Promoters recognized by forkhead proteins exist for individual 21U-RNAs

Mol Cell. 2012 Sep 14;47(5):734-45. doi: 10.1016/j.molcel.2012.06.021. Epub 2012 Jul 19.


C. elegans 21U-RNAs are equivalent to the piRNAs discovered in other metazoans and have important roles in gametogenesis and transposon control. The biogenesis and molecular function of 21U-RNAs and piRNAs are poorly understood. Here, we demonstrate that transcription of each 21U-RNA is regulated separately through a conserved upstream DNA motif. We use genomic analysis to show that this motif is associated with low nucleosome occupancy, a characteristic of many promoters that drive expression of protein-coding genes, and that RNA polymerase II is localized to this nucleosome-depleted region. We establish that the most conserved 8-mer sequence in the upstream region of 21U-RNAs, CTGTTTCA, is absolutely required for their individual expression. Furthermore, we demonstrate that the 8-mer is specifically recognized by Forkhead family (FKH) transcription factors and that 21U-RNA expression is diminished in several FKH mutants. Our results suggest that thousands of small noncoding transcription units are regulated by FKH proteins.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Caenorhabditis elegans / genetics*
  • Forkhead Transcription Factors / metabolism*
  • Gene Expression Profiling
  • Nucleosomes / genetics
  • Promoter Regions, Genetic / genetics*
  • RNA Polymerase II / metabolism
  • RNA, Helminth / genetics*
  • RNA, Small Interfering / genetics*


  • Forkhead Transcription Factors
  • Nucleosomes
  • RNA, Helminth
  • RNA, Small Interfering
  • RNA Polymerase II

Associated data

  • GEO/GSE38253