Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize
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Updated: Jun 19, 2026

Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development
Published on: March 5, 2017
Axel A Elling1, Xing Wang Deng
1Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
Abstract:
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.
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