Chromatin Accessibility Profiling in Whole Caenorhabditis elegans L4 Larvae

Area of Science:

• Molecular Biology
• Genomics
• Developmental Biology

Background:

• Chromatin accessibility is crucial for fundamental cellular processes like transcription and DNA repair.
• The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is a powerful tool for profiling genome-wide chromatin accessibility.
• Existing ATAC-seq methods face challenges in Caenorhabditis elegans due to the nematode's cuticle, hindering cell dissociation.

Purpose of the Study:

• To develop and optimize a protocol for performing ATAC-seq on whole Caenorhabditis elegans worms.
• To overcome technical barriers associated with cell dissociation in C. elegans for ATAC-seq analysis.
• To facilitate genome-wide chromatin accessibility studies in C. elegans under various conditions.

Main Methods:

• Synchronized L4 stage C. elegans cultures were used.
• The protocol involves cuticle disruption, enzymatic dissociation, and cell suspension preparation.
• Permeabilized nuclei undergo Tn5 transposition, followed by PCR amplification and library purification for next-generation sequencing.

Main Results:

• The optimized protocol requires a small worm pellet (30 µL) and can be completed within one day.
• The method yields 5,000-9,000 chromatin accessibility peaks in the Bristol N2 reference strain.
• The streamlined workflow is adaptable to different developmental stages and FACS-purified cell populations.

Conclusions:

• This optimized ATAC-seq protocol significantly reduces technical barriers for studying chromatin accessibility in whole C. elegans.
• The method enables broader investigation of genome-wide chromatin accessibility in response to genetic and environmental factors in a whole-organism context.
• This advancement expands research opportunities in C. elegans epigenetics and gene regulation.