Cooperation of Multiple Chromatin Modifications Can Generate Unanticipated Stability of Epigenetic States inArabidopsis     

Abstract

Epigenetic changes of gene expression can potentially be reversed by developmental programs, genetic manipulation, or pharmacological interference. However, a case of transcriptional gene silencing, originally observed in tetraploid Arabidopsis thaliana plants, created an epiallele resistant to many mutations or inhibitor treatments that activate many other suppressed genes. This raised the question about the molecular basis of this extreme stability. A combination of forward and reverse genetics and drug application provides evidence for an epigenetic double lock that is only alleviated upon the simultaneous removal of both DNA methylation and histone methylation. Therefore, the cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic states and contributes to heritable diversity of gene expression patterns.

Arabidopsis SET DOMAIN GROUP2Is Required for H3K4 Trimethylation and Is Crucial for Both Sporophyte and Gametophyte Development

“…Curiously, sdg2-1 shows slightly elevated polyploidy levels but reduced cell size. Ploidydependent epigenetic regulation has been reported to be involved in differential reprogramming of orthologous gene expression and in stable silencing of epialleles (Lee and Chen, 2001;Baubec et al, 2010). Based on its global effect on H3K4me3 deposition, it is reasonable to speculate that SDG2 is involved in regulation of chromatin structure and gene expression in diploid and polyploid cells, playing important roles in the coordination of cell division, differentiation, and expansion to determinate organ size.…”

Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming

“…Tissue upregulated genes were defined as having log 2 -fold change $ 1 in one versus the other tissue. First, we estimated the effects of the transposonsilencing machinery by testing mutants for DECREASED DNA METHYLATION1 (DDM1), KRYPTONITE (KYP), and HISTONE DEACETYLASE6 (HDA6) (Baubec et al, 2010;Inagaki et al, 2010;Popova et al, 2013), which lead to a loss of DNA methylation, a loss of H3K9me2, and a gain of histone acetylation at heterochromatic loci, respectively. There was no clear correlation (maximum r = 0.040) between transcription in pollen relative to leaves and transcriptional changes induced by ddm1, kyp, and hda6 for all tested groups (Supplemental Figures 4A to 4C).…”

“…Throughout the study, we used the following ATH1 cDNA microarrays (Affymetrix): wild-type Arabidopsis development data produced by the AtGenExpress consortium (Schmid et al, 2005), Arabidopsis pollen development and sperm cell data sets NASCARRAYS-48 Twell, 2003, 2004), the ddm1-12 data set deposited at the Gene Expression Omnibus (GEO) as GSE18977 (Baubec et al, 2010), the kyp GEO data set GSE22957 (Inagaki et al, 2010), the clf, swn, and clf swn GEO data set GSE20256, and the hda6 (rts1-1) data set NASCARRAYS-538 (Popova et al, 2013). The raw data were processed and normalized using the robust multiarray averaging method (Irizarry et al, 2003) in R software (www.R-project.org) using Bioconductor (www.bioconductor.org) and the affy package.…”

Transgene Expression and Transgene-Induced Silencing in Diploid and Autotetraploid Arabidopsis

“…The inactivated HPT allele is associated with both DNA methylation and heterochromatic histone modifications and can be reactivated only when both of these modifications are reversed (Mittelsten Scheid et al 2003;Hetzl et al 2007;Baubec et al 2010). The authors proposed that DNA methylation and histone modifications cooperate to form a ''double lock'' on ploidyassociated transcriptional inactivation (Baubec et al 2010), but how these mechanisms are initiated remains unknown.…”