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E-GEOD-25237 - The DNA damage response transcriptome of the moss Physcomitrella patens

Status
Released on 10 November 2010, last updated on 3 April 2013
Organism
Physcomitrella patens
Samples (2)
Protocols (4)
Description
The moss Physcomitrella patens is remarkable for the ease with which mutant alleles of any gene can be generated by highly efficient homologous recombination-mediated gene targeting. Targeted transgene integration is believed to be mediated through the capture of transforming DNA by the homologous recombination DNA repair pathway. To identify components of this pathway in P. patens we have undertaken a transcriptomic analysis of the response to the sublethal induction of bleomycin-induced DNA double-strand breaks using massively parallel (Illumina) cDNA sequencing. Transcripts significantly increased in bleomycin-treated tissue include a number encoding conserved DNA-DSB components in both the homology-dependent pathway (including Rad51, CTiP, DNA ligase 1, Replication protein A, ATR) and the non-homologous end-joining pathway (including Xrcc4, DNA ligase 4, Ku70, Ku80, PARP). Differentially regulated cell-cycle components include up-regulated Rad9 and Hus1 DNA-damage-related checkpoint proteins and down-regulated D-type cyclins and B-type CDKs, commensurate with the imposition of a checkpoint in the G2 stage of the cell cycle characteristic of homology-dependent DNA-DSB repair. Comparison of the DNA damage transcriptome of P. patens with that of A. thaliana reveals significant up-regulation of a number of P. patens genes encoding ATP-dependent chromatin remodelling helicases of the SNF-2 class. These represent candidates for investigation of their role in mediating efficient gene targeting in P. patens. Gene expression profiling monitored by transcript abundance in control tissue and tissue treated with the DNA-DSB inducing agent, bleomycin
Experiment type
RNA-seq of coding RNA 
Contacts
John William Whitaker <drjohnwhitaker@gmail.com>, Andrew C Cuming, John W Whitaker, Yasuko Kamisugi
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-25237.idf.txt
Sample and data relationshipE-GEOD-25237.sdrf.txt
Additional data (1)E-GEOD-25237.additional.1.zip
Links