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Widespread regulation of translation by elongation pausing in heat shock

ABSTRACT: Widespread regulation of translation by elongation pausing in heat shock

PROVIDER: PRJNA147613 | ENA |

REPOSITORIES: ENA

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Widespread regulation of translation by elongation pausing in heat shock

Project description:RNA-seq and ribosome footprinting libraries of mouse 3T3 and human 293T cellsrelated to Shalgi et al. 2013 36bases paired-end RNA-seq, and ribosome footprinting libraries for: 3T3 cells - Control, 8 hours of mild heat shock (42) and 2 hours of severe heat shock (44) - in replicates, as well as 3T3 cells treated by mild followed by severe heat shock. In addition, 3T3 cells treated with Hsp70 inhibitor VER-155008 (Massey et al. 2010), and 293T cells transfected with Hspa1a or GFP, before and after 2 hours of severe heat shock.

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Widespread regulation of translation by elongation pausing in heat shock

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Widespread Alterations in Translation Elongation in the Brain of Fmr1 Knock-Out Mice

Project description:FMRP is a polysome-associated RNA-binding protein encoded by Fmr1 and lost in Fragile X syndrome. Increasing evidence suggests that FMRP regulates both translation initiation and elongation, but the gene-specificity of these effects is unclear. To elucidate the effects of FMRP loss on translation, we used ribosome profiling for genome-wide measurements of ribosomal occupancy and positioning in the cortex of Fmr1 knock-out mice. We found a remarkably coherent reduction in ribosome footprint abundance per mRNA for previously identified, high-affinity mRNA binding partners of FMRP, and an increase for terminal oligo-pyrimidine (TOP) motif-containing genes canonically controlled by mTOR-4EBP-eIF4E signaling. Amino acid motif- and gene-level analyses both showed a widespread reduction of translational pausing in Fmr1 knock-out mice. Our findings are consistent with a model of FMRP-mediated regulation of both translation initiation through eIF4E and elongation that is disrupted in Fragile X syndrome.

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Transformation of elongation factor 1Bdelta into heat shock response transcription factor by alternative splicing

Project description:Protein translation factors play crucial roles in a variety of stress responses. Here, we show that the eukaryotic elongation factor 1Bdelta (eEF1Bdelta) changes its structure and function from a translation factor into a heat shock response transcription factor by alternative splicing. While eEF1Bdelta is specifically localized in the cytoplasm, the long isoform of eEF1Bdelta (eEF1BdeltaL) is localized in the nucleus and induces heat shock element (HSE)-containing genes in cooperation with heat-shock transcription factor 1 (HSF1). Moreover, the N-terminal domain of eEF1BdeltaL binds with NF-E2-related factor 2 (Nrf2) and induces stress response heme oxygenase 1 (HO-1). Specific inhibition of eEF1BdeltaL with siRNA completely inhibits Nrf2-dependent HO-1 induction. In addition, eEF1BdeltaL directly binds to HSE oligo DNA in vitro and associates with HSE containing the HO-1-enhancer region in vivo. Thus, the transcriptional role of eEF1BdeltaL could provide new insights into the molecular mechanism of stress responses. We performed microarray analysis to compare the gene expression induced by eEF1Bdelta1 or eEF1BdeltaL overexpression. HEK293 cells transfected with expression plasmids encoding flag-tagged-eEF1Bdelta1 or eEF1BdeltaL protein

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Project description:Transcriptional regulation in eukaryotes commonly occurs at promoter-proximal regions wherein transcriptionally engaged RNA Polymerase II (Pol II) pauses before proceeding towards productive elongation. The roles of chromatin in this process remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6 regulates transcription elongation by binding to Pol II and anchoring the Negative ELongation Factor NELF, thereby preventing the release of Pol II towards elongation. Absence of SIRT6, or conditions of glucose deprivation, lead to increased levels of acetylated histone H3 at lysines 9 (H3K9ac) and 56 (H3K56ac), activation of the CDK9 kinase, phosphorylation of NELF and Pol II, and recruitment of the transcription factors MYC and BRD4, the PAF1 Complex, as well as several positive elongation factors, in turn releasing Pol II into productive elongation. Collectively, we identified SIRT6 as the first pausing-dedicated histone deacetylase, regulating intragenic H3K9ac and H3K56ac as critical chromatin modifications modulating transcriptional pausing and elongation.

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