SEE: A Method for Predicting the Dynamics of Chromatin Conformation Based on Single-Cell Gene Expression

Overview

Journal Adv Sci (Weinh)

Date 2025 Jan 8

PMID 39778075

Authors

Minghong Li

Yurong Yang

Rucheng Wu

Haiyan Gong

Zan Yuan

Jixin Wang

Erping Long

Xiaotong Zhang

Yang Chen

Affiliations

Soon will be listed here.

Abstract

The dynamics of chromatin conformation involve continuous and reversible changes within the nucleus of a cell, which participate in regulating processes such as gene expression, DNA replication, and damage repair. Here, SEE is introduced, an artificial intelligence (AI) method that utilizes autoencoder and transformer techniques to analyze chromatin dynamics using single-cell RNA sequencing data and a limited number of single-cell Hi-C maps. SEE is employed to investigate chromatin dynamics across different scales, enabling the detection of (i) rearrangements in topologically associating domains (TADs), and (ii) oscillations in chromatin interactions at gene loci. Additionally, SEE facilitates the interpretation of disease-associated single-nucleotide polymorphisms (SNPs) by leveraging the dynamic features of chromatin conformation. Overall, SEE offers a single-cell, high-resolution approach to analyzing chromatin dynamics in both developmental and disease contexts.

Citing Articles

SEE: A Method for Predicting the Dynamics of Chromatin Conformation Based on Single-Cell Gene Expression.

Li M, Yang Y, Wu R, Gong H, Yuan Z, Wang J Adv Sci (Weinh). 2025; 12(8):e2406413.

PMID: 39778075 PMC: 11848634. DOI: 10.1002/advs.202406413.

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