Argonaute proteins of the PIWI clade are central to transposon silencing in animal gonads. Their target specificity is defined by 23-30 nt PIWI interacting RNAs (piRNAs), which mostly originate from discrete genomic loci termed piRNA clusters. Here, we show that a complex composed of Rhino, Deadlock, and Cutoff (RDC) defines dual-strand piRNA clusters genome-wide in Drosophila ovaries. The RDC is anchored to H3K9me3-marked chromatin in part via Rhino's chromodomain. Depletion of Piwi results in loss of the RDC and small RNAs at a subset of piRNA clusters, demonstrating a feedback loop between Piwi and piRNA source loci. Intriguingly, profiles of RNA polymerase II occupancy, nascent transcription, and steady-state RNA levels reveal that the RDC licenses noncanonical transcription of dual-strand piRNA clusters. Likely, this process involves 5' end protection of nascent RNAs and suppression of transcription termination. Our data provide key insight into the regulation and evolution of piRNA clusters.
Sample name | Organism | Experiment title | Sample type | Library instrument | Attributes | |||||||||||||||||||||||||||||||||||||||||||||||||
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chip antibody | chip antibody vendor | development stage | germline knock-down | molecule subtype | sex | source name | tissue | |||||||||||||||||||||||||||||||||||||||||||||||
ribosomal RNA depleted total RNA from control germline knock-down ovaries, replicate 1 | Drosophila melanogaster | GSM1346535: ribosomal RNA depleted total RNA from control germline knock-down ovaries, replicate 1; Drosophila melanogaster; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | 4-6 days old adult | control | female | ribosomal RNA depleted total RNA from control germline knock-down ovaries | ovary | |||||||||||||||||||||||||||||||||||||||||||||
5'-capped RNA from control germline knock-down ovaries | Drosophila melanogaster | GSM1346542: 5'-capped RNA from control germline knock-down ovaries; Drosophila melanogaster; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | 4-6 days old adult | control | female | 5'-capped RNA from control germline knock-down ovaries | ovary | |||||||||||||||||||||||||||||||||||||||||||||
nascent RNA from global nuclear run on (GRO) in rhino germline knock-down ovaries | Drosophila melanogaster | GSM1346541: nascent RNA from global nuclear run on (GRO) in rhino germline knock-down ovaries; Drosophila melanogaster; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | 4-6 days old adult | rhino | female | nascent RNA from global nuclear run on (GRO) in rhino germline knock-down ovaries | ovary | |||||||||||||||||||||||||||||||||||||||||||||
nascent RNA from global nuclear run on (GRO) in control germline knock-down ovaries | Drosophila melanogaster | GSM1346540: nascent RNA from global nuclear run on (GRO) in control germline knock-down ovaries; Drosophila melanogaster; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | 4-6 days old adult | control | female | nascent RNA from global nuclear run on (GRO) in control germline knock-down ovaries | ovary | |||||||||||||||||||||||||||||||||||||||||||||
small RNAs from a Piwi-IP in piwi germline knock-down ovaries (=somatic piRNAs) | Drosophila melanogaster | GSM1346534: small RNAs from a Piwi-IP in piwi germline knock-down ovaries (=somatic piRNAs); Drosophila melanogaster; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | 4-6 days old adult | piwi | small RNA | female | small RNAs from a Piwi-IP in piwi germline knock-down ovaries (=somatic piRNAs) | ovary |