Control of growth and gut maturation by HoxD genes and the associated lncRNA Haglr.

During embryonic development, Hox genes participate in the building of a functional digestive system in metazoans, and genetic conditions involving these genes lead to important, sometimes lethal, growth retardation. Recently, this phenotype was obtained after deletion of Haglr, the Hoxd antisense growth-associated long noncoding RNA (lncRNA) located between Hoxd1 and Hoxd3 In this study, we have analyzed the function of Hoxd genes in delayed growth trajectories by looking at several nested targeted deficiencies of the mouse HoxD cluster. Mutant pups were severely stunted during the suckling period, but many recovered after weaning. After comparing seven distinct HoxD alleles, including CRISPR/Cas9 deletions involving Haglr, we identified Hoxd3 as the critical component for the gut to maintain milk-digestive competence. This essential function could be abrogated by the dominant-negative effect of HOXD10 as shown by a genetic rescue approach, thus further illustrating the importance of posterior prevalence in Hox gene function. A role for the lncRNA Haglr in the control of postnatal growth could not be corroborated

Phylogenomics and Genome Annotation

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Repository/R-Forge/DateTimeStamp 2012-12-11 16:03:18

Suggests ade4, segmented Description Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Include also utilities for sequence data management under the ACNUC system. License GPL (> = 2

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Background Most eukaryotic genes are subject to alternative splicing (AS), which may contribute to the production of protein variants or to the regulation of gene expression via nonsense-mediated messenger RNA (mRNA) decay (NMD). However, a fraction of splice variants might correspond to spurious transcripts and the question of the relative proportion of splicing errors to functional splice variants remains highly debated. Results We propose a test to quantify the fraction of AS events corresponding to errors. This test is based on the fact that the fitness cost of splicing errors increases with the number of introns in a gene and with expression level. We analyzed the transcriptome of the intron-rich eukaryote Paramecium tetraurelia. We show that in both normal and in NMD-deficient cells, AS rates strongly decrease with increasing expression level and with increasing number of introns. This relationship is observed for AS events that are detectable by NMD as well as for those that are not, which invalidates the hypothesis of a link with the regulation of gene expression. Our results show that in genes with a median expression level, 92–98% of observed splice variants correspond to errors. We observed the same patterns in human transcriptomes and we further show that AS rates correlate with the fitness cost of splicing errors. Conclusions These observations indicate that genes under weaker selective pressure accumulate more maladaptive substitutions and are more prone to splicing errors. Thus, to a large extent, patterns of gene expression variants simply reflect the balance between selection, mutation, and drift

Assessing Recent Selection and Functionality at Long Non-Coding RNA Loci in the Mouse Genome

This work was supported by the Biotechnology and Biological Sciences Research Council and The Wellcome Trust. A.N. was supported by the Swiss National Science Foundation (Grant: PZ00P3_142636). H.K. was supported by the European Research Council Starting (Grant: 242597, SexGenTransEvolution) and the Swiss National Science Foundation (Grants: 130287 and 146474).Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs has identified approximately 200 functional loci across the Eukarya, general surveys have found only modest or no evidence of long-term evolutionary conservation. Although this lack of conservation suggests that most lncRNAs are nonfunctional, the possibility remains that some represent recent evolutionary innovations. We examine recent selection pressures acting on lncRNAs in mouse populations. We compare patterns of within-species nucleotide variation at approximately 10,000 lncRNA loci in a cohort of the wild house mouse, Mus musculus castaneus, with between-species nucleotide divergence from the rat (Rattus norvegicus). Loci under selective constraint are expected to show reduced nucleotide diversity and divergence. We find limited evidence of sequence conservation compared with putatively neutrally evolving ancestral repeats (ARs). Comparisons of sequence diversity and divergence between ARs, protein-coding (PC) exons and lncRNAs, and the associated flanking regions, show weak, but significantly lower levels of sequence diversity and divergence at lncRNAs compared with ARs. lncRNAs conserved deep in the vertebrate phylogeny show lower within-species sequence diversity than lncRNAs in general. A set of 74 functionally characterized lncRNAs show levels of diversity and divergence comparable to PC exons, suggesting that these lncRNAs are under substantial selective constraints. Our results suggest that, in mouse populations, most lncRNA loci evolve at rates similar to ARs, whereas older lncRNAs tend to show signals of selection similar to PC genes.PostprintPeer reviewe

Etude des patrons d'évolution asymétrique dans les séquences d'ADN

This thesis analyses the effect of two essential cellular mechanisms, replication and transcription, on the base composition of DNA sequences. These two processes function asymmetrically on the two DNA strands, and they have as a consequence an asymmetric nucleotide composition in genomic sequences. Moreover, they act in a coordinated manner on genomes, thus the estimation of their respective effects can be difficult. First, we studied the co-orientation between replication and transcription in prokaryotes. We proposed a method for the study of base composition biases which can separate these two sources of asymmetry. We show that the effect of replication on base composition can be highly variable even between closely related species. We then studied the substitution pattern in transcribed regions and around replication origins, in human, with special emphasis on the effect of the 5'-3' nucleotide context. Patterns of context-dependent asymmetric substitutions are similar for replication and transcription. The variation of substitution rate with the expression pattern suggests the presence of context-dependent asymmetric repair mechanisms. We proposed a computational approach for the study of the substitution pattern in microsatellites. We prove that transcribed microsatellites are subject to asymmetric evolution.Cette thèse étudie l'effet de deux processus cellulaires essentiels, la réplication et la transcription, sur la composition en nucléotides des séquences d'ADN. Ces mécanismes ont un fonctionnement asymétrique par rapport aux deux brins d'ADN, et ils ont comme conséquence une composition asymétrique dans les séquences. Nous avons étudié la co-orientation entre réplication et transcription chez les procaryotes. Nous proposons une méthode pour l'étude des biais de composition qui découple ces deux sources d'asymétrie. Nous montrons que les biais associés à la réplication sont très variables, même entre espèces proches. Nous avons ensuite analysé le patron de substitution dans les régions transcrites et autour des origines de réplication du génome humain, et notamment l'effet du contexte 5'-3'. Les biais de voisinage sont similaires pour l'asymétrie associée à la réplication et à la transcription. La variation des taux de substitutions en fonction du patron d'expression des gènes suggère qu'un biais de réparation asymétrique et contexte-dépendant pourrait être en jeu. Enfin, nous avons proposé une méthode de calcul du patron de substitution dans des séquences à composition biaisée: les microsatellites. Nous avons démontré que les microsatellites transcrits sont sujets au mêmes processus asymétriques que les régions non-répétées

Évolution et fonctionnalité des éléments non-codants dans les génomes des vertébrés

RapportriceIl me semble que l'écriture d'un chapitre de remerciements est toujours difficile. Dans mon cas, cela est dû au grand nombre de personnes que j'aimerais remercier comme il se doit, mais aussi à la peur de ne pas trouver les mots justes pour exprimer toute ma reconnaissance. Tout au long de ma carrière de recherche, j'ai eu la chance d'être entourée par des personnes extraordinaires, qui m'ont fourni d'excellents modèles à suivre et qui m'ont soutenue lors des étapes difficiles. Ici je fais le choix de les présenter dans un ordre chronologique approximatif, sachant que lorsque des ambiguïtés temporelles se sont présentées, toutes les dates pertinentes ont été retenues (oui, une description précise du matériel et méthodes est importante même dans le chapitre de remerciements).Je remercie donc les enseignant.e.s et les chercheur.e.s qui m'ont fait découvrir la bioinformatique, lors de mes études à l'INSA de Lyon. Parmi les nombreux noms qui me viennent à l'esprit, je dois citer Guillaume Beslon, Hubert Charles, Laurent Duret, Christian Gautier, Carole Knibbe, Jean Lobry et Marie-France Sagot. J'ai découvert la bioinformatique lorsque nous étions jeunes toutes les deux. C'est grâce à ces enseignant.e.s et chercheur.e.s que j'ai acquis une grande affection pour ce domaine de recherche, que je garde encore aujourd'hui.Je remercie les collègues qui m'ont entourée et encadrée de près ou de loin lors de ma thèse au LBBE. A commencer bien sûr par Jean Lobry, mon directeur de thèse, qui m'a accordé une confiance demesurée et qui m'a soutenue lors de mes nombreux écarts par rapport au chemin établi. Je remercie également Laurent Duret, avec qui j'ai eu la chance de travailler lors de ma dernière année de thèse et pendant un peu de temps après. Depuis ce moment, Laurent n'a cessé de m'impressionner par son immense culture, sa rigueur scientifique, sa brillance et sa modestie, le tout couronné par un don pour les jeux de mots que j'essaye vainement d'imiter (tout comme le reste de ses qualités). C'est également lors de ma thèse que j'ai rencontré Bastien Boussau, qui est rapidement devenu un modèle pour moi, en plus d'un collaborateur et ami, et à qui je dois énormément. Travailler avec Bastien reste toujours très stimulant et je me réjouis de pouvoir le rejoindre dans notre future équipe de recherche.Je remercie les collègues et collaborateur.rice.s suisses, que j'ai rencontré.e.s lors de mon séjour post-doctoral à Lausanne : Henrik Kaessmann et Denis Duboule, qui m'ont accueillie dans leurs laboratoires respectifs et qui m'on fait découvrir de nouvelles façons de faire de la recherche ; Fabrice Darbellay et Rita Amândio, qui m'ont appris de nouvelles approches pour l'étude des longs ARNs non-codants ; Markus Heim, qui m'a permis de faire de la recherche un peu plus appliquée que d'habitude. Je remercie Magali Soumillon, une super-héroïne qui peut faire à la fois de la bioinformatique de haut niveau, des expériences complexes en biologie moléculaire et du pilotage automobile extrême.</div

Comparative transcriptomics analyses across species, organs and developmental stages reveal functionally constrained lncRNAs

AbstractBackgroundTranscription of long non-coding RNAs (lncRNAs) is pervasive, but their functionality is disputed. As a class, lncRNAs show little selective constraint and negligible phenotypic effects upon perturbation. However, key biological roles were demonstrated for individual lncRNAs. Most validated lncRNAs were implicated in gene expression regulation, in pathways related to cellular pluripotency, differentiation and organ morphogenesis, suggesting that functional lncRNAs may be more abundant in embryonic development, rather than in adult organs.ResultsHere, we perform a multi-dimensional comparative transcriptomics analysis, across five developmental time-points (two embryonic stages, newborn, adult and aged individuals), four organs (brain, kidney, liver and testes) and three species (mouse, rat and chicken). Overwhelmingly, lncRNAs are preferentially expressed in adult and aged testes, consistent with the presence of permissive transcription during spermatogenesis. LncRNAs are often differentially expressed among developmental stages and are less abundant in embryos and newborns compared to adult individuals, in agreement with a requirement for tighter expression control and less tolerance for noisy transcription early in development. However, lncRNAs expressed during embryonic development show increased levels of evolutionary conservation, both in terms of primary sequence and of expression patterns, and in particular at their promoter regions. We find that species-specific lncRNA transcription is frequent for enhancer-associated loci and occurs in parallel with expression pattern changes for neighboring protein-coding genes.ConclusionsWe show that functionally constrained lncRNA loci are enriched in developing organ transcriptomes, and propose that many of these loci may function in an RNA-independent manner.</jats:sec

Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs

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