MEG3 noncoding RNA: a tumor suppressor

Abstract

Maternally expressed gene 3 (MEG3) is an imprinted gene belonging to the imprinted DLK1-MEG3 locus located at chromosome 14q32.3 in humans. Its mouse ortholog, Meg3, also known as gene trap locus 2 (Gtl2), is located at distal chromosome 12. The MEG3 gene encodes a long noncoding RNA (lncRNA) and is expressed in many normal tissues. MEG3 gene expression is lost in an expanding list of primary human tumors and tumor cell lines. Multiple mechanisms contribute to the loss of MEG3 expression in tumors, including gene deletion, promoter hypermethylation, and hypermethylation of the intergenic differentially methylated region. Re-expression of MEG3 inhibits tumor cell proliferation in culture and colony formation in soft agar. This growth inhibition is partly the result of apoptosis induced by MEG3. MEG3 induces accumulation of p53 (TP53) protein, stimulates transcription from a p53-dependent promoter, and selectively regulates p53 target gene expression. Maternal deletion of the Meg3 gene in mice results in skeletal muscle defects and perinatal death. Inactivation of Meg3 leads to a significant increase in expression of angiogenesis-promoting genes and microvessel formation in the brain. These lines of evidence strongly suggest that MEG3 functions as a novel lncRNA tumor suppressor.

Figure 1

(A) Schematic representation of the DLK1–MEG3 locus on human chromosome 14. The DLK1–MEG3 locus is w~837 kb long and consists of three known protein-coding genes including DLK1, RTL1, and DIO3, noncoding RNAs including at least three lncRNAs, and numerous small nucleolar RNAs (snoRNAs) and micro-RNAs (miRNAs). The maternal chromosome is in red and the paternal chromosome in blue. Differentially methylated regions are shown as circles. Filled circle, methylated; open circle, unmethylated. (B) The MEG3 gene is 35 kb long and consists of ten exons. The IG-DMR is ~13 kb upstream of the MEG3 gene. The MEG3-DMR overlaps with the MEG3 promoter.

Figure 2

Hypermethylation of the MEG3 promoter in NFAs. Region 4 of the MEG3 promoter contains 33 CpG dinucleotides. The methylation status of the first 16 CpGs are shown (Zhao et al. 2005). The percentage of methylated CpGs in tumors is in red and that in normal pituitaries is in blue.

Figure 3

Schematic representation of MEG3 RNA isoforms generated by alternative splicing. The common exons are in red. Exon 3a contains 40 extra nucleotides at the 3′-end of the exon 3, which is in gold color. The prevalence of each MEG3 RNA isoform is the average of values from five human tissues and cell lines (Zhang et al. 2010b).

Figure 4

MEG3 RNA folding is predicted by Mfold. The stems and loops of folding are categorized into three groups designated as M1, M2, and M3.