Study of changes in chromosomal interaction patterns of Flowering Locus C gene upon vernalization
ABSTRACT: The experiment was performed to test the hypothesis that the chromosomal interaction pattern of FLOWERING LOCUS C (FLC) Arabidopsis thaliana gene (At5g10140) changes its epigenetic state throughout vernalization.
Project description:Falster is a Danish perennial ryegrass ecotype with strong vernalization requirement, while Veyo is an Italian variety with no requirement for vernalization in order to flower. The transcriptome of these two perennial ryegrass genotypes with contrasting vernalization requirements was studied during primary (vernalization and short day conditions), and secondary induction (higher temperature and long day conditions) using an RNA-Seq approach, in order to reveal transcripts with expression profiles indicative of a role in floral induction, both in the promotion and repression of flowering.
Project description:We used high throughput sequencing of coding RNA to identify systematic patterns of expression during vernalization in meristems of lily bulbs that were treated with cold temperature for increasing periods of time. cDNA libraries were constructed from bulbs stored at 25 degrees Celsius (control) and at 4 degrees Celsius for 2, 5, 7 and 9 weeks
Project description:Vernalization, the requirement of long-term exposure to low environmental temperature for flowering, is a typical epigenetic phenomenon in plants. Histone modifications have been analyzed for key vernalization genes, but genome-wide regulation remains unclear. Here, we performed global analysis of histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) trimethylation with Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) during and after vernalization to obtain complete view of histone modification fluctuation both on whole genome scale and for single genes, even different regions of genes. The critical role of H3K27me3 was revealed. During vernalization H3K27me3 regulation concentrated on a few biological processes, with two essential environmental responses, transcription regulation and anti-stress reactions, being main targets, as indicated by change pattern and GO analysis. The regulation of H3K4me3, however, showed no obvious focus. For gene expression, H3K27me3 is involved in multiple trends of control. H3K4me3, however, mainly focuses on unidirectional regulation. After vernalization most of H3K27me3 changes were kept, but relatively small proportion of H3K4me3 changes could be maintained, as shown by multiple-level analysis, suggesting the active role of H3K27me3 in epigenetic memory. Vernalization-induced histone modification changes were uncovered for VRN3, a gene integrating vernalization/photoperiod signals, suggesting its regulation role at epigenetic level. Memory-related genes were genome-widely identified and a high proportion of them showed quantitative response to vernalization-treatment, suggesting broad existence of this mechanism. Our studies shed new light on epigenetic role of H3K27me3 and VRN3 in vernalization, revealed mechanism underlying epigenetic memory, which helps us to further understand vernalization, a mechanism with great potential in agriculture. Overall design: Examination of 2 different histone modifications (H3K4me3 and H3K27me3) in 3 differently vernalized Brachypodium seedlings (V0,V30 and V30N). And another one H3K4me3 sequencing in non-vernalized seedlings (H3K4me3_V0_2) is the biological replication.
Project description:The aim of this experiment was to identify transcripts upregulated during vernalization in Lolium perenne plants. Illumina Genome Analyzer II RNA-Seq data was generated from leaf samples collected before vernalization, and after the start of cold treatment, at 2 days, 4 weeks and 9 weeks.
Project description:Stem cells are defined by their ability to self-renew and produce daughter cells that proliferate and mature. These maturing cells transition from a proliferative state to a terminal state through the process of differentiation. In the Arabidopsis thaliana root the transcription factors SCARECROW and SHORTROOT regulate specification of the bi-potent stem cell that gives rise to the cortical and endodermal progenitors. Subsequent progenitor proliferation and differentiation generates mature endodermis, marked by the Casparian Strip: a cell wall modification that prevents ion diffusion into and out of the vasculature. We identified a transcription factor, MYB36 that regulates the transition from proliferation to differentiation in the endodermis. We show that SCARECROW directly activates MYB36 expression, which in turn directly regulates essential Casparian Strip formation genes. In addition, MYB36 represses extra divisions within the endodermis. Our results demonstrate that MYB36 is a critical positive regulator of differentiation and negative regulator of cell proliferation. 12 samples analyzed: 3 biological replicates each from 1) wild type (Col-0) whole root, 2) mutant (myb36-1) whole root, 3) wild type (Col-0) sorted endodermis, 4) mutant (myb36-1) sorted endodermis
Project description:Gene expression was assyed in seedlings of isogenic barley lines differing in vernalization requirement. Seedlings were harvested after 5 days germination in darkness at 20 degrees. Seedlings were then subjected to 1 day at 4 degrees after 5 days germination in darkness at 20. Genotypes include the winter barley parent Dairokakku, and isogenic lines carrying a deletion of VRN2, active VRN1 allleles (VRN1-10, or VRN1-8) or an active allele of FT1/VRN3. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Ben Trevaskis. The equivalent experiment is BB97 at PLEXdb.] Overall design: genetic line: +VRN1-10 - temperature: 20 C(3-replications); genetic line: +VRN1-10 - temperature: 4 C(3-replications); genetic line: -VRN2 - temperature: 20 C(3-replications); genetic line: -VRN2 - temperature: 4 C(3-replications); genetic line: +VRN1-8 - temperature: 20 C(3-replications); genetic line: +VRN1-8 - temperature: 4 C(3-replications); genetic line: +FT1/VRN3 - temperature: 20 C(3-replications); genetic line: +FT1/VRN3 - temperature: 4 C(3-replications); genetic line: Parent (winter type) - temperature: 20 C(3-replications); genetic line: Parent (winter type) - temperature: 4 C(3-replications)
Project description:The maintained vegetative phase (mvp) mutant has a non-flowering phenotype caused by deletions including, but not limited to, the genes CYS, PHYC and VRN1. However the impact of these deletions on flowering genes and global gene expression is still unknown. In this study, we showed that these deletions caused the up-regulation of several pathogenesis related (PR) and jasmonate responsive genes using microarray analysis. Our results raise the hypothesis that jasmonates may be involved in flowering. To confirm this hypothesis, the methyl-jasmonate (MeJA) and jasmonic acid (JA) content in mvp and wild type plants was measured. The content of JA was comparable in all plants while the content of MeJA was higher in mvp plants. Our transcriptomic and chemical analyses of the mvp mutants plants reveal that the deletion of the major vernalization gene TaVRN1 induces the up-regulation of the major biotic stress related genes and the accumulation of MeJA. In addition, our results demonstrate an important role of MeJA during vernalization and flowering in wheat. A total of 3 biological replicates (R1, R2 and R3) for each condition (wild type (control) and mvp mutant (mutant) ) were used for microarray analyses. Each biological replicate sample was obtained by pooling three wild type plants (control) or five mvp plants (mutant) from different plants harvested randomly. The different biological samples of einkorn spring wheat whole aerial part were ground in dry ice to fine powder and total RNA was extracted with trizol (Invitrogen, Burlington, ON, CA). Total RNA was cleaned using RNeasy plant mini kit (Qiagen) and integrity was determined on agarose gel and on a bioanalyser (Agilent 2100). Synthesized cDNAs were transcribed to cRNAs with the 3’IVT labelling kit (Santa Clara, CA, USA) and hybridized to the Affymetrix wheat genome array (Santa Clara, Ca, USA) at the McGill University and Génome Québec Innovation Centre (Montreal, Qc, CA). The experimental design consisted of three biological replicates for each of the two conditions, 1: The einkorn wheat (Triticum monococcum L. 2n = 2x = 14, AmAm) wild type plants (control) and 2: the mvp plants (mutant). Thus, a total of 3 biological samples from each of the two conditions described above were used for hybridizations.