockdown studies reveal little to no cis-acting effect of SENCR on FLI1 or neighboring gene expression. RNA-sequencing experiments in smooth muscle cells after SENCR knockdown disclose decreased expression of Myocardin and numerous smooth muscle contractile genes, whereas several promigratory genes are increased. Reverse transcription PCR and Western blotting experiments validate several differentially expressed genes after SENCR knockdown. Loss-of-function studies in scratch wound and Boyden chamber assays support SENCR as an inhibitor of smooth muscle cell migration. CONCLUSIONS: SENCR is a new vascular cell-enriched, cytoplasmic lncRNA that seems to stabilize the smooth muscle cell contractile phenotype.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNA expression
Investigative techniques and equipment > assays > RNA-seq
CSHL Authors:
Communities: CSHL Cancer Center Program > Gene Regulation and Cell Proliferation
CSHL labs > Spector lab
CSHL Cancer Center Shared Resources > Microscopy Service
Depositing User: Matt Covey
Date Deposited: 07 Mar 2014 16:53
Last Modified: 28 Oct 2015 16:23
PMCID: PMC4024079
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29571

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