Journal
MOLECULAR CELL
Volume 47, Issue 5, Pages 734-745Publisher
CELL PRESS
DOI: 10.1016/j.molcel.2012.06.021
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Funding
- National Institutes of Health-National Center for Research Resources
- Leukemia and Lymphoma Society [3260-07]
- Arnold and Mabel Beckman Foundation
- NIH [1 DP2 OD006412-01]
- United States Public Health Service from the National Cancer Institute [P01-CA42063]
- National Cancer Institute [P30-CA14051]
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C. elegans 21U-RNAs are equivalent to the piRNAs discovered in other metazoans and have important roles in gannetogenesis 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.
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