A thymus-specific noncoding RNA, Thy-ncR1, is a cytoplasmic riboregulator of MFAP4 mRNA in immature T-cell lines

Kazuma Aoki,Tetsuro Hirose,Akira Harashima,Miho Sano,Masayoshi Kibata,Shuji Nakamura,Takahide Yokoi

doi:10.1186/1471-2199-11-99

Abstract

BackgroundPostgenomic transcriptome analyses have identified large numbers of noncoding (nc)RNAs in mammalian cells. However, the biological function of long ncRNAs in mammalian cells remains largely unknown. Our recent expression profiling of selected human long ncRNAs revealed that a majority were expressed in an organ-specific manner, suggesting their function was linked to specific physiological phenomena in each organ. We investigated the characteristics and function of ncRNAs that were specifically expressed in the thymus, the site of T-cell selection and maturation.ResultsExpression profiling of 10 thymus-specific ncRNAs in 17 T-cell leukemia cell lines derived from various stages of T-cell maturation revealed that HIT14168 ncRNA, named Thy-ncR1, was specifically expressed in cell lines derived from stage III immature T cells in which the neighbouring CD1 gene cluster is also specifically activated. The Thy-ncR1 precursor exhibited complex alternative splicing patterns and differential usage of the 5' terminus leading to the production of an estimated 24 isoforms, which were predominantly located in the cytoplasm. Selective RNAi knockdown of each Thy-ncR1 isoform demonstrated that microfibril-associated glycoprotein 4 (MFAP4) mRNA was negatively regulated by two major Thy-ncR1 isoforms. Intriguingly, the MFAP4 mRNA level was controlled by a hUPF1-dependent mRNA degradation pathway in the cytoplasm distinct from nonsense-mediated decay.ConclusionsThis study identified Thy-ncR1 ncRNA to be specifically expressed in stage III immature T cells in which the neighbouring CD1 gene cluster was activated. Complex alternative splicing produces multiple Thy-ncR1 isoforms. Two major Thy-ncR1 isoforms are cytoplasmic riboregulators that suppress the expression of MFAP4 mRNA, which is degraded by an uncharacterized hUPF1-dependent pathway.

Highlights

Postgenomic transcriptome analyses have identified large numbers of noncodingRNAs in mammalian cells
The thymus-specific noncoding RNAs (ncRNAs), Thy-ncR1, is expressed in a subset of leukemia T-cell lines To identify long ncRNAs that are involved in thymusspecific physiological events, we examined a microarray dataset obtained using our original microarray to monitor the expression of human non-protein coding transcripts selected from the H-Invitational database http:// www.h-invitational.jp/hinv/ahg-db/index.jsp[26]. ncRNA-like transcripts that were predominantly expressed in the thymus were selected based on a simple comparison of the microarray signals from human thymus, brain, liver, and testis
The thymus-specificity of each transcript was validated by quantitative reverse transcription polymerase chain reaction using total RNA samples prepared from 11 human organs, including the 4 listed above (Additional file 1 Fig. S1)

Summary

Introduction

Postgenomic transcriptome analyses have identified large numbers of noncoding (nc)RNAs in mammalian cells. The biological function of long ncRNAs in mammalian cells remains largely unknown. A major subset of ncRNAs associates with specific chromosomal loci, where they may play a role in altering chromosomal structure and regulating gene expression. The PRC2 complex was found to associate with hundreds of large intergenic non-coding RNAs (lincRNAs) that were identified by a genome-wide search based on the histone H3K36 code [13]. These data indicate a general long ncRNA function in epigenetic control of gene expression. The MENε/b ncRNAs are essential for nuclear paraspeckle formation through their interaction with specific RNA-binding proteins [14,15,16]

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