Molecular Cell
Volume 47, Issue 5, 14 September 2012, Pages 734-745
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Article
Promoters Recognized by Forkhead Proteins Exist for Individual 21U-RNAs

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Summary

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.

Highlights

► A conserved 21U-RNA upstream motif is depleted of nucleosomes ► The CTGTTTCA core of the upstream motif is required for 21U-RNA expression ► Forkhead proteins bind the CTGTTTCA motif and stimulate 21U-RNA production ► Pol II initiates 21U-RNA transcription downstream of the CTGTTTCA motif

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Present address: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA