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Article Addendum

Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize

Axel A. Elling and Xing Wang Deng

Epigenetic modifications and small RNAs play an important role in gene regulation. Here, we discuss results of our Solexa/Illumina 1G sequencing-based survey of DNA methylation, activating and repressive histone modifications, small RNAs and mRNA in the maize genome. We analyze tissue-specific epigenetic patterns, discuss antagonistic relationships between repressive epigenetic marks and highlight synergistic relationships between activating histone modifications. We discuss our observation that small RNAs show a tissue-specific distribution in maize. Whereas 24-nucleotide long small interfering RNAs (siRNAs) accumulated preferentially in shoots, 21-nucleotide long micro RNAs (miRNAs) were the most abundant group in roots, which follows the transcript level of mop1. Furthermore, we discuss the possibility that a novel class of 22-nucleotide siRNAs might originate from long double-stranded RNAs in an RNA-dependent RNA polymerase (RdRP)-independent manner. This supports the intriguing possibility that maize possesses at least two distinct pathways to generate siRNAs, one of which relies on RdRP and a second one that might be RdRP-independent.

Addendum to: Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 2009; 21:1053-69. PMID: 19376930.

Authors

Axel A. Elling

Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, Connecticut USA

Xing Wang Deng Corresponding author: xingwang.deng@yale.edu

Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, Connecticut USA