Drosophila Ge-1 Promotes P Body Formation and oskar mRNA Localization

mRNA localization coupled with translational control is a widespread and conserved strategy that allows the localized production of proteins within eukaryotic cells. In Drosophila, oskar (osk) mRNA localization and translation at the posterior pole of the oocyte are essential for proper patterning of the embryo. Several P body components are involved in osk mRNA localization and translational repression, suggesting a link between P bodies and osk RNPs. In cultured mammalian cells, Ge-1 protein is required for P body formation. Combining genetic, biochemical and immunohistochemical approaches, we show that, in vivo, Drosophila Ge-1 (dGe-1) is an essential gene encoding a P body component that promotes formation of these structures in the germline. dGe-1 partially colocalizes with osk mRNA and is required for osk RNP integrity. Our analysis reveals that although under normal conditions dGe-1 function is not essential for osk mRNA localization, it becomes critical when other components of the localization machinery, such as staufen, Drosophila decapping protein 1 and barentsz are limiting. Our findings suggest an important role of dGe-1 in optimization of the osk mRNA localization process required for patterning the Drosophila embryo

Early Experience of Helical Tomotherapy for Hepatobiliary Radiotherapy

Helical tomotherapy (HT), an image-guided, intensity-modulated, radiation therapy technique, allows for precise targeting while sparing normal tissues. We retrospectively assessed the feasibility and tolerance of the hepatobiliary HT in 9 patients. A total dose of 54 to 60 Gy was prescribed (1.8 or 2 Gy per fraction) with concurrent capecitabine for 7 patients. There were 1 hepatocarcinoma, 3 cholangiocarcinoma, 4 liver metastatic patients, and 1 pancreatic adenocarcinoma. All but one patient received previous therapies (chemotherapy, liver radiofrequency, and/or surgery). The median doses delivered to the normal liver and to the right kidney were 15.7 Gy and 4.4 Gy, respectively, below the recommended limits for all patients. Most of the treatment-related adverse events were transient and mild in severity. With a median followup of 12 months, no significant late toxicity was noted. Our results suggested that HT could be safely incorporated into the multidisciplinary treatment of hepatobiliary or pancreatic malignant disease

Systematic mapping of rRNA 2'-O methylation during frog development and involvement of the methyltransferase Fibrillarin in eye and craniofacial development in Xenopus laevis..

peer reviewedRibosomes are essential nanomachines responsible for protein production. Although ribosomes are present in every living cell, ribosome biogenesis dysfunction diseases, called ribosomopathies, impact particular tissues specifically. Here, we evaluate the importance of the box C/D snoRNA-associated ribosomal RNA methyltransferase fibrillarin (Fbl) in the early embryonic development of Xenopus laevis. We report that in developing embryos, the neural plate, neural crest cells (NCCs), and NCC derivatives are rich in fbl transcripts. Fbl knockdown leads to striking morphological defects affecting the eyes and craniofacial skeleton, due to lack of NCC survival caused by massive p53-dependent apoptosis. Fbl is required for efficient pre-rRNA processing and 18S rRNA production, which explains the early developmental defects. Using RiboMethSeq, we systematically reinvestigated ribosomal RNA 2'-O methylation in X. laevis, confirming all 89 previously mapped sites and identifying 15 novel putative positions in 18S and 28S rRNA. Twenty-three positions, including 10 of the new ones, were validated orthogonally by low dNTP primer extension. Bioinformatic screening of the X. laevis transcriptome revealed candidate box C/D snoRNAs for all methylated positions. Mapping of 2'-O methylation at six developmental stages in individual embryos indicated a trend towards reduced methylation at specific positions during development. We conclude that fibrillarin knockdown in early Xenopus embryos causes reduced production of functional ribosomal subunits, thus impairing NCC formation and migration

Ribosomal RNA 2′O-methylation as a novel layer of inter-tumour heterogeneity in breast cancer

International audienceRecent epitranscriptomics studies unravelled that ribosomal RNA (rRNA) 2′O-methylation is an additional layer of gene expression regulation highlighting the ribosome as a novel actor of translation control. However, this major finding lies on evidences coming mainly, if not exclusively, from cellular models. Using the innovative next-generation RiboMeth-seq technology, we established the first rRNA 2′O-methylation landscape in 195 primary human breast tumours. We uncovered the existence of compulsory/stable sites, which show limited inter-patient variability in their 2′O-methylation level, which map on functionally important sites of the human ribosome structure and which are surrounded by variable sites found from the second nucleotide layers. Our data demonstrate that some positions within the rRNA molecules can tolerate absence of 2′O-methylation in tumoral and healthy tissues. We also reveal that rRNA 2′O-methylation exhibits intra- and inter-patient variability in breast tumours. Its level is indeed differentially associated with breast cancer subtype and tumour grade. Altogether, our rRNA 2′O-methylation profiling of a large-scale human sample collection provides the first compelling evidence that ribosome variability occurs in humans and suggests that rRNA 2′O-methylation might represent a relevant element of tumour biology useful in clinic. This novel variability at molecular level offers an additional layer to capture the cancer heterogeneity and associates with specific features of tumour biology thus offering a novel targetable molecular signature in cancer

Structural and functional analysis of the Rous Sarcoma virus negative regulator of splicing and demonstration of its activation by the 9G8 SR protein

Retroviruses require both spliced and unspliced RNAs for replication. Accumulation of Rous Sarcoma virus (RSV) unspliced RNA depends upon the negative regulator of splicing (NRS). Its 5′-part is considered as an ESE binding SR proteins. Its 3′-part contains a decoy 5′-splice site (ss), which inhibits splicing at the bona fide 5′-ss. Only the 3D structure of a small NRS fragment had been experimentally studied. Here, by chemical and enzymatic probing, we determine the 2D structure of the entire RSV NRS. Structural analysis of other avian NRSs and comparison with all sequenced avian NRSs is in favour of a phylogenetic conservation of the NRS 2D structure. By combination of approaches: (i) in vitro and in cellulo splicing assays, (ii) footprinting assays and (iii) purification and analysis of reconstituted RNP complex, we define a small NRS element retaining splicing inhibitory property. We also demonstrate the capability of the SR protein 9G8 to increase NRS activity in vitro and in cellulo. Altogether these data bring new insights on how NRS fine tune splicing activity

Ribosomal RNA-based epitranscriptomic regulation of chondrocyte translation and proteome in osteoarthritis

OBJECTIVE: Osteoarthritis-related cartilage extracellular matrix remodeling is dependent on changes in chondrocyte protein expression. Yet, the role of ribosomes in chondrocyte translation regulation is unknown. In this exploratory study, we investigated ribosomal RNA (rRNA) epitranscriptomic-based ribosome heterogeneity in human articular chondrocytes and its relevance for osteoarthritis. METHODS: Sequencing-based rRNA 2'-O-methylation profiling analysis (RiboMethSeq) was performed on non-OA primary human articular chondrocytes (n = 5) exposed for 14 days to osteoarthritic synovial fluid (14 donors, pooled, 20% v/v). The SW1353 SNORD71 KO cell pool was generated using LentiCRISPRv2/Cas9. The mode of translation initiation and fidelity were determined by dual-luciferase reporters. The cellular proteome was analyzed by LC-MS/MS and collagen type I protein expression was evaluated by immunoblotting. Loading of COL1A1 mRNA into polysomes was determined by sucrose gradient ultracentrifugation and fractionation. RESULTS: We discovered that osteoarthritic synovial fluid instigates site-specific changes in the rRNA 2'-O-me profile of primary human articular chondrocytes. We identified five sites with differential 2'-O-me levels. The 2'-O-me status of 5.8S-U14 (one of identified differential 2'-O-me sites; decreased by 7.7%, 95% CI [0.9-14.5%]) was targeted by depleting the level of its guide snoRNA SNORD71 (50% decrease, 95% CI [33-64%]). This resulted in an altered ribosome translation modus (e.g., CrPV IRES, FC 3, 95% CI [2.2-4.1]) and promoted translation of COL1A1 mRNA which led to increased levels of COL1A1 protein (FC 1.7, 95% CI [1.3-2.0]). CONCLUSIONS: Our data identify a novel concept suggesting that articular chondrocytes employ rRNA epitranscriptomic mechanisms in osteoarthritis development

Estimates of ozone return dates from Chemistry-Climate Model Initiative simulations

We analyse simulations performed for the Chemistry-Climate Model Initiative (CCMI) to estimate the return dates of the stratospheric ozone layer from depletion caused by anthropogenic stratospheric chlorine and bromine. We consider a total of 155 simulations from 20 models, including a range of sensitivity studies which examine the impact of climate change on ozone recovery. For the control simulations (unconstrained by nudging towards analysed meteorology) there is a large spread (±20DU in the global average) in the predictions of the absolute ozone column. Therefore, the model results need to be adjusted for biases against historical data. Also, the interannual variability in the model results need to be smoothed in order to provide a reasonably narrow estimate of the range of ozone return dates. Consistent with previous studies, but here for a Representative Concentration Pathway (RCP) of 6.0, these new CCMI simulations project that global total column ozone will return to 1980 values in 2049 (with a 1σ uncertainty of 2043–2055). At Southern Hemisphere mid-latitudes column ozone is projected to return to 1980 values in 2045 (2039–2050), and at Northern Hemisphere mid-latitudes in 2032 (2020–2044). In the polar regions, the return dates are 2060 (2055–2066) in the Antarctic in October and 2034 (2025–2043) in the Arctic in March. The earlier return dates in the Northern Hemisphere reflect the larger sensitivity to dynamical changes. Our estimates of return dates are later than those presented in the 2014 Ozone Assessment by approximately 5–17 years, depending on the region, with the previous best estimates often falling outside of our uncertainty range. In the tropics only around half the models predict a return of ozone to 1980 values, around 2040, while the other half do not reach the 1980 value. All models show a negative trend in tropical total column ozone towards the end of the 21st century. The CCMI models generally agree in their simulation of the time evolution of stratospheric chlorine and bromine, which are the main drivers of ozone loss and recovery. However, there are a few outliers which show that the multi-model mean results for ozone recovery are not as tightly constrained as possible. Throughout the stratosphere the spread of ozone return dates to 1980 values between models tends to correlate with the spread of the return of inorganic chlorine to 1980 values. In the upper stratosphere, greenhouse gas-induced cooling speeds up the return by about 10–20 years. In the lower stratosphere, and for the column, there is a more direct link in the timing of the return dates of ozone and chlorine, especially for the large Antarctic depletion. Comparisons of total column ozone between the models is affected by different predictions of the evolution of tropospheric ozone within the same scenario, presumably due to differing treatment of tropospheric chemistry. Therefore, for many scenarios, clear conclusions can only be drawn for stratospheric ozone columns rather than the total column. As noted by previous studies, the timing of ozone recovery is affected by the evolution of N2O and CH4. However, quantifying the effect in the simulations analysed here is limited by the few realisations available for these experiments compared to internal model variability. The large increase in N2O given in RCP 6.0 extends the ozone return globally by ∼15 years relative to N2O fixed at 1960 abundances, mainly because it allows tropical column ozone to be depleted. The effect in extratropical latitudes is much smaller. The large increase in CH4 given in the RCP 8.5 scenario compared to RCP 6.0 also lengthens ozone return by ∼15 years, again mainly through its impact in the tropics. Overall, our estimates of ozone return dates are uncertain due to both uncertainties in future scenarios, in particular those of greenhouse gases, and uncertainties in models. The scenario uncertainty is small in the short term but increases with time, and becomes large by the end of the century. There are still some model–model differences related to well-known processes which affect ozone recovery. Efforts need to continue to ensure that models used for assessment purposes accurately represent stratospheric chemistry and the prescribed scenarios of ozone-depleting substances, and only those models are used to calculate return dates. For future assessments of single forcing or combined effects of CO2, CH4, and N2O on the stratospheric column ozone return dates, this work suggests that it is more important to have multi-member (at least three) ensembles for each scenario from every established participating model, rather than a large number of individual models

METTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer

Newly growing evidence highlights the essential role that epitranscriptomic marks play in the development of many cancers; however, little is known about the role and implications of altered epitranscriptome deposition in prostate cancer. Here, we show that the transfer RNA N-7-methylguanosine (m(7)G) transferase METTL1 is highly expressed in primary and advanced prostate tumours. Mechanistically, we find that METTL1 depletion causes the loss of m(7)G tRNA methylation and promotes the biogenesis of a novel class of small non-coding RNAs derived from 5'tRNA fragments. 5'tRNA-derived small RNAs steer translation control to favour the synthesis of key regulators of tumour growth suppression, interferon pathway, and immune effectors. Knockdown of Mettl1 in prostate cancer preclinical models increases intratumoural infiltration of pro-inflammatory immune cells and enhances responses to immunotherapy. Collectively, our findings reveal a therapeutically actionable role of METTL1-directed m(7)G tRNA methylation in cancer cell translation control and tumour biology