Project description:In order to identify differentially expressed genes in developing seeds of Arabidopsis thaliana three different stages of seed development were analysed (9-10, 10-11 and 12-13 days after flower opening) for two Arabidopsis thaliana accessions, Col-0 and C24. For each stage and accession three biological replicates were analysed.
Project description:Eukaryotic genomes are heavily regulated by epigenetic marks that often act to modulate the transcriptional control of genetic elements. In Arabidopsis thaliana the ATXR5 and ATXR6 histone methyltransferases, and their cognate H3K27 monomethylation mark, act in transcriptional silencing while also maintaining genome stability by preventing generation of excess DNA corresponding to pericentromeric heterochromatin. In this study we characterize the atxr5 atxr6 transcriptome and its relationship to the DNA damage response which suggests that the atxr5 atxr6 transcriptional defects may be epistatic to the genome instability defects in the mutants. In addition we isolate several factors that modulate both the transcriptional and genomic instability phenotypes of atxr5 atxr6 mutants, which suggest a mechanism for atxr5 atxr6-induced extra DNA involving conflicts between the replicative and transcriptional processes in the cell. PolyA RNA sequencing (RNA-seq), whole-genome resequencing (DNA-seq), and whole-genome bisulfite sequencing (methyl-seq) was performed on Arabidospsis thaliana mutant and wildtype plants. DNA-seq was used to characterize DNA copy number and map EMS-induced mutations, RNA-seq was used to quantify transcript abundance and map EMS-induced mutations, and methyl-seq was used to assess DNA methylation. Details of the relationship between samples in this series and figures in the associated manuscript can be found in Supplemental Table 4 of the associated manuscript. Unless otherwise noted in the description all lines are ecotype Columbia, and all genotypes should be assumed homozygous unless otherwise indicated with a '/'.
Project description:To gain further insights into a larger number of processes potentially altered by high nickel (Ni), we performed a transcriptional profiling of whole roots of Arabidopsis thaliana accession Columbia-0 (Col-0) exposed to 100 µM nickel, a concentration that induces slight chlorosis and intermediate inhibition of root and shoot growth.
Project description:In order to identify differentially expressed genes in developing seeds of Arabidopsis thaliana three different stages of seed development were analysed (9-10, 10-11 and 12-13 days after flower opening) for two Arabidopsis thaliana accessions, Col-0 and C24. For each stage and accession three biological replicates were analysed.