The maize regulatory landscape at single molecule resolution

The evolution of the maize genome is intertwined with that of mobile DNA elements, yet the highly repetitive architecture of these mobile elements has limited our understanding of how these elements are organizing Maize genome regulation.impacting the precise which play a central role in is largely composed of repetitive DNA, including many retrotransposons and DNA transposons, posing challenges for short-read mapping of regulatory regions by ATAC-seq. Here, we demonstrate applied long-read the single-molecule chromatin fiber sequencing (, long-read assay Fiber-seq) for uniquely resolving the to maize to determine accessible chromatin regions and CpG methylation landscape of the maize genome, including XX% of the annotated mobile elements. irrespective of mappability. We demonstrate that Fiber-seq markedly improves our annotation of the maize regulatory grammer - enabling the single-nucleotide and single-molecule precise mapping of regulatory architectures that have escaped detection by short-read methods. doubling the number of maize grammer provides single-nucleotide, and single-molecule precise mapping of maize gene regulation aWe uncover discovered twice the number of accessible chromatin regions with Fiber-seq compared to matched ATAC-seq samples. However Notably, we find that only a small percentage of the additional accessible chromatin regions were due to low mappability. Instead, Fiber-seq detected a large number of regulatory elements that escaped detection by ATAC-seq due to size and frequency of occupancy. Overall, we find that recently transposed intact LTRs frequently encode stereotypical coupled accessible elements that do not impact the expression of neighboring genes. Notably, LTRs that lose this coupled architecture often exhibit hyper-CpG methylation directly within their accessible elements. Finally, we show that diffuse gene body chromatin accessibility and hypoCpG methylation guides the insertion landscape of DNA transposons, including those described by Barbara McClintock. Together, these findings provide insights to how mobile elements behave within and interact with the maize genome.