Biology subjects

Santos-Gonzalez, J.

Publications and source records attributed to Santos-Gonzalez, J..

8 recordsLinked to original sources

bioRxiv2024

Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm

Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals--tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-- both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, underscoring the need for cautious interpretation of the connection between TEs and genomic imprinting.

plant biology↗

bioRxiv2023

The molecular basis of parental conflict driven regulation of endosperm cellularization

The endosperm is a seed tissue supporting embryo growth, similar to the placenta in mammals. It originates after fertilization of the maternal central cell by one of the paternal sperm cells. In the early stages of Arabidopsis thaliana seed development, nuclei divisions in the endosperm are not followed by cellularization. After a defined number of mitotic cycles, the endosperm cellularizes and stops dividing. The timing of endosperm cellularization impacts on final seed size and is differentially controlled by maternal and paternal genome contributions. While increased maternal genome dosage causes early endosperm cellularization and the formation of small seeds, the opposite is caused by increased paternal genome dosage. The parental factors controlling the differential timing of endosperm cellularization remain largely unexplored. Here, we show that a family of maternally expressed auxin response factors (ARFs) promotes endosperm cellularization and regulates final seed size. One-Sentence SummaryEndosperm cellularization is under antagonistic parental control that converges on Auxin Response Factors.

plant biology↗

bioRxiv2020

Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy

Polycomb Repressive Complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) and methylation of histone 3 on lysine 9 (H3K9me) are two repressive epigenetic modifications that are typically localized in distinct regions of the genome. For reasons unknown, however, they co-occur in some organisms and special tissue types. In this study, we show that maternal alleles marked by H3K27me3 in the Arabidopsis endosperm were targeted by the H3K27me3 demethylase REF6 and became activated during germination. In contrast, maternal alleles marked by H3K27me3, H3K9me2, and CHGm were protected from REF6 targeting and remained silenced. Our study unveils that combinations of different repressive epigenetic modifications time a key adaptive trait by modulating access of REF6.

molecular biology↗

bioRxiv2020

Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block

Hybridization of plants that differ in number of chromosome sets (ploidy) frequently causes endosperm failure and seed arrest, a phenomenon referred to as triploid block. Mutation in NRPD1, encoding the largest subunit of the plant-specific RNA Polymerase IV (Pol IV), can suppress the triploid block. Pol IV generates short RNAs required to guide de novo methylation in the RNA-directed DNA methylation (RdDM) pathway. In this study, we found that the ability of mutants in the RdDM pathway to suppress the triploid block depends on their degree of inbreeding. While nrpd1 is able to suppress in the first homozygous generation, mutants in RDR2, NRPE1, and DRM2 require at least one additional round of inbreeding to exert a suppressive effect. Inbreeding of nrpd1 was connected with a transgenerational loss of non-CG DNA methylation on sites jointly regulated by CHROMOMETHYLASES 2 and 3. Our data thus reveal that loss of RdDM function differs in its effect in early and late generations and that Pol IV acts at an early stage of triploid block establishment. One-sentence summaryInbreeding of mutants impaired in RdDM components transgenerationally enhanced their ability to suppress the triploid block.

genetics↗

bioRxiv2019

Functional role of Polymerase IV during pollen development in Capsella

In Arabidopsis thaliana, the DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA (sRNA) transcripts. These transcripts are processed by DICER-LIKE 3 into 24-nt small interfering RNAs (siRNAs) that guide RNA-dependent DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nt epigenetically-activated siRNAs (easiRNAs) that likely silence TEs by post-transcriptional mechanisms. Despite this proposed functional role, loss of Pol IV function in Arabidopsis does not cause a discernable pollen defect. Here, we show that loss of NRPD1, encoding the largest subunit of Pol IV in the Brassicaceae Capsella rubella, causes post-meiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were depleted in Capsella nrpd1 microspores. In wild-type background, we found that the same TEs produced 21/22-nt and 24-nt siRNAs, leading us to propose that Pol IV is generating the direct precursors for 21-24-nt siRNAs, which are targeted by different DICERs. Arrest of Capsella nrpd1 microspores was accompanied by deregulation of genes targeted by Pol IV-dependent siRNAs. The distance of TEs to genes was much closer in Capsella rubella compared to Arabidopsis thaliana, providing a possible explanation for the essential role of Pol IV for pollen development in Capsella. Our study in Capsella uncovers a functional requirement of Pol IV in microspores, emphasizing the relevance of investigating different plant models. One-sentence summaryLoss of Polymerase IV function in Capsella rubella causes microspore arrest, revealing an important functional role of Polymerase IV during pollen development. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Claudia Kohler (Claudia.Kohler@slu.se)

plant biology↗

bioRxiv2019

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

MADS-box transcription factors are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of molecular domestication of these elements, which by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.

plant biology↗

bioRxiv2018

Epigenetic signatures associated with imprinted paternally-expressed genes in the Arabidopsis endosperm

BackgroundImprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression.\n\nResultsIn this study, we show that imprinted paternally-expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Based on the presence of this epigenetic signature on maternal alleles we were able to predict known PEGs at high accuracy and identified several new PEGs that we confirmed using INTACT-based transcriptomes generated in this study.\n\nConclusionsThe presence of the three repressive epigenetic marks, H3K27me3, H3K9me2, and CHG methylation on the maternal alleles in the endosperm serves as a specific epigenetic signature that allows to predict genes with parental-specific gene expression. Our study reveals that there are substantially more PEGs than previously identified, indicating that paternal-specific gene expression is of higher functional relevance than currently estimated. The combined activity of PRC2-mediated H3K27me3 together with the heterochromatic H3K9me3 has also been reported to silence the maternal Xist locus in mammalian preimplantation embryos, suggesting convergent employment of both pathways during the evolution of genomic imprinting.

genetics↗

bioRxiv2017

Paternal easiRNAs regulate parental genome dosage in Arabidopsis

The regulation of parental genome dosage is of fundamental importance in animals and plants, exemplified by X chromosome inactivation and dosage compensation. The \"triploid block\" is a classical example of dosage regulation in plants that establishes a reproductive barrier between species differing in chromosome number 1,2. This barrier acts in the endosperm, an ephemeral tissue that nurtures the developing embryo and induces the abortion of hybrid seeds through a yet unknown mechanism. Interploidy hybridizations involving diploid (2x) maternal parents and tetraploid (4x) pollen donors cause failure in endosperm cellularization, leading to embryo arrest 3. Here we show that paternal epigenetically activated small interfering RNAs (easiRNAs) are responsible for the establishment of the triploid block-associated seed abortion in Arabidopsis thaliana. Paternal loss of the plant-specific RNA polymerase IV suppressed easiRNA formation and rescued triploid seeds by restoring small RNA-directed DNA methylation at transposable elements (TEs), correlating with reduced expression of paternally expressed imprinted genes (PEGs). We propose that excess of paternally derived easiRNAs in diploid pollen prevents establishment of DNA methylation, leading to triploid seed abortion. Our data further suggest that easiRNAs form a quantitative signal for chromosome number and their balanced dosage is required for post-fertilization genome stability and seed viability.

plant biology↗