Plant RNases T2, but not Dicer-like proteins, are major players of tRNA-derived fragments biogenesis

RNA fragments deriving from tRNAs (tRFs) exist in all branches of life and the repertoire of their biological functions regularly increases. Paradoxically, their biogenesis remains unclear. The human RNase A, Angiogenin, and the yeast RNase T2, Rny1p, generate long tRFs after cleavage in the anticodon region. The production of short tRFs after cleavage in the D or T regions is still enigmatic. Here, we show that the Arabidopsis Dicer-like proteins, DCL1-4, do not play a major role in the production of tRFs. Rather, we demonstrate that the Arabidopsis RNases T2, called RNS, are key players of both long and short tRFs biogenesis. Arabidopsis RNS show specific expression profiles. In particular, RNS1 and RNS3 are mainly found in the outer tissues of senescing seeds where they are the main endoribonucleases responsible of tRNA cleavage activity for tRFs production. In plants grown under phosphate starvation conditions, the induction of RNS1 is correlated with the accumulation of specific tRFs. Beyond plants, we also provide evidence that short tRFs can be produced by the yeast Rny1p and that, in vitro, human RNase T2 is also able to generate long and short tRFs. Our data suggest an evolutionary conserved feature of these enzymes in eukaryotes

VLTI status update: a decade of operations and beyond

We present the latest update of the European Southern Observatory's Very Large Telescope interferometer (VLTI). The operations of VLTI have greatly improved in the past years: reduction of the execution time; better offering of telescopes configurations; improvements on AMBER limiting magnitudes; study of polarization effects and control for single mode fibres; fringe tracking real time data, etc. We present some of these improvements and also quantify the operational improvements using a performance metric. We take the opportunity of the first decade of operations to reflect on the VLTI community which is analyzed quantitatively and qualitatively. Finally, we present briefly the preparatory work for the arrival of the second generation instruments GRAVITY and MATISSE.Comment: 10 pages, 7 figures, Proceedings of the SPIE, 9146-1

Event-Related Potential Effects of Object Recognition depend on Attention and Part-Whole Configuration

The effects of spatial attention and part-whole configuration on recognition of repeated objects were investigated with behavioral and event-related potential (ERP) measures. Short-term repetition effects were measured for probe objects as a function of whether a preceding prime object was shown as an intact image or coarsely scrambled (split into two halves) and whether or not it had been attended during the prime display. In line with previous behavioral experiments, priming effects were observed from both intact and split primes for attended objects, but only from intact (repeated sameview) objects when they were unattended. These behavioral results were reflected in ERP waveforms at occipital–temporal locations as more negative-going deflections for repeated items in the time window between 220 and 300 ms after probe onset (N250r).Attended intact images showed generally more enhanced repetition effects than split ones. Unattended images showed repetition effects only when presented in an intact configuration, and this finding was limited to the right-hemisphere electrodes. Repetition effects in earlier (before 200 ms) time windows were limited to attended conditions at occipito-temporal sites during the N1, a component linked to the encoding of object structure, while repetition effects at central locations during the same time window (P150) were found for attended and unattended probes but only when repeated in the same intact configuration. The data indicate that view-generalization is mediated by a combination of analytic (part-based) representations and automatic view-dependent representations

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Entre silence, naissance et dégradation : vers la caractérisation de nouveaux mécanismes relatifs à la biologie des ARN de transfert et assurant l'homéostasie de la cellule végétale.

My thesis project aimed at figuring out new physiological aspects related to transfer RNA (tRNAs) biology in plants. It was divided in two parts. The first one consisted in describing from an evolutionarily point of view the genomic layout of plant tRNA genes (tDNAs) onto nuclear chromosomes. Contrasting with non-plant organisms, plant nuclear tDNAs exhibit a higher order in their chromosomal scattering. This is due to centromeric regions exclusion combined to highly conserved inter-tDNA distances and tDNA repeat clusters occurrences. Moreover, that part consisted in deciphering elements of nuclear tDNA transcriptional regulation. We brought evidences of epigenetic silencing mechanisms at clustered tDNA loci. As a perspective, we propose tDNAs might play a role in three-dimensional genomes orchestration. The second aspect referred to characterizing the biogenesis and functions of small non-coding RNAs deriving from tRNAs: tRFs. The results obtained demonstrate that RNases T2 as the predominant molecular actors for their biogenesis.Mon projet de thèse visait à caractériser de nouveaux aspects physiologiques relatifs à la biologie des ARN de transfert (ARNt) chez les plantes. Il se composait de deux chapitres. Le premier chapitre avait pour objectif de décrire d’un point de vue évolutif l’organisation génomique des gènes d’ARNt nucléaires (ADNt) de plantes, et caractériser les pendants moléculaires régulant leur expression. Par rapport aux autres organismes vivants, ce travail a permis de révéler une haute organisation des ADNt sur les chromosomes de plantes se caractérisant par : des déserts géniques au niveau des centromères, des distances inter-ADNt homogènes, et la présence de clusters d’ADNt répétés. Aussi, ce travail a permis de décrire les premières évidences d’un silencing épigénétique de l’expression d’ADNt de plantes organisés en clusters de répétitions. La conjonction de ces résultats suggère un rôle potentiel des ADNt dans l’orchestration des génomes tridimensionnels de plantes. Le deuxième chapitre avait pour objectif de caractériser la biogenèse et les fonctions de petits ARN non-codants dérivant d’ARNt, les tRF, chez A. thaliana. Ce travail a permis de montrer que les RNases T2 sont les principaux acteurs de leur biogenèse

Between silence, birth and degradation : towards the characterization of new mechanisms related to transfer RNA biology and ensuring plant cell homeostasis

Mon projet de thèse visait à caractériser de nouveaux aspects physiologiques relatifs à la biologie des ARN de transfert (ARNt) chez les plantes. Il se composait de deux chapitres. Le premier chapitre avait pour objectif de décrire d’un point de vue évolutif l’organisation génomique des gènes d’ARNt nucléaires (ADNt) de plantes, et caractériser les pendants moléculaires régulant leur expression. Par rapport aux autres organismes vivants, ce travail a permis de révéler une haute organisation des ADNt sur les chromosomes de plantes se caractérisant par : des déserts géniques au niveau des centromères, des distances inter-ADNt homogènes, et la présence de clusters d’ADNt répétés. Aussi, ce travail a permis de décrire les premières évidences d’un silencing épigénétique de l’expression d’ADNt de plantes organisés en clusters de répétitions. La conjonction de ces résultats suggère un rôle potentiel des ADNt dans l’orchestration des génomes tridimensionnels de plantes. Le deuxième chapitre avait pour objectif de caractériser la biogenèse et les fonctions de petits ARN non-codants dérivant d’ARNt, les tRF, chez A. thaliana. Ce travail a permis de montrer que les RNases T2 sont les principaux acteurs de leur biogenèse.My thesis project aimed at figuring out new physiological aspects related to transfer RNA (tRNAs) biology in plants. It was divided in two parts. The first one consisted in describing from an evolutionarily point of view the genomic layout of plant tRNA genes (tDNAs) onto nuclear chromosomes. Contrasting with non-plant organisms, plant nuclear tDNAs exhibit a higher order in their chromosomal scattering. This is due to centromeric regions exclusion combined to highly conserved inter-tDNA distances and tDNA repeat clusters occurrences. Moreover, that part consisted in deciphering elements of nuclear tDNA transcriptional regulation. We brought evidences of epigenetic silencing mechanisms at clustered tDNA loci. As a perspective, we propose tDNAs might play a role in three-dimensional genomes orchestration. The second aspect referred to characterizing the biogenesis and functions of small non-coding RNAs deriving from tRNAs: tRFs. The results obtained demonstrate that RNases T2 as the predominant molecular actors for their biogenesis

Between silence, birth and degradation : towards the characterization of new mechanisms related to transfer RNA biology and ensuring plant cell homeostasis

Mon projet de thèse visait à caractériser de nouveaux aspects physiologiques relatifs à la biologie des ARN de transfert (ARNt) chez les plantes. Il se composait de deux chapitres. Le premier chapitre avait pour objectif de décrire d’un point de vue évolutif l’organisation génomique des gènes d’ARNt nucléaires (ADNt) de plantes, et caractériser les pendants moléculaires régulant leur expression. Par rapport aux autres organismes vivants, ce travail a permis de révéler une haute organisation des ADNt sur les chromosomes de plantes se caractérisant par : des déserts géniques au niveau des centromères, des distances inter-ADNt homogènes, et la présence de clusters d’ADNt répétés. Aussi, ce travail a permis de décrire les premières évidences d’un silencing épigénétique de l’expression d’ADNt de plantes organisés en clusters de répétitions. La conjonction de ces résultats suggère un rôle potentiel des ADNt dans l’orchestration des génomes tridimensionnels de plantes. Le deuxième chapitre avait pour objectif de caractériser la biogenèse et les fonctions de petits ARN non-codants dérivant d’ARNt, les tRF, chez A. thaliana. Ce travail a permis de montrer que les RNases T2 sont les principaux acteurs de leur biogenèse.My thesis project aimed at figuring out new physiological aspects related to transfer RNA (tRNAs) biology in plants. It was divided in two parts. The first one consisted in describing from an evolutionarily point of view the genomic layout of plant tRNA genes (tDNAs) onto nuclear chromosomes. Contrasting with non-plant organisms, plant nuclear tDNAs exhibit a higher order in their chromosomal scattering. This is due to centromeric regions exclusion combined to highly conserved inter-tDNA distances and tDNA repeat clusters occurrences. Moreover, that part consisted in deciphering elements of nuclear tDNA transcriptional regulation. We brought evidences of epigenetic silencing mechanisms at clustered tDNA loci. As a perspective, we propose tDNAs might play a role in three-dimensional genomes orchestration. The second aspect referred to characterizing the biogenesis and functions of small non-coding RNAs deriving from tRNAs: tRFs. The results obtained demonstrate that RNases T2 as the predominant molecular actors for their biogenesis

Transfection of small non-coding RNAs into Arabidopsis thaliana protoplasts

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