Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the  delineation of DNA structure by DNA sequence (SS-Seq)
We developed an efficient method to map DNA supercoils that quantifies genome-wide incorporation of biotinylated psoralen using high throughput DNA sequencing and applied it to C. elegans. We discovered that GC-rich regions flanked by sharp GC/AT boundaries delineate the extent of negative supercoiling at transcription start sites, the regions of DNA accessibility and the positioning of nucleosomes.  We also discovered that promoters with either paused or non-paused RNA polymerase II (Pol II) exhibit the same level of supercoiling, revealing that supercoiling at transcription start sites is neither the cause nor consequence of Pol II pausing.  Furthermore, we found that a condensin complex that mediates X-chromosome dosage compensation in C. elegans creates local negative supercoils at its high-occupancy binding sites on X but does not create large domains of supercoiling across X to achieve dosage compensation.  We also developed a new high-throughput method to map single-stranded DNA and alternative DNA structures, including Z DNA. The approach combines potassium permanganate footprinting and a technique to sequence rare double-stranded breaks.  We discovered that GC-rich regions flanked by sharp GC/AT boundaries determine the width of single-stranded DNA regions at transcription start sites.  Moreover, AT-rich sequences bordered by a change in GC content delineate Z DNA at transcription end sites and in introns as well as non-B DNA at trans-splicing acceptor sites that comprise the 5' ends of most mature mRNAs in C. elegans.  Our analysis suggests that a sharp transition in GC content rather than the GC content by itself creates alternative DNA structures. Overall design: We performed potassium permanganate footprinting in C. elegans wild type and dosage compensation defective embryos, starved first stage larvae and larvae treated with a-amanitin to inhibit transcription.