Practical NicE-seq workflow for chromatin accessibility analysis in plants

Open chromatin profiling identifies regulatory DNA regions that are accessible to transcription factors and other proteins, offering insights into gene regulation. Although ATAC-seq is commonly used for mapping open chromatin, standard techniques such as DNase-seq and ATAC-seq have limitations, including the need for large cell numbers or fresh (unfixed) samples. NicE-seq offers an alternative approach by using nicking endonucleases combined with polymerase-mediated biotin labeling. Here, we present a detailed analysis framework for NicE-seq data in plants using Arabidopsis thaliana as our reference species, adapted from the nf-core/atacseq pipeline with specific modifications. We emphasize the analytical differences between NicE-seq and ATAC-seq, describe data processing workflows, and illustrate methods for peak calling, annotation, and integration with transcriptomic data. This computational resource aims to guide researchers in applying NicE-seq, providing a basis for selecting between NicE-seq and ATAC-seq in plant epigenomic research, especially when working with challenging samples such as archived tissues or small cell populations.