Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice

Abstract

Background: mPing is an endogenous MITE in the rice genome, which is quiescent under normal conditions but can be induced towards mobilization under various stresses. The cellular mechanism responsible for modulating the activity of mPing remains unknown. Cytosine methylation is a major epigenetic modification in most eukaryotes, and the primary function of which is to serve as a genome defense system including taming activity of transposable elements (TEs). Given that tissue-culture is capable of inducing both methylation alteration and mPing transposition in certain rice genotypes, it provides a tractable system to investigate the possible relationship between the two phenomena.

Tissue Culture-Induced Novel Epialleles of aMybTranscription Factor Encoded bypericarp color1in Maize

“…Consistent with activation of transposable elements are changes in their epigenetic status; reduced methylation has been reported to correspond to the active state of several transposons in tissue culture (Cheng et al 2006;Ngezahayo et al 2009). Although tissue culture-induced chromatin modifications have been shown to occur in many types of sequences, the extent to which these modifications affect the expression of nontransposon sequences remains unclear.…”

Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications

“…When over-expressed in tobacco, the gene was able to confer cell division and callus formation properties, instead of root organogenesis in an auxin-rich medium, Leal et al (2006) Fluorescent in situ hybridization (FISH) Gernand et al (2007) 2 DNA sequence changes Restriction fragment length polymorphism (RFLP) Andreev et al (2005) Inter-simple sequence repeats markers (ISSR) Sreedhar et al (2007) Random amplified polymorphic DNA (RAPD) Jin et al (2008) Microsatellites or simple sequence repeat (SSR) Jin et al (2008) Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) Kour et al (2009) Amplified fragment length polymorphism (AFLP) Li et al (2007) Next generation sequencing of genomic DNA libraries Jiang et al (2011) 3 DNA sequence-specific changes Inter-retrotransposon amplified polymorphism (IRAP) Smýkal et al (2007) Sequence-specific amplification polymorphism (SSAP) Kour et al (2009) Transposon display Ngezahayo et al (2009) 4 RNA expression changes Differential display Linkiewicz et al (2004) Suppression subtractive hybridization Zeng et al (2006) EST array or Gene Chip hybridization Che et al (2006a, b) cDNA macroarray hybridization Singla et al (2007) Genome-scale microarray hybridization Bao et al (2009) Kaeppler and Phillips (1993a, b) and Jaligot et al 2002 Methylation-sensitive restriction fragment length polymorphism (metRFLP) Bednarek et al (2007) Methylation-sensitive amplification polymorphism (MSAP) Kour et al (2009) Based on treatment with the restriction enzyme McrBC, which only cleaves DNA at 5-methylcytosine Tanurdzic et al (2008) DNA degradation followed by reversed-phase high-performance liquid chromatography (RP-HPLC) Kubis et al (2003) DNA degradation followed by high performance capillary electrophoresis (HPCE) Berdasco et al (2008) Based on bisulfite treatment, which changes un-methylated cytosines into uracil, and sequencing Ngezahayo et al (2009) Transposon methylation display (TMD) Ngezahayo et al (2009) 9 Chromatin condensation Fluorescent in situ hybridization (FISH) Koukalova et...…”

Epigenetics in plant tissue culture

“…In maize, the activation is passed on for two sexual generations (Brettell and Dennis 1991). The miniature inverted repeat transposable element (MITE) mPing becomes activated in rice, e.g., in callus culture, which is correlated with alterations in cytosine methylation (Ngezahayo et al 2009). The retroelement Tos17 becomes active in rice suspension cultures, supposedly as a consequence of changes in the epigenetic modifications that silence it.…”