Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions

Endocrinology. 2010 Mar;151(3):939-47. doi: 10.1210/en.2009-0657. Epub 2009 Dec 23.


Maternally expressed gene 3 (MEG3) is an imprinted gene highly expressed in the human pituitary. However, MEG3 expression is lost in human gonadotroph-derived pituitary adenomas and most human tumor cell lines. Expression of MEG3 in tumor cells results in growth suppression, p53 protein increase, and activation of p53 downstream targets. The MEG3 gene encodes a noncoding RNA of approximately 1700 nucleotides. There are 12 different MEG3 gene transcripts, generated by alternative splicing. They contain the common exons 1-3 and exons 8-10, but each uses one or more exons 4-7 in a different combination in the middle. MEG3 isoform expression patterns are tissue and cell type specific. Functionally, each isoform stimulates p53-mediated transactivation and suppresses tumor cell growth. We analyzed the secondary RNA folding structure of each MEG3 isoform, using the computer program mfold. All MEG3 RNA isoforms contain three distinct secondary folding motifs M1, M2, and M3. Deletion analysis showed that motifs M2 and M3 are important for p53 activation. Furthermore, a hybrid MEG3 RNA, containing a piece of artificially synthesized sequence different from the wild type but folding into a similar secondary structure, retained the functions of both p53 activation and growth suppression. These results support the hypothesis that a proper folding structure of the MEG3 RNA molecule is critical for its biological functions. This study establishes for the first time the structure-function relationship of a large noncoding RNA and provides a first look into the molecular mechanisms of the biological functions of a large noncoding RNA.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cell Line
  • DNA, Complementary / chemistry
  • Gene Expression
  • Humans
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Pituitary Neoplasms / metabolism
  • Proteins / genetics*
  • Proteins / metabolism
  • RNA, Long Noncoding
  • RNA, Untranslated / chemistry*
  • Structure-Activity Relationship
  • Tumor Suppressor Protein p53 / metabolism


  • DNA, Complementary
  • MEG3 non-coding RNA, human
  • Proteins
  • RNA, Long Noncoding
  • RNA, Untranslated
  • Tumor Suppressor Protein p53