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:This study is a high-level comparison of the embryonic brains of Homo sapiens, Macaca mulatta, and Mus musculus using scRNA-seq. This submission includes the novel Macaca mulatta scRNA-seq generated for this study between PCD40 and 100. The supplementary h5ad file contains the meta-atlas including processed data from all 3 species, with annotations from the publication.
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: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: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: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:mRNA decay is a key determinant of gene regulation, initiated by the shortening of mRNA poly(A) tails by the CCR4-NOT deadenylation complex. Specificity is achieved through RNA adaptors—RNA-binding proteins that recruit CCR4-NOT to specific substrate mRNAs in a regulated manner. However, the molecular mechanisms underlying this specificity remain unclear in many cases. In this study, we applied crosslinking MS to investigate the interaction between the fission yeast RNA-binding protein Puf3 and the Ccr4-Not complex.