Biology subjects

Schon, M. A.

Publications and source records attributed to Schon, M. A..

8 recordsLinked to original sources

bioRxiv2026

The SAUERKRAUT transposable element acceleratesArabidopsis floral transition

Salt stress alters plant development, including the floral transition, but regulation of timing of flowering by salt is poorly understood at the molecular level. To identify genetic loci regulating the floral transition under high soil salinity, we performed a genome-wide association study (GWAS) in Arabidopsis thaliana and identified natural variation at the UGT74E1-UGT74E2-BT3 (UUB) locus that correlates with bolting time specifically in response to salt stress. Genetic analysis revealed BT3 as a novel repressor of the floral transition in control conditions. Similarly, the putative IBA glycosylases UGT74E1 & UGT74E2 delay the floral transition in control conditions. Furthermore, we identified that IBA homeostasis regulators TOB1 and ECH2/IBR10 play a key role in the floral transition, and that ECH2/IBR10 are required for the early flowering phenotype of the ugt74e1/ugt74e2 double mutant, indicating that UGT74E1 & UGT74E2 delay flowering by altering IBA homeostasis. A pangenome analysis of the UUB locus revealed variation in the occurrence of the DNA transposon SAUERKRAUT (SKRT). CRISPR-mediated SKRT deletion in Col-0 affected gene expression both within and outside the UUB locus and caused a salt-dependent delayed floral transition. The delayed bolting phenotype of the skrt-2 mutant also depends on ECH2/IBR10 function, indicating that SKRT accelerates the floral transition by altering IBA homeostasis. Finally, targeted demethylation of SKRT resulted in delayed floral transition under salt stress. Taken together, our data show a role for SKRT and its DNA methylation levels in the salt-dependent bolting time response in Arabidopsis, revealing a novel molecular mechanism to control flowering in adverse conditions.

plant biology↗

bioRxiv2026

Genome-wide mapping of DCP2-dependent 5' cap footprints in Arabidopsis thaliana

mRNA decapping mediated by DCP2 is a key mechanism controlling RNA stability and gene expression in eukaryotes, including plants. Despite its central role in regulating plant development and stress responses, the repertoire of mRNA 5 caps targeted by DCP2 remains undefined. Here, we combined in vitro decapping treatment with 5-end enriched and full-length transcriptome sequencing of DCP2-deficient mutants to comprehensively characterize the mRNA capping landscape in Arabidopsis thaliana. We mapped over 13,000 high-confidence capped transcripts at nucleotide resolution, revealing distinct 5 cap signatures in both wild type and dcp2 seedlings. Most caps were localized near annotated transcription start sites, validating the accuracy of our approach. Loss of DCP2 led to a substantial accumulation of capped mRNAs, including 275 capped transcripts originating from previously unannotated loci. It also increased prevalence of multi-capped genes highlighting the role of DCP2-mediated decapping in removing unwanted transcripts. Integration of these data with degradome resources revealed that targets of co-translational and cytosolic XRN4-dependent decay, as well as of nonsense-mediated decay, were enriched among capped mRNAs specifically accumulated in dcp2. These findings suggest that mRNA degradation in these decay pathways is mediated through decapping. In addition, this study provides a valuable resource for transcript annotation and isoform-aware analysis of RNA turnover. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/709597v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@3569a2org.highwire.dtl.DTLVardef@aa2ca3org.highwire.dtl.DTLVardef@58a27forg.highwire.dtl.DTLVardef@1147350_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2024

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function

Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs-named premeiotic 24-nt phasiRNAs-have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). To determine whether premeiotic 24-nt phasiRNAs are also present in maize and related species and begin to characterize their biogenesis and function, we performed a comparative transcriptome and degradome analysis of premeiotic and meiotic anthers from five maize inbred lines and three teosinte species/subspecies. Our data indicate that a substantial subset of the 24-nt phasiRNA loci in maize and teosinte are already highly expressed at premeiotic phase. The premeiotic 24-nt phasiRNAs are similar to meiotic 24-nt phasiRNAs in genomic origin and dependence on DCL5 for biogenesis, however, premeiotic 24-nt phasiRNAs are unique in that they are likely (i) not triggered by microRNAs, (ii) not loaded by AGO18 proteins, and (iii) not capable of mediating cis-cleavage. In addition, we also observed a group of premeiotic 24-nt phasiRNAs in rice using previously published data. Together, our results indicate that the premeiotic 24-nt phasiRNAs constitute a unique class of reproductive phasiRNAs and are present more broadly in the grass family (Poaceae) than previously known. SIGNIFICANCEWe previously reported two classes of reproductive phasiRNAs in maize, the premeiotic 21-nt phasiRNAs and the meiotic 24-nt phasiRNAs. Here we report a third class of reproductive phasiRNAs - premeiotic 24-nt phasiRNAs - that are present in the Zea genus, including all five maize inbred lines and three teosinte species/subspecies that we examined, plus rice. We show that in the Zea genus the premeiotic 24-nt phasiRNAs are distinct from the meiotic 24-nt phasiRNAs in triggering mechanism, effector protein, and molecular function.

plant biology↗

bioRxiv2022

Precise Transcript Reconstruction with End-Guided Assembly

Accurate annotation of transcript isoforms is crucial to understand gene functions, but automated methods for reconstructing full-length transcripts from RNA sequencing (RNA-seq) data remain imprecise. We developed Bookend, a software package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5' and 3' ends. Through end-guided assembly with Bookend we demonstrate that correct modeling of transcript start and end sites is essential for precise transcript assembly. Furthermore, we discovered that utilization of end-labeled reads present in full-length single-cell RNA-seq (scRNA-seq) datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells (mESCs) can produce end-to-end transcript annotations of comparable quality to reference annotations in these model organisms. Summary statementBookend is a generalized framework that utilizes RNA 5' and 3' end information hidden in RNA-seq datasets to accurately reconstruct transcriptomes including those from single cells.

bioinformatics↗

bioRxiv2021

Innate, translation-dependent silencing of an invasive transposon in Arabidopsis

Co-evolution between hosts and parasites genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence-degeneration and, ultimately, loss-of-autonomy of most transposable elements (TEs). Recognition of newly-invasive plant TEs, by contrast, involves an innate antiviral-like silencing response. To investigate this responses activation, we studied the single-copy element EVADE (EVD), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically-reactivated. In Ty1/Copia-elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full-length genomic flGAG-POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly-nuclear flGAG-POL, during which an unusually intense ribosomal stalling event coincides precisely with the starting-point of sRNA production exclusively on shGAG. mRNA breakage occurring at this starting-point yields unconventional 5OH RNA fragments that evade RNA-quality-control and concomitantly likely stimulate RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) to initiate sRNA production. This hitherto-unrecognized "translation-dependent silencing" (TdS) is independent of codon-usage or GC-content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against de novo invasive TEs that underlies their associated sRNA patterns.

plant biology↗

bioRxiv2021

Gene Expression Variation in Arabidopsis Embryos at Single-Nucleus Resolution

Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos. Summary statementA transcriptome atlas of Arabidopsis embryos constructed from single nuclei reveals cell-specific epigenetic and transcriptional regulatory features.

plant biology↗

bioRxiv2019

MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis

MicroRNAs (miRNAs) are short non-coding RNAs that mediate the repression of target transcripts in plants and animals. Although miRNAs are required throughout plant development, relatively little is known regarding their embryonic functions. To systematically characterize embryonic miRNAs in Arabidopsis thaliana, we developed or applied high-throughput sequencing based methods to profile hundreds of miRNAs and associated targets throughout embryogenesis. We discovered dozens of miRNAs that dynamically cleave and repress target transcripts including 30 that encode transcription factors. Transcriptome analyses indicated that these miRNA:target interactions have a profound impact on embryonic gene expression programs, and we further demonstrated that the miRNA-mediated repression of six transcription factors were individually required for embryo morphogenesis. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.

developmental biology↗

bioRxiv2018

The embryonic transcriptome of Arabidopsis thaliana

Cellular differentiation is associated with changes in transcript populations. Accurate quantification of transcriptomes during development can thus provide global insights into differentiation processes including the fundamental specification and differentiation events operating during plant embryogenesis. However, multiple technical challenges have limited the ability to obtain high quality early embryonic transcriptomes, namely the low amount of RNA obtainable and contamination from surrounding endosperm and seed-coat tissues. We compared the performance of three low-input mRNA sequencing (mRNA-seq) library preparation kits on 0.1 to 5 nanograms (ng) of total RNA isolated from Arabidopsis thaliana (Arabidopsis) embryos and identified a low-cost method with superior performance. This mRNA-seq method was then used to profile the transcriptomes of Arabidopsis embryos across eight developmental stages. By comprehensively comparing embryonic and post-embryonic transcriptomes, we found that embryonic transcriptomes do not resemble any other plant tissue we analyzed. Moreover, transcriptome clustering analyses revealed the presence of four distinct phases of embryogenesis which are enriched in specific biological processes. We also compared zygotic embryo transcriptomes with publicly available somatic embryo transcriptomes. Strikingly, we found little resemblance between zygotic embryos and somatic embryos derived from late-staged zygotic embryos suggesting that the molecular basis of somatic and zygotic embryogenesis are distinct from each other. In addition to the biological insights gained from our systematic characterization of the Arabidopsis embryonic transcriptome, we provide a data-rich resource for the community to explore.\n\nKey MessageArabidopsis embryos possess unique transcriptomes relative to other plant tissues including somatic embryos, and can be partitioned into four transcriptional phases with characteristic biological processes.

genomics↗