Assaying Chromatin Accessibility Using ATAC-Seq in Invertebrate Chordate Embryos

Area of Science:

• Developmental Biology
• Evolutionary Biology
• Genomics

Background:

• Cis-regulatory elements (CREs) control gene expression crucial for animal development and evolution.
• Understanding CREs across species and developmental stages is key to deciphering evolutionary mechanisms.
• The Assay for Transposase-Accessible Chromatin (ATAC-seq) is a high-resolution technique for genome-wide CRE detection.

Purpose of the Study:

• To establish a detailed ATAC-seq protocol for invertebrate chordate marine embryos.
• To provide a streamlined bioinformatic workflow for analyzing ATAC-seq data.
• To demonstrate the utility of ATAC-seq in identifying functional CREs in developmental pathways.

Main Methods:

• A step-by-step ATAC-seq protocol optimized for low cell input (<10^5 cells) and rapid execution (1 day).
• Application of the protocol to amphioxus and tunicate embryos.
• Development of a bioinformatic pipeline for ATAC-seq data analysis.

Main Results:

• Successful genome-wide identification of CREs in open chromatin regions of marine invertebrate embryos.
• Demonstrated efficiency of the protocol and pipeline in detecting CREs associated with the Wnt signaling pathway.
• Validated the method's applicability using drug-perturbed embryos.

Conclusions:

• The developed ATAC-seq protocol and bioinformatic pipeline are effective for identifying functional CREs in diverse animal embryos.
• This approach facilitates the study of gene regulation and evolutionary processes across a broad range of animal lineages.
• The method is adaptable for investigating other signaling pathways and gene mutants in developmental studies.