Project description:HISTONE MONOUBIQUITINATION1 (HUB1) and its ortholog HUB2 regulate expression of genes involved in flowering, dormancy and circadian clock. HUB1 and HUB2 interact with two RNA-binding proteins KHD and SPEN. Phenotype analysis of the knock-down khd1-1, knock-out spen3-1, and knock-out hub mutants suggested that KHD and SPEN may contribute to flowering- and circadian clock-related functions that are also target of HUB1/2 activity. Transcriptome analysis was performed using RNA extracted from shoot apices of 10-day-old seedlings. After library preparation by TruSeq, RNA was sequenced on the Illumina HiSeq.
Project description:Analysis of the transcriptomes of nearly ripe siliques (18-19 DAP) of the rdo2-1, rdo3 and hub1-2 (rdo4) mutants in comparison with wild-type Ler, using Affymetrix GeneChip Arabidopsis ATH1 Genome Array.
Project description:ngs2018_05_tor-analysis of arabidopsis mutants tor/lst8/yak1/maktor-Analysis of Arabidopsis insertion and suppressor mutants linked to the TOR signaling pathway.-Comparison of in vitro grown plantlets for lst8, yak1 mutants and double mutants corresponding to suppressor lines. Comparison of in vitro grown plantlets for mutants affected in LST8 interacting proteins (MAKTOR) compared to wild type.
Project description:ra08-01_cpl1 - transcriptome analysis of fry2 mutants - Compare the transcriptome of 2 mutants affected in FRY2 (fry2-1 and 14-5sep) to control plants. - The Arabidopsis 14-5sep mutant was isolated as overexpressing a NII::LUC construct fusing a tobacco nitrite reductase gene with the luciferase reporter gene. This mutant overexpressed also the endogenous Arabidopsis nitrite reductase gene. Map-based cloning showed that the 14-5 sep mutant was affected in the FRY2 gene. Transciptome analysis was performed on both the 14-5sep and the fry2-1 mutants and their respective controls (either the C24 ecotype containing the RD29A::LUC transgene for fry2-1 or the Col0 accession containing the NII::LUC transgene for the 14-5sep mutant) to analyze which genes are differentially expressed in the mutants versus control plants. Keywords: gene knock out
Project description:In this experiment, we knocked down the expression of Split Ends (SPEN), a gene that we found was involved in the regulation of primary cilia formation, in MCF10A cells, to evaluate its effects on transcription. Split Ends (SPEN) is a transcriptional coregulator that have formerly identified as a tumour suppressor gene in ER-positive breast cancers. We expect the knockdown of SPEN in MCF10A cells to be accompanied with the down-regulation of genes involved in ciliogenesis as we observed that SPEN knockdown decreases primary cilia formation in those cells. We chose MCF10A cells because they harbour lots of primary cilia and therefore represent a good model to study the effect of SPEN on primary cilia formation.
Project description:Autophagy is an essential cellular process in eukaryotes that degrades and recycles macromolecules and organelles. Defects in autophagy is known to affect metabolism, including the lipidome. Genetic approaches have identified a series of AuTophaGy-related (ATG) genes in Arabidopsis. In this study we used WT (ecotype Col-0) and two Arabidopsis autophagy-defective mutants, atg7 and atg9 to perform a multi-omics study on the effect of nitrogen starvation treatment, which induces autophagy. Specifically, we have quantified ~100 lipids from leaf and root tissues of WT, atg7 and atg9 mutant plants, under either autophagy-inducing conditions (-N) or normal nitrogen conditions (+N). The lipid species we quantified include: DGDG, MGDG, LPC, LPE, PE, LPG, PC, PA, PG, PI, and PS. Our study sheds lights on the understanding of the relationships between autophagy and metabolism, especially lipid metabolism.