{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR953/SRR953381/SRR953381.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR953/SRR953384/SRR953384.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR953/SRR953383/SRR953383.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR953/SRR953377/SRR953377.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR953/SRR953379/SRR953379.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR953/SRR953382/SRR953382.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR953/SRR953380/SRR953380.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR953/SRR953378/SRR953378.fastq.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics","Multiomics"],"center_name":["Alla Grishok, Biochemistry and Molecular Biophysics, Columbia University"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA215422"],"scientific_name":["Caenorhabditis elegans"],"tag":["xref:PubMed:24681887"],"long_description":["Argonaute proteins and their small RNA co-factors short interfering RNAs (siRNAs) are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) antisense to germline transcripts and associates with chromatin in a siRNA-dependent manner. However, its role in gene expression regulation remains controversial. Here, we used a genome-wide profiling of nascent RNA transcripts to demonstrate that the CSR-1 RNAi pathway promotes sense-oriented Pol II transcription. Moreover, a loss of CSR-1 function resulted in global increase in antisense transcription and ectopic transcription of silent chromatin domains, which led to reduced chromatin incorporation of centromere-specific histone H3. Based on these findings, we propose that the CSR-1 pathway has a role in maintaining the directionality of active transcription thereby propagating the distinction between transcriptionally active and silent genomic regions. Overall design: GRO-seq (Global Run-On sequencing) for detection of nascent transcripts. Two biological replicates were generated for csr-1 hypomorphic mutant and the corresponding WT samples using ~300,000 worms for each experiment, and two biological replicates were prepared for drh-3 (ne4253) mutant and the corresponding WT samples using ~100,000 worms for each experiment. The GRO-seq were performed in late L3/early L4 stage worms. (8 samples total)"],"repository":["ENA"],"additional_accession":[]},"is_claimable":false,"name":"Caenorhabditis elegans","description":"Global effects of the CSR-1 RNA interference pathway on transcriptional landscape","dates":{"last_updated":"2025-09-24","first_public":"2014-02-28"},"accession":"PRJNA215422","cross_references":{"GEO":["GSE49946"],"taxon":["6239"],"PubMed":["24681887"]}}