Project description:In Trypanosoma brucei, most mitochondrial mRNAs undergo U-insertion/deletion editing, and 3′ adenylation and uridylation. The internal sequence changes and terminal extensions are coordinated: Pre-editing addition of the short (A) tail protects the edited transcript against 3′-5′ degradation, while post-editing A/U-tailing renders mRNA competent for ribosome recruitment. Participation of a poly(A) binding protein (PABP) in coupling of editing and 3′ modification processes has been inferred, but its identity and mechanism of action remained elusive. We report identification of KPAF4, a pentatricopeptide repeat-containing PABP which sequesters the A-tail and impedes exonucleolytic degradation. Conversely, KPAF4 inhibits uridylation of A-tailed transcripts and, therefore, premature A/U-tailing of partially-edited mRNAs. This quality check point prevents translation of incompletely edited mRNAs. Our findings also implicate the RNA editing substrate binding complex (RESC) in mediating the interaction between the 5′-end bound pyrophosphohydrolase MERS1 and 3′-end associated KPAF4 to enable mRNA circularization. This event is critical for transcript stability during the editing process.
Project description:The Drosophila ubiquitin receptor dDsk2 associates to chromatin and stabilizes binding of the euchromatic dHP1c/WOC/ROW-complex (dHP1EU) to the transcription-start site (TSS) of active genes ChIP-Seq peak calling of WOC, ROW, Z4, HP1c and Dsk2 against Input sample in Drosophila melanogaster S2 cells
Project description:Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Here, we characterized the RNA-binding landscape of three broadly expressed PABs in Arabidopsis thaliana. We observed substantial variation in the AtPAB-binding efficiency among mRNAs, which can be partly explained by the guanosine (G) content of poly(A) tails. AtPAB-binding efficiency of a gene was positively associated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibited a greater reduction in translational efficiency when AtPAB is depleted. Our study provides a new mechanism that translational efficiency of a gene can be regulated through G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.
Project description:Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054. ArrayExpress Submission Date: Apr 07 2010 ArrayExpress Release Date: Apr 08 2010 Publication Author List: Dominic Schmidt; Michael D Wilson; Benoit Ballester; Petra C Schwalie; Gordon D Brown; Aileen Marshall; Claudia Kutter; Stephen Watt; Celia P Martinez-Jimenz; Sarah MacKay; Iannis Talianidis; Paul Flicek; Duncan T Odom Publication Title: Transcription factor binding evolution in five vertebrates Person Roles: submitter Person Last Name: Flicek Person First Name: Paul Person Email: flicek@ebi.ac.uk Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Person Affiliation: EBI
Project description:The Drosophila ubiquitin receptor dDsk2 associates to chromatin and stabilizes binding of the euchromatic dHP1c/WOC/ROW-complex (dHP1EU) to the transcription-start site (TSS) of active genes
Project description:Deep Sequencing of mRNA from the Drosophila melanogaster S2-DRSC cells that have been RNAi depleted of mRNAs encoding RNA binding proteins. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Analysis of Poly(A)+ RNA from S2-DRSC Cells depleted of mRNAs encoding RNA binding proteins
Project description:Epstein-Barr virus (EBV) expresses several mRNAs produced from intronless genes that could be unfavorably translated in front of cellular spliced mRNAs. To overpass these limitations, the virus encodes a RNA-binding protein (RBP), EB2, which is already known to facilitate nuclear mRNAs export and to increase their translational yield. Here we show that EB2 binds both nuclear and cytoplasmic cap-binding complexes (respectively, CBC and eIF4F), and the poly(A)-binding protein (PABP) to enhance translation initiation of a given mRNP. Interestingly, such effect can be obtained only if EB2 was initially bound to the native mRNPs in the nucleus. We also demonstrate that the EB2-eIF4F-PABP association renders the translation of these mRNPs less sensitive to inhibitors of initiation. Taken together, our new data suggest that EB2 binds and stabilizes cap-binding complexes to increase mRNP translation and demonstrate the importance of the mRNP assembly process in the nucleus to promote translation in the cytoplasm.
Project description:Pabpc1 is the major cytoplasmic poly(A) binding protein in mammalian cells. Pabpc1 functions have been characterized predominantly in context of its binding to 3’ poly(A) tails of mRNAs. Here we performed CLIP-seq to identify additional Pabpc1 binding sites within mammalian mRNAs that may impact on gene regulation. Our analysis revealed that Pabpc1 binds directly to the canonical polyadenylation signal on thousands of mRNAs in the mouse transcriptome. Pabpc1 binding was also observed at sites coincident with the translational initiation and termination sites bracketing open reading frames, exemplified by non-polyadenylated replication-dependent histone mRNAs. A less abundant set of Pabpc1 interactions were mapped to A-rich sites within 5’ UTRs in a restricted subset of mRNAs including Pabpc1 itself. Mechanistic analyses of the subset of 5’UTR-Pabpc1 interactions revealed evidence for auto-regulatory and trans-regulatory translational control mediated by defined A/U-rich elements. These data, in their entirety, demonstrate that the repertoire of Pabpc1 binding and actions is substantially broader than previously recognized and has the potential to impact and coordinate post-transcriptional controls over a critical to an array of cellular functions