title: Promoters recognized by forkhead proteins exist for individual 21U-RNAs.
abstract: 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.
authors: Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
authors: Germano
authors: G
authors: Cecere
authors: Grace X Y
authors: GX
authors: Zheng
authors: Andres R
authors: AR
authors: Mansisidor
authors: Katherine E
authors: KE
authors: Klymko
authors: Alla
authors: A
authors: Grishok
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D051858:Forkhead Transcription Factors / Q000378:metabolism*; D020869:Gene Expression Profiling; D009707:Nucleosomes / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012319:RNA Polymerase II / Q000378:metabolism; D018510:RNA, Helminth / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*
chemical_list: D051858:Forkhead Transcription Factors; D009707:Nucleosomes; D018510:RNA, Helminth; D034741:RNA, Small Interfering; D012319:RNA Polymerase II