Retinoblastoma and Its Binding Partner MSI1 Control Imprinting in Arabidopsis

Parental genomic imprinting causes preferential expression of one of the two parental alleles. In mammals, differential sex-dependent deposition of silencing DNA methylation marks during gametogenesis initiates a new cycle of imprinting. Parental genomic imprinting has been detected in plants and relies on DNA methylation by the methyltransferase MET1. However, in contrast to mammals, plant imprints are created by differential removal of silencing marks during gametogenesis. In Arabidopsis, DNA demethylation is mediated by the DNA glycosylase DEMETER (DME) causing activation of imprinted genes at the end of female gametogenesis. On the basis of genetic interactions, we show that in addition to DME, the plant homologs of the human Retinoblastoma (Rb) and its binding partner RbAp48 are required for the activation of the imprinted genes FIS2 and FWA. This Rb-dependent activation is mediated by direct transcriptional repression of MET1 during female gametogenesis. We have thus identified a new mechanism required for imprinting establishment, outlining a new role for the Retinoblastoma pathway, which may be conserved in mammals

Cell cycle status of male and female gametes during Arabidopsis reproduction

Fertilization in Arabidopsis (Arabidopsis thaliana) is a highly coordinated process that begins with a pollen tube delivering the 2 sperm cells into the embryo sac. Each sperm cell can then fertilize either the egg or the central cell to initiate embryo or endosperm development, respectively. The success of this double fertilization process requires a tight cell cycle synchrony between the male and female gametes to allow karyogamy (nuclei fusion). However, the cell cycle status of the male and female gametes during fertilization remains elusive as DNA quantification and DNA replication assays have given conflicting results. Here, to reconcile these results, we quantified the DNA replication state by DNA sequencing and performed microscopic analyses of fluorescent markers covering all phases of the cell cycle. We show that male and female Arabidopsis gametes are both arrested prior to DNA replication at maturity and initiate their DNA replication only during fertilization.M.I. and C.M. were supported by the French National Research Agency (ANR-15-CE12-0012; ANR-21-CE20-0047). Y.V. was supported by a Marie Skłodowska-Curie Actions (MSCA) Individual Fellowship (101028014). C.G. was supported by RTI2018-094793-B-I00 and PID2021-123319NBI00 by the Ministerio de Ciencia e Innovación (MICIN and FEDER), and by AdG_833617 (European Research Council). This project has received funding from Austrian Science Fund (FWF) including the Lise Meitner program to M.B. M1818 and grant I2363 B16 to F.B. and core funding from the Austrian Academy of Sciences to F.B. and A.S

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome

<p>Abstract</p> <p>Background</p> <p>Since the finishing of the sequencing of the <it>Arabidopsis thaliana </it>genome, the Arabidopsis community and the annotator centers have been working on the improvement of gene annotation at the structural and functional levels. In this context, we have used the large CATMA resource on the Arabidopsis transcriptome to search for genes missed by different annotation processes. Probes on the CATMA microarrays are specific gene sequence tags (GSTs) based on the CDS models predicted by the Eugene software. Among the 24 576 CATMA v2 GSTs, 677 are in regions considered as intergenic by the TAIR annotation. We analyzed the cognate transcriptome data in the CATMA resource and carried out data-mining to characterize novel genes and improve gene models.</p> <p>Results</p> <p>The statistical analysis of the results of more than 500 hybridized samples distributed among 12 organs provides an experimental validation for 465 novel genes. The hybridization evidence was confirmed by RT-PCR approaches for 88% of the 465 novel genes. Comparisons with the current annotation show that these novel genes often encode small proteins, with an average size of 137 aa. Our approach has also led to the improvement of pre-existing gene models through both the extension of 16 CDS and the identification of 13 gene models erroneously constituted of two merged CDS.</p> <p>Conclusion</p> <p>This work is a noticeable step forward in the improvement of the Arabidopsis genome annotation. We increased the number of Arabidopsis validated genes by 465 novel transcribed genes to which we associated several functional annotations such as expression profiles, sequence conservation in plants, cognate transcripts and protein motifs.</p

Chromatin dynamics during interphase and cell division:similarities and differences between model and crop plants

Genetic information in the cell nucleus controls organismal development, responses to the environment and finally ensures own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organisation of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to the genome size, ploidy and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organisation and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits

Molecular regulation of embryo development in Norway spruce

Plant embryogenesis is mainly concerned with establishing the apical-basal and radial tissue patterns of the future adult plant and accumulating food reserves required for seed germination. The present work describes the isolation of putative transcription factors expressed during somatic embryo development in the gymnosperm Norway spruce (Picea abies). Two Norway spruce homeobox (PaHB) genes belonging to the homeodomain-glabra2 (HD-GL2) family, were isolated. Both genes display a highly conserved intron pattern characteristic of their phylogenetically related angiosperm HD-GL2 genes. The two predicted gymnosperm proteins are also highly similar to the angiosperm HD-GL2 proteins. In proembryogenic masses, both genes are expressed in all embryogenic cells. In early maturing somatic embryos, PaHBl becomes restricted to the protoderm layer and PaHB2 is not expressed. At a later stage, PaHBl expression remains on the protoderm whereas PaHB2 transcripts are mainly detected in the underlying cortical layers. A stepwise peripheral to central radial patterning takes place during embryo development in Norway spruce. Ectopic expression of PaHBl led to an early block in somatic embryo development suggesting that the inner layers of the embryos must be devoid of PaHBl to proceed through embryogenesis. The conservation of protoderm-specific expression in HD-GL2 and lipid transfer protein {LTP) genes from divergent plants suggests putative common cis-regulatory elements in these genes. Sequence comparisons between the isolated PaHBl, Pal8 (encoding a predicted LTP) promoters and the angiosperm counterparts allowed us to identify candidate motifs for protoderm expression. The AtMLl promoter and PaHBl promoter, both fused to the reporter gene GUS, were transferred into Norway spruce and Arabidopsis respectively, enaling reporter gene analysis. The Norway spruce viviparousl (Pavpl) single-copy gene shows similar gene structure and protein domain organization as the angiosperm counterparts. The expression profile of Pavpl further suggests a similar role of vpl genes in maturation and desiccation processes in seed plants

DNA Methylation Readers in Plants

International audienc

Evolution of CG Methylation Maintenance Machinery in Plants

Cytosine methylation is an epigenetic mark present in most eukaryotic genomes that contributes to the regulation of gene expression and the maintenance of genome stability. DNA methylation mostly occurs at CG sequences, where it is initially deposited by de novo DNA methyltransferases and propagated by maintenance DNA methyltransferases (DNMT) during DNA replication. In this review, we first summarize the mechanisms maintaining CG methylation in mammals that involve the DNA Methyltransferase 1 (DNMT1) enzyme and its cofactor, UHRF1 (Ubiquitin-like with PHD and RING Finger domain 1). We then discuss the evolutionary conservation and diversification of these two core factors in the plant kingdom and speculate on potential functions of novel homologues typically observed in land plants but not in mammals

The two male gametes share equal ability to fertilize the egg cell in Arabidopsis thaliana

10.1016/j.cub.2008.11.025Current Biology19

The Female Gametophyte and the Endosperm Control Cell Proliferation and Differentiation of the Seed Coat in Arabidopsis

Double fertilization of the female gametophyte produces the endosperm and the embryo enclosed in the maternal seed coat. Proper seed communication necessitates exchanges of signals between the zygotic and maternal components of the seed. However, the nature of these interactions remains largely unknown. We show that double fertilization of the Arabidopsis thaliana female gametophyte rapidly triggers sustained cell proliferation in the seed coat. Cell proliferation and differentiation of the seed coat occur in autonomous seeds produced in the absence of fertilization of the multicopy suppressor of ira1 (msi1) mutant. As msi1 autonomous seeds mostly contain autonomous endosperm, our results indicate that the developing endosperm is sufficient to enhance cell proliferation and differentiation in the seed coat. We analyze the effect of autonomous proliferation in the retinoblastoma-related1 (rbr1) female gametophyte on seed coat development. In contrast with msi1, supernumerary nuclei in rbr1 female gametophytes originate mainly from the endosperm precursor lineage but do not express an endosperm fate marker. In addition, defects of the rbr1 female gametophyte also reduce cell proliferation in the ovule integuments before fertilization and prevent further differentiation of the seed coat. Our data suggest that coordinated development of the seed components relies on interactions before fertilization between the female gametophyte and the surrounding maternal ovule integuments and after fertilization between the endosperm and the seed coat