Chromatin Accessibility Profiling in Whole Caenorhabditis elegans L4 Larvae

Chromatin accessibility plays essential roles in transcription, DNA repair, and chromosome segregation. Hyper-accessible regions usually correlate with active promoters and enhancers, facilitating transcription factor binding and regulatory activity. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) enables genome-wide profiling of chromatin accessibility with very few cells. However, its implementation in Caenorhabditis elegans is limited by the nematode's rich collagen cuticle that complicates cell dissociation. Here, we present an optimized protocol for performing ATAC-seq in whole worms at the L4 stage. The procedure begins with synchronized cultures and involves cuticle disruption, enzymatic dissociation, and cell-suspension preparation. Permeabilized nuclei are then subjected to Tn5 transposition, followed by polymerase chain reaction (PCR) amplification and purification of next-generation sequencing (NGS)-ready libraries. This protocol requires 30 µL of worm pellet, can be completed in one day, and generates 5,000-9,000 accessibility peaks in the Bristol N2 reference strain. This streamlined workflow can be adapted to other developmental stages or FACS-purified cell populations. By reducing technical barriers to ATAC-seq in C. elegans, this method expands opportunities to study genome-wide chromatin accessibility in response to genetic and environmental perturbations in a whole-organism context.