# Practical NicE-seq workflow for chromatin accessibility analysis in plants

## TL;DR

This paper introduces a NicE-seq workflow for studying chromatin accessibility in plants, offering an alternative to ATAC-seq for challenging samples.

## Contribution

A modified computational framework for NicE-seq data analysis in plants, adapted from ATAC-seq pipelines.

## Key findings

- NicE-seq is suitable for chromatin accessibility profiling in plants with limited or archived samples.
- The workflow includes peak calling, annotation, and integration with transcriptomic data.
- The framework is adapted from nf-core/atacseq with plant-specific modifications.

## Abstract

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.