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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 Fordhead family (FKH) transcription factors and that 21U-RNA expression is diminished in several FKH mutants. Our results demonstrate a novel paradigm for simultaneous regulation of thousands of small non-coding transcription units.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE38253 | GEO | 2012/05/29

SECONDARY ACCESSION(S): PRJNA167637

REPOSITORIES: GEO

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Promoters Recognized by Forkhead Proteins Exist for Individual 21U-RNAs

Project description: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 Fordhead family (FKH) transcription factors and that 21U-RNA expression is diminished in several FKH mutants. Our results demonstrate a novel paradigm for simultaneous regulation of thousands of small non-coding transcription units. Comparisons of H3 and H2B positions on Chromosome 4 relative to the positions of 21U-RNAs.

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C. elegans piRNAs are processed from capped-small RNAs transcribed at promoters throughout the genome

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