Caractérisation fonctionnelle de JMJ24, une déméthylase d'histone de la famille JUMONJI, chez Arabidopsis thaliana

Cette dernière décennie a vu augmenter le nombre d études portant sur la caractérisation des protéines JUMONJI (JMJ) et montrant leur rôle prépondérant dans la régulation des gènes et le développement des organismes. Ces protéines sont capables de déméthyler certains résidus des queues des histones et ont été organisées en groupes phylogénétiques en fonction de la conservation de leur domaine catalytique. Pour chaque clade entre un et trois substrats spécifiques ont pu être identifiés. De la sous famille KDM3, dont le résidu cible est H3K9, seul un membre, IBM1, a été caractérisé chez Arabidopsis. Cette étude montre que la mutation de JMJ24, un autre membre de ce groupe, entraine une augmentation de la taille des racines, cotylédons et organes floraux, suggérant un rôle dans le contrôle du développement à différents stades. De plus, l analyse de l expression tissulaire indique que JMJ24 est exprimé dans le phloème, en cohérence avec l effet pléiotropique de sa mutation. Enfin, nos données suggèrent une interaction entre JMJ24 et d autres protéines JMJ, telles JMJ14 et IBM1, mais aussi une interaction avec les protéines DCL, impliquées dans la régulation des gènes et des éléments transposables.Numerous studies over the last decade have reported the characterization of the JUMONJI (JMJ) proteins, showing their critical importance in regulating genes and organism s development. These proteins are able to demethylate a subset of histone tail residues and were clustered into distinct groups using a phylogenetic analysis based on their catalytic domain conservation. Furthermore, modification of one to three specific residues has been attributed to each JMJ group. Within the KDM3 subfamily, of which target is the H3K9 residue, only one member, IBM1, was first characterized in Arabidopsis. In this report, we showed that the mutation of JMJ24, another member of this subfamily, resulted in an increase of the root length, cotyledon and floral organ size, suggesting that JMJ24 functions is needed at different developmental stage. In addition, the analysis of the tissue-specific expression of JMJ24 indicated that the gene is expressed within the phloem of all organs, correlating with the pleiotropic effect of the gene mutation. Last, our data also suggested that JMJ24 interacts with other JMJ protein like JMJ14 and IBM1, but also with the DCL proteins knowing to be involved in genes and transposable elements regulation.PARIS11-SCD-Bib. électronique (914719901) / SudocSudocFranceF

Analysis of GT-3a identifies a distinct subgroup of trihelix DNA-binding transcription factors in Arabidopsis

AbstractTrihelix DNA-binding factors (or GT factors) bind to GT elements found in the promoters of many plant genes. Although the binding specificity and the transcriptional activity of some members (e.g. GT-1 and GT-2) have been studied, the regulatory function of this family of transcription factors remains largely unknown. In this work, we have characterised a new GT factor, namely GT-3a, and a closely related member, GT-3b. We show that (1) they can form either homo- or heterodimers but do not interact with GT-1; (2) they are predominantly expressed in floral buds and roots; (3) GT-3a cannot bind to the binding sites of GT-1 or GT-2, but binds to the cab2 and rbcS-1A gene promoters via the 5′-GTTAC sequence, which has been previously shown to be the core of the Site 1 type of GT elements. These results suggest that GT-3a and GT-3b belong to a distinct subgroup of GT factors and that each subgroup of GT factors binds to a functionally distinct type of cis-acting GT elements

The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Histone acetyltransferases (HATs) play critical roles in the regulation of chromatin structure and gene expression. Arabidopsis genome contains 12 HAT genes, but the biological functions of many of them are still unknown. In this work, we studied the evolutionary relationship and cellular functions of the two Arabidopsis HAT genes homologous to the MYST family members.</p> <p>Results</p> <p>An extensive phylogenetic analysis of 105 MYST proteins revealed that they can be divided into 5 classes, each of which contains a specific combination of protein modules. The two Arabidopsis MYST proteins, HAM1 and HAM2, belong to a "green clade", clearly separated from other families of HATs. Using a reverse genetic approach, we show that <it>HAM1 </it>and <it>HAM2 </it>are a functionally redundant pair of genes, as single Arabidopsis <it>ham1 </it>and <it>ham2 </it>mutants displayed a wild-type phenotype, while no double mutant seedling could be recovered. Genetic analysis and cytological study revealed that <it>ham1ham2 </it>double mutation induced severe defects in the formation of male and female gametophyte, resulting in an arrest of mitotic cell cycle at early stages of gametogenesis. RT-PCR experiments and the analysis of transgenic plants expressing the <it>GUS </it>reporter gene under the <it>HAM1 </it>or the <it>HAM2 </it>promoter showed that both genes displayed an overlapping expression pattern, mainly in growing organs such as shoots and flower buds.</p> <p>Conclusion</p> <p>The work presented here reveals novel properties for MYST HATs in Arabidopsis. In addition to providing an evolutionary relationship of this large protein family, we show the evidence of a link between MYST and gamete formation as previously suggested in mammalian cells. A possible function of the Arabidopsis MYST protein-mediated histone acetylation during cell division is suggested.</p

The Role of Histone Methylation and H2A.Z Occupancy during Rapid Activation of Ethylene Responsive Genes

Ethylene signaling pathway leads to rapid gene activation by two hierarchies of transcription factors with EIN3/EIL proteins as primary ones and ERF proteins as secondary ones. The role of chromatin modifications during the rapid gene activation is not known. In this work we studied trimethylated histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3), two opposite histone methylation marks for gene activity, during the induction course of three ethylene-responsive genes (ERF1, AtERF14 and ChiB). We found that the three genes displayed different histone modification profiles before induction. After induction, H3K4me3 was increased in the 5′ region and the gene body of ERF1, while H3K27me3 was decreased in the promoter of AtERF14. But the modification changes were later than the gene activation. Analysis of other rapidly inducible ERF genes confirmed the observation. In addition, histone H2A.Z occupancy on the three genes and the association of the H3K27me3-binding protein LHP1 with AtERF14 and ChiB were not affected by the inductive signal. However, the mutation of genes encoding H2A.Z and LHP1 attenuated and enhanced respectively the induction of target genes and altered H3K4me3. These results indicate that the induction of ethylene-responsive genes does not require immediate modulation of H3K4me3 and H3K27me3 and dissociation of LHP1 and H2A.Z from the targets, and suggest that the chromatin structure of the genes before induction is committed for transcriptional activation and that H3K4me3 is not required for ethylene-responsive gene activation, but may serve as a mark for gene activity

Altered Levels of Histone Deacetylase OsHDT1 Affect Differential Gene Expression Patterns in Hybrid Rice

Hybrids between different inbred varieties display novel patterns of gene expression resulted from parental variation in allelic nucleotide sequences. To study the function of chromatin regulators in hybrid gene expression, the histone deacetylase gene OsHDT1 whose expression displayed a circadian rhythm was over-expressed or inactivated by RNAi in an elite rice parent. Increased OsHDT1 expression did not affect plant growth in the parent but led to early flowering in the hybrid. Nonadditive up-regulation of key flowering time genes was found to be related to flowering time of the hybrid. Over-expression of OsHDT1 repressed the nonadditive expression of the key flowering repressors in the hybrid (i.e. OsGI and Hd1) inducing early flowering. Analysis of histone acetylation suggested that OsHDT1 over-expression might promote deacetylation on OsGI and Hd1 chromatin during the peak expression phase. High throughput differential gene expression analysis revealed that altered OsHDT1 levels affected nonadditive expression of many genes in the hybrid. These data demonstrate that nonadditive gene expression was involved in flowering time control in the hybrid rice and that OsHDT1 level was important for nonadditive or differential expression of many genes including the flowering time genes, suggesting that OsHDT1 may be involved in epigenetic control of parental genome interaction for differential gene expression

Non-Standard Errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

Non-standard errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

Organisation et expression de genes chloroplastiques et nucleaires codant pour des proteines ribosomiques du chloroplaste d'epinard

SIGLECNRS T Bordereau / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Rôle des histone-acétyltransférases dans le développement d'Arabidopsis thaliana

Les histone-acétyltransférases sont des enzymes capables d acétyler les histones ainsi que certaines protéines non-histones. Elles fonctionnent au sein de complexes multiprotéiques liés à la régulation de la transcription des gènes. L acétylation des histones participe également au remodelage de la chromatine, mécanisme largement impliqué dans le contrôle du développement des plantes. L objectif de ce travail était d étudier le rôle des histone-acétyltransférases dans différents aspects du développement d Arabidopsis thaliana. Dans cette optique, les phe notypes de deux mutants d histone-acétyltransférases ont été analysés. Tout d abord, la mutation du gène AtGCN5 induit un phénotype pléiotrope et notamment une anomalie du développement floral avec des transformations homéotiques. Ces caractéristiques s accompagnent d une expansion du domaine d expression dans le méristème floral de deux gènes clés, WUSCHEL et AGAMOUS. Ces résultats nous ont permis d impliquer AtGCN5 dans le contrôle de l activité du méristème floral. Parallèlement, la mutation d AtGCN5 affecte la réponse de la plante à la lumière. Un phénotype similaire est obtenu lors de la mutation du gène HAF2 qui code pour le facteur de transcription TAF1. AtGCN5 et TAF1 interviennent tous les deux dans la photomorphogenèse et l activation de la transcription des gènes photo-inductibles. Cette régulation impliquerait leur fonction d acétylation des nucléosomes au niveau des promoteurs de ces gènes, mais aussi leur rôle de médiateur au sein de complexes transcriptionnels. Ces résultats révèlent les histone-acétyltransférases comme de nouveaux régulateurs de mécanismes spécifiques du développement de la plante.Histone acetyltransferase are enzymes able to acetylate histone and non-histone proteins. They usually function as part of multiprotein complexes involved in gene transcriptional regulation. Histone acetylation also plays a role in chromatin remodelling, a mechanism that is greatly involved in the control of plant development. The aim of this work was to study the role of histone acetyltransferase in different aspects of Arabidopsis thaliana development. Therefore, the phenotypes of two histone acetyltransferase mutants were analysed. First of all, the mutation of AtGCN5 gene induces a pleiotropic phenotype and, particularly, a defect in floral development with homeotic transformations. These effects are accompanied by an expansion of the expression domain in the floral meristem of two key genes of this developmental aspect, WUSCHEL and AGAMOUS. These results showed that AtGCN5 is involved in the floral meristem activity. On the other hand, AtGCN5 mutation also affects the light response pathways. A similar phenotype was obtained with the mutation of HAF2 gene encoding TAF1, a transcription cofactor showing a histone acetyltransferase activity. Both AtGCN5 and TAF1 promote photomorphogenesis and transcription activation of light-induced genes. This regulation seems to involve their nucleosome acetylation function on the promoters and also a mediation function within transcriptional complexes. These results reveal that histone acetyltransferases are new regulators of plant specific developmental mechanisms.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Génomique fonctionnelle de facteurs de transcription de la famille GT chez Arabidopsis thaliana (caractérisation du facteur GT-3a)

AMIENS-BU Sciences (800212103) / SudocSudocFranceF