Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA

Robert D. Bell, Xiaochun Long, Mingyan Lin, Jan H. Bergmann, Vivek Nanda, Sarah L. Cowan, Qian Zhou, Yu Han, David L. Spector, Deyou Zheng, Joseph M. Miano

Research output: Contribution to journalArticle

139 Citations (Scopus)

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 (RNA-seq) 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-seq 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.

Original languageEnglish (US)
Pages (from-to)1249-1259
Number of pages11
JournalArteriosclerosis, Thrombosis, and Vascular Biology
Volume34
Issue number6
DOIs
StatePublished - 2014

Fingerprint

Long Noncoding RNA
Blood Vessels
Smooth Muscle Myocytes
Genes
RNA Sequence Analysis
Reverse Transcription
Cell Movement
RNA
Phenotype
Gene Expression
Polymerase Chain Reaction
Fluorescence In Situ Hybridization
Vascular Smooth Muscle
Smooth Muscle
Coronary Vessels
Endothelial Cells
Complementary DNA
Western Blotting

Keywords

  • cell migration
  • endothelial cells
  • myocytes, smooth muscle
  • RNA sequence
  • RNA, long noncoding

ASJC Scopus subject areas

  • Cardiology and Cardiovascular Medicine

Cite this

Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. / Bell, Robert D.; Long, Xiaochun; Lin, Mingyan; Bergmann, Jan H.; Nanda, Vivek; Cowan, Sarah L.; Zhou, Qian; Han, Yu; Spector, David L.; Zheng, Deyou; Miano, Joseph M.

In: Arteriosclerosis, Thrombosis, and Vascular Biology, Vol. 34, No. 6, 2014, p. 1249-1259.

Research output: Contribution to journalArticle

Bell, RD, Long, X, Lin, M, Bergmann, JH, Nanda, V, Cowan, SL, Zhou, Q, Han, Y, Spector, DL, Zheng, D & Miano, JM 2014, 'Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA', Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 34, no. 6, pp. 1249-1259. https://doi.org/10.1161/ATVBAHA.114.303240
Bell, Robert D. ; Long, Xiaochun ; Lin, Mingyan ; Bergmann, Jan H. ; Nanda, Vivek ; Cowan, Sarah L. ; Zhou, Qian ; Han, Yu ; Spector, David L. ; Zheng, Deyou ; Miano, Joseph M. / Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. In: Arteriosclerosis, Thrombosis, and Vascular Biology. 2014 ; Vol. 34, No. 6. pp. 1249-1259.
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AU - Bell, Robert D.

AU - Long, Xiaochun

AU - Lin, Mingyan

AU - Bergmann, Jan H.

AU - Nanda, Vivek

AU - Cowan, Sarah L.

AU - Zhou, Qian

AU - Han, Yu

AU - Spector, David L.

AU - Zheng, Deyou

AU - Miano, Joseph M.

PY - 2014

Y1 - 2014

N2 - 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 (RNA-seq) 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-seq 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.

AB - 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 (RNA-seq) 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-seq 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.

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KW - endothelial cells

KW - myocytes, smooth muscle

KW - RNA sequence

KW - RNA, long noncoding

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