# Centromere-size reduction and chromatin state dynamics following intergenomic hybridization in cotton

## TL;DR

This study explores how centromeres change in size and structure when transferred between cotton species, revealing key epigenetic factors involved in their adaptation.

## Contribution

The study reveals novel epigenetic mechanisms, including H3K36me2 dynamics and chromatin reorganization, that underlie centromere adaptation following intergenomic hybridization in cotton.

## Key findings

- Ga centromeres consistently reduced in size when transferred into the Gh background.
- Elevated H3K36me2 levels and altered chromatin accessibility correlate with centromere stability.
- Hi-C analysis shows reorganized 3D chromatin architecture linked to new topologically associating domains.

## Abstract

Centromeres are pivotal for accurate chromosome segregation, yet their regulation and evolutionary dynamics remain poorly understood. Here, we investigate centromeres of the diploid species Gossypium anomalum (Ga, B-genome) that were transferred into tetraploid cotton G. hirsutum (Gh, AD-genome) as either an additional or integrated chromosome, as well as in synthetic allohexaploid (AABBDD) lines. We demonstrate consistent size reduction for all Ga centromeres in the Gh background. Histone modification profiling across 10 marks revealed heightened levels of both active and repressive chromatin marks within the Ga centromeres when transferred into the Gh background, particularly for H3K36me2. The centromeric histone modification perturbation extended into pericentromeric regions, with variable CENH3-binding domains consistently exhibiting a more pronounced increase in histone modification levels compared to stable centromere regions, highlighting the role of histone modification elevation in centromere dynamics. In addition, we observed enhanced chromatin accessibility and the presence of non-B-form DNA motifs, such as A-phased DNA repeats within stable centromere domains that are correlated with centromere stability. Hi-C analysis reveals a reorganized 3D chromatin architecture within the introgression line centromeres, including the formation of new topologically associating domains linked to H3K36me2 dynamics, emphasizing the importance of H3K36me2 in centromere organization. Together, these findings elucidate epigenetic mechanisms underlying centromere composition following intergenomic hybridization and allopolyploid formation, offering insights into centromere evolution in plants and its myriad epigenetic and potentially functional dimensions.

Centromeres are crucial for ensuring accurate chromosome segregation during cell division, yet their adaptability and regulatory mechanisms are not well understood. In cotton species, hybridization can lead to significant alterations in centromere characteristics, raising important questions about the underlying processes driving these adaptations. In our study, we focus on the centromeres of Gossypium anomalum when integrated into the Gossypium hirsutum genome, revealing a consistent reduction in centromere size. Our analysis uncovers substantial changes in histone modifications and chromatin architecture, particularly with elevated levels of H3K36me2 and enhanced chromatin accessibility. Additionally, we document alterations in topologically associating domains that are linked to these histone modification dynamics. These epigenetic changes appear to play a critical role in centromere stability and functionality, providing insights into how centromeres adapt during intergenomic hybridization and allopolyploid formation. This research enhances our understanding of centromere dynamics in plants, shedding light on the complex interplay of epigenetic factors that influence centromere adaptation and stability.