Phosphorylation of histone deacetylase 7 by protein kinase D mediates T cell receptor–induced Nur77 expression and apoptosis

The molecular basis of thymocyte negative selection, a crucial mechanism in establishing central tolerance, is not yet resolved. Histone deacetylases (HDACs) have emerged as key transcriptional regulators in several major developmental programs. Recently, we showed that the class IIa member, HDAC7, regulates negative selection by repressing expression of Nur77, an orphan nuclear receptor involved in antigen-induced apoptosis of thymocytes. Engagement of the T cell receptor (TCR) alleviates this repression through phosphorylation-dependent nuclear exclusion of HDAC7. However, the identity of the TCR-activated kinase that phosphorylates and inactivates HDAC7 was still unknown. Here, we demonstrate that TCR-induced nuclear export of HDAC7 and Nur77 expression is mediated by activation of protein kinase D (PKD). Indeed, active PKD stimulates HDAC7 nuclear export and Nur77 expression. In contrast, inhibition of PKD prevents TCR-mediated nuclear exclusion of HDAC7 and associated Nur77 activation. Furthermore, we show that HDAC7 is an interaction partner and a substrate for PKD. We identify four serine residues in the NH2 terminus of HDAC7 as targets for PKD. More importantly, a mutant of HDAC7 specifically deficient in phosphorylation by PKD, inhibits TCR-mediated apoptosis of T cell hybridomas. These findings indicate that PKD is likely to play a key role in the signaling pathways controlling negative selection

Les oncoprotéines FET remodèlent l'épissage alternatif des sarcomes en détournant le complexe LASR

The FET (FUS, EWSR1, TAF15) genes are commonly involved in chromosomal translocations resulting in their fusion with various transcription factors (TF) genes. These genomic abnormalities are hallmarks of several sarcomas and leukemias, and are found along few other alterations in these neoplasms. The chimeric proteins encoded by these fusion genes share a similar architecture, with a strong aminoterminal transactivation domain derived from FET proteins, and a carboxyterminal DNA-binding domain derived from the TF partner. As this structure is reminiscent of that of a TF, the oncogenic potential of FET fusion proteins has been first attributed to their ability to reprogram transcription. However, this transcriptional role is not sufficient to fully explain how these oncoproteins single-handedly drive various cancers. Indeed, growing evidence points towards novel post-transcriptional roles for FET fusions, notably in the alternative splicing of pre-mRNA. Such a function has previously been studied for the prototypical FET fusion EWSR1::FLI1, the main driver of Ewing sarcoma. Interestingly, RBFOX2, an RNA-binding protein (RBP) governing alternative splicing as part of a large assembly of splicing regulators (LASR) complex, has been identified as a key functional partner of EWSR1::FLI1. In this project, we aim to determine whether the pre-mRNA alternative splicing function observed for EWSR1::FLI1 could be a shared mechanism promoting FET fusion-driven oncogenesis. RNA-sequencing of various FET-translocated sarcoma cell lines showed that thousands of alternative splicing events are induced when the expression of the corresponding fusion is prevented. This suggests that FET fusions inforce a specific splicing landscape in their corresponding sarcoma. In addition, we showed that a representative panel of FET fusions promoted exon inclusion of a reporter minigene, but only when directly tethered onto its pre-mRNA, suggesting that the control of splicing by FET fusions might be direct and might rely on its recruitment onto pre-mRNA. As FET fusions lack canonical RNA-binding domains, we hypothesized that endogenous recruitment could be mediated indirectly via an RBP. By performing luciferase-based protein complementation assays, we demonstrated that almost all FET fusions could interact with RBFOX2. Surprisingly, RBFOX2 appeared to preferentially interact with the C-terminal domains of the fusions, which are derived from a wide range of unrelated TFs. RBFOX2 is known to function as part of a hetero-multimeric splicing complex called LASR. Based on our genome-wide splicing analysis analysis, we found that RNA-binding motifs of RBFOX2 and other members of the LASR complex were found enriched in the proximity of differentially regulated cassette exons. We further validated that members of LASR co-immunoprecipitated with FET fusions. Finally, we confirmed the importance of RBFOX2 and other LASR components in the modulation of splicing of endogenous and cancer-related gene targets of FET fusions. Altogether, our work provided evidence supporting a direct role in splicing for FET fusions by interacting with the LASR complex. Although the mechanisms by which the oncoproteins and LASR collaborate to promote oncogenesis remain unclear, we have established a moonlighting function for these driver fusion proteins that could be crucial in our understanding of the tumorigenesis of multiple neoplasms

Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels.

peer reviewed[en] BACKGROUND: Extracellular vesicles (EVs) are released by nearly every cell type and have attracted much attention for their ability to transfer protein and diverse RNA species from donor to recipient cells. Much attention has been given so far to the features of EV short RNAs such as miRNAs. However, while the presence of mRNA and long noncoding RNA (lncRNA) transcripts in EVs has also been reported by multiple different groups, the properties and function of these longer transcripts have been less thoroughly explored than EV miRNA. Additionally, the impact of EV export on the transcriptome of exporting cells has remained almost completely unexamined. Here, we globally investigate mRNA and lncRNA transcripts in endothelial EVs in multiple different conditions. RESULTS: In basal conditions, long RNA transcripts enriched in EVs have longer than average half-lives and distinctive stability-related sequence and structure characteristics including shorter transcript length, higher exon density, and fewer 3' UTR A/U-rich elements. EV-enriched long RNA transcripts are also enriched in HNRNPA2B1 binding motifs and are impacted by HNRNPA2B1 depletion, implicating this RNA-binding protein in the sorting of long RNA to EVs. After signaling-dependent modification of the cellular transcriptome, we observed that, unexpectedly, the rate of EV enrichment relative to cells was altered for many mRNA and lncRNA transcripts. This change in EV enrichment was negatively correlated with intracellular abundance, with transcripts whose export to EVs increased showing decreased abundance in cells and vice versa. Correspondingly, after treatment with inhibitors of EV secretion, levels of mRNA and lncRNA transcripts that are normally highly exported to EVs increased in cells, indicating a measurable impact of EV export on the long RNA transcriptome of the exporting cells. Compounds with different mechanisms of inhibition of EV secretion affected the cellular transcriptome differently, suggesting the existence of multiple EV subtypes with different long RNA profiles. CONCLUSIONS: We present evidence for an impact of EV physiology on the characteristics of EV-producing cell transcriptomes. Our work suggests a new paradigm in which the sorting and packaging of transcripts into EVs participate, together with transcription and RNA decay, in controlling RNA homeostasis and shape the cellular long RNA abundance profile

DHX15-independent roles for TFIP11 in U6 snRNA modification, U4/U6.U5 tri-snRNP assembly and pre-mRNA splicing fidelity

International audienceThe U6 snRNA, the core catalytic component of the spliceosome, is extensively modified post-transcriptionally, with 2’-O-methylation being most common. However, how U6 2’-O-methylation is regulated remains largely unknown. Here we report that TFIP11, the human homolog of the yeast spliceosome disassembly factor Ntr1, localizes to nucleoli and Cajal Bodies and is essential for the 2’-O-methylation of U6. Mechanistically, we demonstrate that TFIP11 knockdown reduces the association of U6 snRNA with fibrillarin and associated snoRNAs, therefore altering U6 2′-O-methylation. We show U6 snRNA hypomethylation is associated with changes in assembly of the U4/U6.U5 tri-snRNP leading to defects in spliceosome assembly and alterations in splicing fidelity. Strikingly, this function of TFIP11 is independent of the RNA helicase DHX15, its known partner in yeast. In sum, our study demonstrates an unrecognized function for TFIP11 in U6 snRNP modification and U4/U6.U5 tri-snRNP assembly, identifying TFIP11 as a critical spliceosome assembly regulator

Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses

Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL), whereas HTLV-2, highly similar to HTLV-1, causes no known overt disease. HTLV gene products are engaged in a dynamic struggle of activating and antagonistic interactions with host cells. Investigations focused on one or a few genes have identified several human factors interacting with HTLV viral proteins. Most of the available interaction data concern the highly investigated HTLV-1 Tax protein. Identifying shared and distinct host-pathogen protein interaction profiles for these two viruses would enlighten how they exploit distinctive or common strategies to subvert cellular pathways toward disease progression.Comparative StudyJournal ArticleResearch Support, N.I.H. ExtramuralResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Phosphorylation of p65(RelA) on Ser547 by ATM Represses NF-κB-Dependent Transcription of Specific Genes after Genotoxic Stress

The NF-κB pathway is involved in immune and inflammation responses, proliferation, differentiation and cell death or survival. It is activated by many external stimuli including genotoxic stress. DNA double-strand breaks activate NF-κB in an ATM-dependent manner. In this manuscript, a direct interaction between p65(RelA) and the N-terminal extremity of ATM is reported. We also report that only one of the five potential ATM-(S/T)Q target sites present in p65, namely Ser547, is specifically phosphorylated by ATM in vitro. A comparative transcriptomic analysis performed in HEK-293 cells expressing either wild-type HA-p65 or a non-phosphorylatable mutant HA-p65S547A identified several differentially transcribed genes after an etoposide treatment (e.g. IL8, A20, SELE). The transcription of these genes is increased in cells expressing the mutant. Substitution of Ser547 to alanine does not affect p65 binding abilities on the κB site of the IL8 promoter but reduces p65 interaction with HDAC1. Cells expressing p65S547A have a higher level of histone H3 acetylated on Lys9 at the IL8 promoter, which is in agreement with the higher gene induction observed. These results indicate that ATM regulates a sub-set of NF-κB dependent genes after a genotoxic stress by direct phosphorylation of p65

Class IIa histone deacetylases: conducting development and differentiation.

The emergence of specialized cell types and their organisation into organs and tissues involve the temporal modulation of many genes that are essential for coordinating the correct timing of instructive signals. These transcriptional changes are orchestrated with a precision that reminds that of a classical symphony. Extracellular signals are transmitted to key integrators, which then orchestrate activation or repression of specific genes. In the last decade, class IIa HDACs have emerged as crucial regulators in various developmental and differentiation processes. This review focuses on the latest studies that have provided new insights into the biological functions of class IIa HDACs and discusses important aspects of their regulation. Elucidating cellular and molecular mechanisms by which functions of class IIa HDACs are modulated could potentially lead to new therapeutic opportunities for various diseases