Identification of Transposable Element Families in Zea Mays that Exhibit Tissue-Specific Variation in Chromatin Structure

Transposable elements (TEs) make up a large portion of the maize genome. Some of these elements have been shown to be active in different tissues or developmental stages. Transposon activity, thought to involve changes in chromatin structure, is associated with more accessible or “open” states. Differential Nuclease Sensitivity profiling (DNS-seq) was developed in the Bass Lab to identify MNase-hypersensitive regions of open chromatin. The Bass Lab applied DNS-seq and peak calling to four distinct B73 tissues: root tip (RT), coleoptile node (CN), ear shoot (ES), and endosperm (EN). Chromatin accessibility data is often used to study gene regulation; however, in this study it was used to study transposon biology. Transposable element families were examined to determine whether they exhibit tissue-specific changes in chromatin structure. I analyzed two hundred five abundant transposable element families by calculating the number of base pairs of each that intersected with open chromatin, classified as MNase hypersensitive footprints (DNS-seq positive peaks, iSeg-BC1). For comparison, a probability distribution was generated from a 100-iteration control in which the peak positions were shuffled. Then z-scores were obtained using the mean and standard deviation of the random-distribution control simulations and the observed intersection scores. The resulting 820 z-scores revealed the statistical degree of enrichment (positive z-scores) or depletion (negative z-scores) of open chromatin for each transposable element family in the four different tissues. I found that some transposable element families, such as puck, milt, bygum, iwik, ilyl, and ebel, appeared to have positive z-scores in only a single tissue, CN. Similarly, ubow and osed were enriched in only ES, whereas ibulaf was enriched in only RT, and none of them for only EN. This study reveals that TE families can exhibit tissue-specific chromatin dynamics, illustrating a novel approach to better understand transposon behavior in maize development.