Abstract
Paramutations represent directed and meiotically-heritable changes in gene regulation leading to apparent violations of Mendelian inheritance. Although the mechanism and evolutionary importance of paramutation behaviors remain largely unknown, genetic screens in maize (Zea mays) identify five components affecting 24 nucleotide RNA biogenesis as required to maintain repression of a paramutant purple plant1 (pl1) allele. Currently, the RNA polymerase IV largest subunit represents the only component also specifying proper development. Here we identify a chromodomain helicase DNA-binding 3 (CHD3) protein orthologous to Arabidopsis (Arabidopsis thaliana) PICKLE as another component maintaining both pl1 paramutation and normal somatic development but without affecting overall small RNA biogenesis. In addition, genetic tests show this protein contributes to proper male gametophyte function. The similar mutant phenotypes documented in Arabidopsis and maize implicate some evolutionarily-conserved gene regulation while developmental defects associated with the two paramutation mutants are largely distinct. Our results show that a CHD3 protein responsible for normal plant ontogeny and sperm transmission also helps maintain meiotically-heritable epigenetic regulatory variation for specific alleles. This finding implicates an intersection of RNA polymerase IV function and nucleosome positioning in the paramutation process.
Highlights
Organismal development requires alleles to undergo controlled transitions between silent and expressed states coordinated by transcription factors, non-coding RNAs, and chromatin regulators interacting with allele-specific regulatory sequences
Funding was provided by awards to J.Brachypodium stacei (Bs).H. from the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service (99-35301-7753, 2001-35301-10641, and 2006-35304-17399), the National Science Foundation (MCB-0419909, -0920623, -1715375) and The Ohio State Foundation
Because repressed Pl1-Rhoades states invariably condition weak pigmentation, mutations disrupting functions required to maintain this repression are identified by increased anthocyanin production [40]
Summary
Organismal development requires alleles to undergo controlled transitions between silent and expressed states coordinated by transcription factors, non-coding RNAs, and chromatin regulators interacting with allele-specific regulatory sequences. SRNAs are typically processed from DNA-dependent RNA polymerase (RNAP) II transcripts, but in multicellular plants, additional RNAP II-related complexes [4,5] having specialized functions in transcriptional regulation [6,7,8,9] generate the majority of siRNA precursors. RNAP II-related RNAPs IV and V collaborate to maintain repressive chromatin states through the action of RNAP IV-derived siRNAs that primarily target TEs and other repetitive sequences for de novo cytosine methylation and subsequent histone modifications via a process termed RNA-directed DNA Methylation (RdDM) [10]. The evolutionary importance of such diversity and regulatory novelty remains completely unknown
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