Project description:Transfer RNA (tRNA)-derived fragments (tRF) are emerging small noncoding (nc) RNAs that, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here we show that pseudouridylation (Ψ) of a stem-cell-enriched tRF subtype, mTOG, selectively inhibits malignant protein synthesis programs, thereby promoting engraftment and differentiation of myelodysplastic syndrome (MDS) hematopoietic stem and progenitor cells (HSPC). Building on evidence that mTOG-Ψ target the polyadenylate-binding protein cytoplasmic 1 (PABPC1), we employed HDX-MS to reveal critical interactions between mTOG and functional RNA-recognition motif (RRM) domains in PABPC1. Mechanistically, this hinders the recruitment of the translational co-activator PABPC1-interacting protein 1 (PAIP1) and strongly represses translation of transcripts sharing 5’UTR pyrimidine-enriched sequences (PES), including 5’ terminal oligopyrimidine tracts (TOP) that encode protein machinery components, and are frequently altered in cancer. Significantly, mTOG dysregulation leads to aberrantly increased 5’PES mRNA translation in malignant MDS-HSPC and is clinically associated with leukemic transformation and reduced patient survival. Taken together, these results define a critical role for tRF and Ψ in difficult-to-treat subsets of MDS characterized by high risk of progression to acute myeloid leukemia.
Project description:Because HES1 maintained PP6 protein level without affecting its mRNA level, we asked if HES1 directly interacted with PP6 in keratinocytes.
Project description:Stress Granule formation has been linked to the resistance of some cancer cells to chemotherapeutic intervention. A number of studies have proposed that certain anti-tumor compounds promote cancer cell survival by inducing Stress Granules formation, leading to increased cellular fitness and apoptosis avoidance. Here we show that a potent fatty acid synthase inhibitor, fasnall, known for its anti-tumor capabilities, triggers the formation of non-canonical Stress Granules with a faster clearing and internal dynamics kinetics independently of fatty acid synthase inhibition. PABPC1 BioID interactomes in fasnall, and arsenite conditions were obtained.
Project description:Ribosome immunoprecipitates of cardiomyocytes isolated from Rpl3l-/- and Rpl3l+/+ mouse hearts were analysed using mass spectrometry.
Project description:The Myc-Max heterodimer has been thought of as a sequence specific DNA binding protein that regulates transcription of a large number of genes. We demonstrate here that the positions of the human genome occupied by Myc-Max correlate with the RNA polymerase II (Pol II) transcription complex rather than to the canonical DNA binding sequence element CACGTG. The heterodimer is positioned slightly upstream of essentially all promoter proximal paused polymerases and is found throughout the transcribed regions of genes. Using a multi-genome analysis of promoter regions we show that the heterodimers are oriented with respect to the direction of transcription with Myc downstream of Max. In strong support of a model in which the Myc is recruited by transcription complexes rather than specific DNA sequences, we found that the difference in affinities of Myc-Max heterodimers for CACGTG versus non-specific DNA is not great enough to drive the pattern of genome occupancy exhibited. A total of 2 ChIP-Seq data for Myc and Max in human HeLa cell.
Project description:PABPC1 mediated protein synthesis control might be important for chronic myeloid leukemia (CML) disease progression. Here, we use the PABPC1 enhanced cross-linking and immunoprecipitation sequencing (eCLIP-seq) to capture PABPC1 directly bound RNAs as well as the ribosome profiling (Ribo-seq) to examine the ribosome protected mRNA fragments in control and PABPC1 silenced K562 cells. We integrated the eCLIP-seq and Ribo-seq data and found that 1496 out of the 6840 PABPC1 directly bound genes, significantly reduced their translation efficiency in PABPC1 silenced K562 cells. Strikingly, the 1496 genes with reduced translational efficiency enriched significant numbers of leukemogenesis oncogenes, such as BCR-ABL1, RPL22, SKP1, and MYCBP. Among them, BCR-ABL1 mRNA translation was the most vigorous, which was also most influenced by PABPC1. Furthermore, we found that PABPC1 inhibition significantly suppressed the BCR-ABL1 downstream gene network in K562 cells (q value<0.001), indicating that BCR-ABL1 might be one of the main targets of PABPC1 in K562 cells.
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