The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae.

BACKGROUND: The angiosperm family Bromeliaceae comprises over 3.500 species characterized by exceptionally high morphological and ecological diversity, but a very low genetic variation. In many genera, plants are vegetatively very similar which makes determination of non flowering bromeliads difficult. This is particularly problematic with living collections where plants are often cultivated over decades without flowering. DNA barcoding is therefore a very promising approach to provide reliable and convenient assistance in species determination. However, the observed low genetic variation of canonical barcoding markers in bromeliads causes problems. RESULT: In this study the low-copy nuclear gene Agt1 is identified as a novel DNA barcoding marker suitable for molecular identification of closely related bromeliad species. Combining a comparatively slowly evolving exon sequence with an adjacent, genetically highly variable intron, correctly matching MegaBLAST based species identification rate was found to be approximately double the highest rate yet reported for bromeliads using other barcode markers. CONCLUSION: In the present work, we characterize Agt1 as a novel plant DNA barcoding marker to be used for barcoding of bromeliads, a plant group with low genetic variation. Moreover, we provide a comprehensive marker sequence dataset for further use in the bromeliad research community.

Molecular memories in the regulation of seasonal flowering: from competence to cessation.

Plants commit to flowering based on endogenous and exogenous information that they can remember across mitotic cell divisions. Here, we review how signal perception and epigenetic memory converge at key integrator genes, and we show how variation in their regulatory circuits supports the diversity of plant lifestyles.

VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis.

Plant B3-domain transcription factors have an important role in regulating seed development, in particular seed maturation and germination. Among the B3 factors, the AFL (ABSCISIC ACID INSENSITIVE3 [ABI3], FUSCA3 [FUS3], and LEAFY COTYLEDON2 [LEC2]) proteins activate the seed maturation program in a complex network, while the VAL (VP1/ABI3-LIKE) 1/2/3 proteins suppress AFL action in order to initiate germination and vegetative development through an as yet unknown mechanism. In addition, the AFL genes and LEAFY COTYLEDON1 (LEC1), referred as seed maturation genes, are epigenetically repressed after germination by the Polycomb group (PcG) machinery via its histone-modifying activities: the histone H3 lysine 27 trimethyltransferase activity of the PcG repressive complex 2 (PRC2) and the E3 H2A monoubiquitin ligase activity of the PRC1. Both histone modifications are required for the repression; however, the underlying mechanism is far from clear, because the localization and the role of H2Aub marks are still unknown. In this work, we demonstrate that VAL proteins and AtBMI1-mediated H2Aub initiate repression of seed maturation genes. After the initial off switch, the repression is maintained by PRC2-mediated H3K27me3. Our results indicate that the regulation of seed maturation genes does not follow the classic hierarchical model proposed for animal PcG-mediated repression, since the PRC1 activity is required for the H3K27me3 modification of these genes. Furthermore, we show different mechanisms to achieve PcG repression in plants, as the repression of genes involved in other processes has different requirements for H2Aub and H3K27me3 marking.

Regulation of the new Arabidopsis imprinted gene AtBMI1C requires the interplay of different epigenetic mechanisms.

Recently, it has been shown that plants contain homologs to the animal Polycomb repressive complex 1 (PRC1) components BMI1 and RING1A/B. In Arabidopsis, there are three BMI1-like genes, two of which, AtBMI1A and B, are required during post-embryonic plant growth to repress embryonic traits and allow cell differentiation. However, little is known about the third BMI1-like gene, AtBMI1C. In this work, we show that AtBMI1C is only expressed during endosperm and stamen development. AtBMI1C is an imprinted gene expressed from the maternal allele in the endosperm but biallelically expressed in stamen. We found that the characteristic expression pattern of AtBMI1C is the result of a complex epigenetic regulation that involves CG DNA methylation, RNA-directed non-CG DNA methylation (RdDM), and PcG activity. Our results show the orchestrated interplay of different epigenetic mechanisms in regulating gene expression throughout development, shedding light on the current hypotheses for the origin and mechanism of imprinting in plant endosperm.

Keeping cell identity in Arabidopsis requires PRC1 RING-finger homologs that catalyze H2A monoubiquitination.

Polycomb group (PcG) proteins form conserved regulatory complexes that modify chromatin to repress the genes that are not required in a specific differentiation status [1]. In animals, the two best-characterized PcG complexes are PRC2 and PRC1, which respectively possess histone 3 lysine 27 (H3K27) trimethyltransferase [2-4] and histone 2A lysine 119 (H2AK119) E3 ubiquitin ligase activities [5-7]. In Arabidopsis, PRC2 activity is also required for the gene silencing mechanism [8]; however, the existence of PRC1 has been questioned, because plant genomes do not encode clear PRC1 components and H2A monoubiquitination has not been detected [6, 9]. Conversely, recent reports have unveiled the presence of homologs to PRC1 components that together with plant-specific proteins could be part of the long-sought PRC1-like complexes [10, 11]. Here we show that the PRC1 RING-finger homologs AtBMI1A and AtBMI1B are implicated in the repression of embryonic and stem cell regulators. Plants impaired in AtBMI1A and AtBMI1B show derepression of embryonic traits in somatic cells, displaying a phenotype similar to plants mutant in PRC2 components [12-14]. Our data demonstrate that the AtBMI1A/B proteins mediate H2A monoubiquitination in Arabidopsis and that this mark, together with PRC2-mediated H3K27 trimethylation, plays a key role in maintaining cell identity.