# Chromatin state architecture governs transcription factor accessibility across plant genomes

## TL;DR

The study shows that chromatin states are conserved in plants and influence where transcription factors bind, affecting gene regulation.

## Contribution

The paper introduces a new index to predict transcription factor binding and reveals conserved chromatin state interactions in plants.

## Key findings

- Chromatin states are functionally conserved across land plants over 450 million years of evolution.
- Transcription factors are grouped based on their chromatin state preferences and biological functions.
- The study identifies potential pioneer factors in plants, which are poorly understood compared to their roles in animals.

## Abstract

The complexity of varied modifications of chromatin composition is integrated in archetypal combinations called chromatin states that predict the local potential for transcription. The degree of conservation of chromatin states has not been established amongst plants, and how they interact with transcription factors is unknown. Here we identify and characterize chromatin states in the flowering plant Arabidopsis thaliana and the bryophyte Marchantia polymorpha, showing a large degree of functional conservation over more than 450 million years of land plant evolution. We used this new resource of conserved plant chromatin states to understand the influence of chromatin states on gene regulation. We established the preferential association of chromatin states with binding sites and activity of transcription factors. These associations define three main groups of transcription factors that bind upstream of the transcription start site, at the + 1 nucleosome or further downstream of the transcription start site and broadly associate with distinct biological functions including a list of potential candidate pioneer factors we know little about in plants, compared to their important roles in animal stem cells and early development.

In eukaryotes, DNA is tightly associated with histone proteins. Histone covalent modifications and histones isoforms, also called histone variants provide most of the complexity of chromatin and associate in specific combinations called chromatin states. Here we establish the broad conservation of chromatin states and their association with transcription in land plants. We design an index that predicts transcription factor binding and identify distinct groups of transcription factors based on their occupation of chromatin states. Our findings suggest that chromatin defines a specific environment that reflects transcriptional activity.