Profiling Dynamic Changes in DNA Accessibility During Axon Regeneration After Optic Nerve Crush in Adult Zebrafish

A time-course series utilizing assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) can be used to detect changes in accessibility of DNA regulatory elements such as promoters and enhancers over the course of regeneration. This chapter describes methods for preparing ATAC-seq libraries from isolated zebrafish retinal ganglion cells (RGCs) following optic nerve crush at selected post-injury time points. These methods have been used for identifying dynamic changes in DNA accessibility that govern successful optic nerve regeneration in zebrafish. This method may be adapted to identify changes in DNA accessibility that accompany other types of insults to RGCs or to identify changes that occur over the course of development.