Characterization of transcriptional enhancers in plants using Arabidopsis thaliana and Zea mays as model species

Enhancers are non-coding regions of the genome controlling the transcription of genes located at distances ranging from kilo to mega bases. Enhancers act mainly as binding platforms for multiple transcription factors and were shown to interact directly with the promoter of their target genes. Since few enhancers are characterized in plants, we developed a pipeline to find new enhancers based on previous knowledge from plant and animal case studies. To do so, the two plant models Arabidopsis thaliana and Zea mays were used. Both functional and genome-wide approaches were used to study known enhancers in A. thaliana and Z. mays and identify putative enhancers in Z. mays. The characterization of novel enhancers in plants provides more insight about gene regulatory networks in plants. In fine, a better understanding of gene regulation could help improving important traits of cultivated plants by conventional breeding or biotechnological improvement. In A. thaliana, enhancers of the FLOWERING LOCUS T (FT) were characterized by inducing DNA methylation using Inverted Repeats (IRs). Indeed, DNA methylation was often associated with the inactivation of cis-regulatory elements such as enhancers and promoters in mammals and for some cases in plants. DNA methylation deposition at the previously characterized enhancer Block C led to downregulation of FT expression and subsequent late flowering phenotype in FT-inducing growth conditions. A novel putative enhancer of FT, named Block E, was found downstream of the gene and shared several features with Block C such as accessible chromatin, conserved sequences among Brassicaceae, and putative transcription factor binding sites present at Block C. Transgenic lines containing an IR targeting a part of Block E displayed a late flowering phenotype, which was not as strong as for Block C, but significantly higher than other lines used as control and displaying a mild late flowering phenotype. We conclude that IR-targeted DNA methylation is a useful tool that can allow characterization of known enhancers and discovery of putative ones. In Z. mays, differential chromatin accessibility, Histone 3 lysine 9 acetylation (H3K9ac) enrichment level, and gene expression profile were obtained for two different tissues (young seedling leaves and husk) in order to define enhancers’ location, activity, and associated genes. Enhancers were previously shown to be in most cases located in accessible chromatin, and to contain associated histone marks such as H3 lysine 27 acetylation (H3K27ac), H3 lysine 4 monomethylation (H3K4me1), or H3K9ac. We first verified whether our data could properly define known or putative enhancers and the expression of their target genes. Indeed, we could find both high chromatin accessibility and H3K9ac enrichment level for the known enhancers of teosinte branched1 (tb1) and booster1 (b1), and the corresponding expression fold change of the target genes across the two tissues. By combining chromatin accessibility and H3K9ac enrichment level data, we could determine ≈2000 candidate enhancers in intergenic regions. We could finally associate for each tissue about 20 differentially expressed genes to about 20 putative tissue-specific enhancers, which will be characterized by transient expression assays in the future

(Tissue) P Systems with Vesicles of Multisets

We consider tissue P systems working on vesicles of multisets with the very simple operations of insertion, deletion, and substitution of single objects. With the whole multiset being enclosed in a vesicle, sending it to a target cell can be indicated in those simple rules working on the multiset. As derivation modes we consider the sequential mode, where exactly one rule is applied in a derivation step, and the set maximal mode, where in each derivation step a non-extendable set of rules is applied. With the set maximal mode, computational completeness can already be obtained with tissue P systems having a tree structure, whereas tissue P systems even with an arbitrary communication structure are not computationally complete when working in the sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for obtaining computational completeness even for tissue P systems working in the sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622

Photoperiod-responsive changes in chromatin accessibility in phloem companion and epidermis cells of Arabidopsis leaves

Photoperiod plays a key role in controlling the phase transition from vegetative to reproductive growth in flowering plants. Leaves are the major organs perceiving day-length signals, but how specific leaf cell types respond to photoperiod remains unknown. We integrated photoperiod-responsive chromatin accessibility and transcriptome data in leaf epidermis and vascular companion cells of Arabidopsis thaliana by combining isolation of nuclei tagged in specific cell/tissue types with assay for transposase-accessible chromatin using sequencing and RNA-sequencing. Despite a large overlap, vasculature and epidermis cells responded differently. Long-day predominantly induced accessible chromatin regions (ACRs); in the vasculature, more ACRs were induced and these were located at more distal gene regions, compared with the epidermis. Vascular ACRs induced by long days were highly enriched in binding sites for flowering-related transcription factors. Among the highly ranked genes (based on chromatin and expression signatures in the vasculature), we identified TREHALOSE-PHOSPHATASE/SYNTHASE 9 (TPS9) as a flowering activator, as shown by the late flowering phenotypes of T-DNA insertion mutants and transgenic lines with phloem-specific knockdown of TPS9. Our cell-type-specific analysis sheds light on how the long-day photoperiod stimulus impacts chromatin accessibility in a tissue-specific manner to regulate plant development

A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment

Most well-characterized cases of adaptation involve single genetic loci. Theory suggests that multilocus adaptive walks should be common, but these are challenging to identify in natural populations. Here, we combine trait mapping with population genetic modeling to show that a two-step process rewired nutrient homeostasis in a population of Arabidopsis as it colonized the base of an active stratovolcano characterized by extremely low soil manganese (Mn). First, a variant that disrupted the primary iron (Fe) uptake transporter gene (IRT1) swept quickly to fixation in a hard selective sweep, increasing Mn but limiting Fe in the leaves. Second, multiple independent tandem duplications occurred at NRAMP1 and together rose to near fixation in the island population, compensating the loss of IRT1 by improving Fe homeostasis. This study provides a clear case of a multilocus adaptive walk and reveals how genetic variants reshaped a phenotype and spread over space and time

Summary statistics of the de novo transcriptome assembly of oak processionary moth (larval stages L2, L4, L5).

Summary statistics of the de novo transcriptome assembly of oak processionary moth (larval stages L2, L4, L5).</p

Benchmarking Universal Single-Copy Orthologues (BUSCO) analysis on the de novo transcriptome assembly of the oak processionary moth (larval stages L2, L4, L5)

Benchmarking Universal Single-Copy Orthologues (BUSCO) analysis on the de novo transcriptome assembly of the oak processionary moth (larval stages L2, L4, L5).</p

Differential gene expression analyses between larval stages of the oak processionary moth (<i>Thaumetopoea processionea</i>).

Differential expressed genes between each stages was performed, in addition to a comparison between the non-allergenic stage L2 and the allergenic stages L4 and L5 using DESeq2 R package. Log fold change shrinkage was performed using the apelgm R package. The lists of differentially expressed genes with an adjusted p-value below 5% for each comparison were summarized for each comparison in this Excel spreadsheet.</p

Trinotate annotation of the de novo transcriptome assembly of the oak processionary moth (larval stages L2, L4, and L5).

Trinotate annotation of the de novo transcriptome assembly of the oak processionary moth (larval stages L2, L4, and L5). Functional annotation of the transcriptome assembly generated by Trinity was performed with Trinotate (v3.2.2).</p

Chromatin and epigenetics in all their states : Meeting report of the first conference on Epigenetic and Chromatin Regulation of Plant Traits - January 14 – 15, 2016 - Strasbourg, France

In January 2016, the first Epigenetic and Chromatin Regulation of Plant Traits conference was held in Strasbourg, France. An all-star lineup of speakers, a packed audience of 130 participants from over 20 countries, and a friendly scientific atmosphere contributed to make this conference a meeting to remember. In this article we summarize some of the new insights into chromatin, epigenetics, and epigenomics research and highlight nascent ideas and emerging concepts in this exciting area of research.</p