Plant Physiol. 2018 Feb 20. pii: pp.01467.2017. doi: 10.1104/pp.17.01467. [Epub ahead of print]
Genomic regions free of nucleosomes are hypersensitive to DNase I digestion. These genomic regions are known as DNase I hypersensitive sites (DHSs) and frequently contain cis-regulatory DNA elements. We developed high-resolution genome-wide DHS maps in maize using a modified DNase-seq technique. Maize DHSs exhibit depletion of nucleosomes and low levels of DNA methylation, and are enriched with conserved non-coding sequences (CNSs). We developed a protoplast-based transient transformation assay to validate the potential enhancer and/or promoter functions associated with DHSs. More than 80% of DHSs overlapping with CNSs showed enhancer function. Strikingly, nearly 25% of maize DHSs were derived from transposable elements (TEs), including both class I and class II transposons. Interestingly, TE-derived DHSs (teDHSs) homologous to retrotransposons were enriched with sequences related to the intrinsic cis-regulatory elements within the long terminal repeats (LTRs) of the retrotransposons. We demonstrate that more than 80% of teDHSs can drive transcription of a reporter gene in protoplast-based transformation assays. These results reveal the wide spread occurrence of TE-derived cis-regulatory sequences and suggest a major role of teDHSs in transcriptional regulation in maize.