Complementarity of end regions increases the lifetime of small RNAs in mammalian cells

PLoS One. 2012;7(9):e44157. doi: 10.1371/journal.pone.0044157. Epub 2012 Sep 12.

Abstract

Two RNAs (4.5SH and 4.5SI) with unknown functions share a number of features: short length (about 100 nt), transcription by RNA polymerase III, predominately nuclear localization, the presence in various tissues, and relatively narrow taxonomic distribution (4 and 3 rodent families, respectively). It was reported that 4.5SH RNA turns over rapidly, whereas 4.5SI RNA is stable in the cell, but their lifetimes remained unknown. We showed that 4.5SH is indeed short-lived (t(1/2)~18 min) and 4.5SI is long-lived (t(1/2)~22 h) in Krebs ascites carcinoma cells. The RNA structures specifying rapid or slow decay of different small cellular RNAs remain unstudied. We searched for RNA structural features that determine the short lifetime of 4.5SH in comparison with the long lifetime of 4.5SI RNA. The sequences of genes of 4.5SH and 4.5SI RNAs were altered and human cells (HeLa) were transfected with these genes. The decay rate of the original and altered RNAs was measured. The complementarity of 16-nt end regions of 4.5SI RNA proved to contribute to its stability in cells, whereas the lack of such complementarity in 4.5SH RNA caused its rapid decay. Possible mechanisms of the phenomenon are discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Half-Life
  • HeLa Cells
  • Humans
  • Mammals / genetics*
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • RNA Stability / genetics*
  • RNA, Small Nuclear / chemistry*
  • RNA, Small Nuclear / genetics*
  • Time Factors
  • Transfection

Substances

  • RNA, Small Nuclear

Grants and funding

The study was supported by the program “Molecular and Cell Biology” of the Russian Academy of Sciences and Russian Foundation for Basic Research (www.rfbr.ru; grant 11-04-00439). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.