The transcriptional response of Arabidopsis to genotoxic stress – a high‐density colony array study (HDCA)

Abstract

SummaryA genome-wide transcription pro®ling of Arabidopsis upon genotoxic stress has been performed using a high-density colony array (HDCA). The array was based on a library of 27 000 cDNA clones derived from Arabidopsis cells challenged with bleomycin plus mitomycin C. The array covers more than 10 000 individual genes (corresponding to at least 40% of Arabidopsis genes). After hybridisation of the HDCA with labelled cDNA probes obtained from genotoxin-treated (bleomycin plus mitomycin C, 6 h) and untreated seedlings, 39 genes revealed an increased and 24 genes a decreased expression among the 3200 highly expressed clones (representing approximately 1200 individual genes because of redundancy of the cDNA library). Of the 4900 clones with a low transcriptional level, the expression of 500 clones was found to be altered and 57 genes with increased and 22 genes with decreased expression were identi®ed by sequence analysis of 135 identi®ed clones. The HDCA results were validated by real-time PCR analysis. For about 80% of genes (34 out of 42), alteration in expression was con®rmed, indicating the reliability of the HDCA for transcription pro®ling. DNA damage and stress-responsive genes encoding, for instance transcription factors (myb protein and WRKY1), the ribonucleotide reductase small subunit (RNR2), thymidine kinase (TK), an AAA-type ATPase, the small subunit of a DNA polymerase and a calmodulin-like protein were found to be strongly upregulated. Also, several genes involved in cell cycle regulation revealed signi®cant alteration in transcription, as detected by real-time PCR analysis, suggesting disturbance of cell cycle progression by mutagen treatment.

E2F RegulatesFASCIATA1, a Chromatin Assembly Gene Whose Loss Switches on the Endocycle and Activates Gene Expression by Changing the Epigenetic Status

“…It is worth noting that CYCB1;1, but not other mitotic cyclins, are up-regulated after DNA-damaging treatment (Chen et al, 2003). A similar response is observed after aphidicolin-induced replication stress, which is not displayed in the atr mutants, defective in the G2 checkpoint (Culligan et al, 2004).…”

“…Both pathways are largely conserved in Arabidopsis and rely on a transduction cascade dependent on ATM and ATR gene products (Garcia et al, 2003;Culligan et al, 2004). Transcriptional up-regulation of certain genes in these pathways is a hallmark of plant DNA damage checkpoint response (Chen et al, 2003;Lafarge and Montane, 2003;DeBlock et al, 2005). We found that the mRNA levels of Ku70, which participates in the G1 checkpoint and NHEJ, did not change.…”

“…4B) or in wild-type plants after damaging treatment, other mitotic cyclins are upregulated in root and aerial organs (Supplemental Fig. S5; Chen et al, 2003;Schö nrock et al, 2006). Finally, we determined by ChIP experiments the epigenetic status of a set of genes that are up-regulated in response to zeocin treatment and also in a constitutive manner in fas1-4 plants.…”

Tissue-specific and DNA damage-responsive expression of the Arabidopsis RAD51 gene promoter in transgenic Arabidopsis and tobacco

“…Many works have been reported on gene regulation of DNA repair genes in response to DNA damage (Chen et al 2003;Molinier et al 2005). However, the promoter functions of DNA repair genes that direct tissue specific and DNA damage-responsive gene expression are not necessarily clear.…”

“…Recent works of DNA repair-related plant genes involved in response to treatment with DNA damaging agents revealed that the induction level of AtRAD51 gene is one of the best among the up-regulated genes that respond to DNA damage (Chen et al 2003;Molinier et al 2005). In order to investigate the DNA damage response of AtRAD51 promoter, a radiomimetic bleomycin, which is known to induce mostly DSBs (Menke et al 2001), and the UV-B radiation, which is reported to result in increased frequencies of homologous recombination in plant (Ries et al 2000), were employed as DNA damaging agents.…”