The PUF family of RNA binding proteins has a conserved role in maintaining stem cell self-renewal. FBF is a C. elegans PUF that is required to maintain germline stem cells (GSCs). To understand how FBF controls GSCs, we sought to identify is target mRNAs. Briefly, we immunoprecipitated FBF-mRNA complexes from worm extracts and then used microarrays to identify the FBF-associated mRNAs. To focus on germline targets of FBF, we used a FBF-GFP transgene under the control of a germline promoter and we used an anti-GFP antibody to purify FBF-GFP from worm extracts. In parallel, we also processed a strain expressing TUBULIN-GFP in the germline to control for mRNAs that non-specifically co-purify with GFP. We found that FBF associates with >1,000 unique mRNAs and likely controls a broad network of key cellular and developmental regulators.
Illumina Genome Analyzer II paired end sequencing; Illumina sequencing of C. elegans dauer exit daf-2(el370) sample 2 DauerExitDAF2-2 polyA+ RNAseq random fragment library RW0001
Illumina Genome Analyzer II paired end sequencing; Illumina sequencing of C. elegans dauer entry daf-2(el370) sample 2 DauerEntryDAF2-2 polyA+ RNAseq random fragment library RW0001
Illumina Genome Analyzer II paired end sequencing; Illumina sequencing of C. elegans dauer daf-2(el370) sample 2 DauerDAF2-2 polyA+ 76bp SE RNAseq random fragment library RW0001
Illumina HiSeq 2000 paired end sequencing; Illumina sequencing of C. elegans dauer daf-2(el370) sample 2-1 DauerDAF2-2-1 polyA+ 100bp PE RNAseq random fragment library RW0001