Integrated ATAC, ChIP, HiC and RNA Sequencing Shed Light on the Chromatin Interactions Puzzle

The chromatin microenvironment is a dynamically balanced system of organismal epigenetic regulation and thus regulation of gene expression. Any heritable modification mechanism in the chromatin can be used as a marker of epigenetic inheritance. The dynamic balance of chromatin is essential to maintain normal cell proliferation, differentiation, metabolism and functional activities.

ATAC-seq, ChIP-seq and Hi-C are techniques to study the mechanisms that govern the dynamic structural and spatial organization of chromatin. And RNA-Seq can be used to identify genes in the genome or to identify which genes are active at a given point in time, and read counts can be used to accurately model relative gene expression levels. In fact, transcriptome data are generally indispensable to study the chromatin dynamics in order to obtain transcriptional information under epigenetic regulation.

ATAC-Seq in Chromatin Accessibility Research

ATAC-seq technology is a technical approach to study nuclear chromatin with easy access to transposases using high-throughput sequencing. Highly active Tn5 transposase is used to insert sequencing junctions into open regions of chromatin, and sequencing of sequences captured by Tn5 transposase is used to infer the accessibility of chromatin regions.

Integrative ATAC-Seq and transcriptome analysis is used to investigate the mechanisms by which the degree of chromatin accessibility reflected by ATAC signaling is associated with the regulation of gene expression, and to assess the plausibility of using chromatin accessibility to elaborate transcriptional levels and even downstream phenotypic changes.

ChIP-Seq in Studying Interactions Between Proteins and DNA

ChIP-seq combines chromatin immunoprecipitation (ChIP) and high-throughput sequencing technologies to sequence target protein-bound DNA fragments, enabling efficient genome-wide detection of DNA regions interacting with histone modifications, transcription factors, etc. It has become an indispensable technique for detecting in vivo interactions between DNA targets and their corresponding transcription factors (TFs), epigenetic histone modifications, and chromatin remodeling.

Because chromatin modification and gene expression regulation are closely related, ChIP-seq for chromatin labeling and transcription factors is often coupled with RNA-seq to extract key features of the role of chromatin modification and transcription factor binding in regulating transcription.

Hi-C Technology in Chromatin Interactions Research

Hi-C technology is a derivative of Chromosome conformation capture (3C), which is a high-throughput-based technique for capturing chromosome conformations, enabling genome-wide capture of spatial interactions between different motifs and studying DNA components regulating genes in three dimensions.

Hi-C and combined RNA-seq analysis can explore the relationship between chromatin spatial conformation and transcription factor regulation.

Integrated ATAC, ChIP and RNA Seq for Multiomic Epigenetic Analysis

With the continuous development and subdivision of epigenomic technologies, the combined study of multi-omics (ATAC-seq, ChIP-seq and RNA-Seq) will help to uncover more valuable differences and variations, and refine the regulatory network of chromosomal feature structure and gene expression.

ATAC-seq can obtain genome-wide chromatin open regions at a certain time and space, and RNA-seq can obtain gene expression information at the same time and space, and by combining the data from the two omics, the upstream regulatory regions affecting gene expression at that time and space can be obtained; and the regulatory element enrichment data and gene expression data can be verified with each other. ATAC-seq can be followed by ChIP-seq for further validation. For example, after ATAC-seq gets the peek, the transcription factor is screened from motif, and then combined with ChIP-seq to see the action site of the transcription factor, we can know whether it acts on the promoter region or the enhancer region.

Integrated ATAC-seq, ChIP-seq and RNA-seq can explore the mechanism of protein regulation of gene expression and provide the possibility to identify transcriptional differences caused by the regulation of transcription initiation.

References:

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2. Gong H, Yang Y, Zhang S, et al. Application of Hi-C and other omics data analysis in human cancer and cell differentiation research. Computational and Structural Biotechnology Journal, 2021, 19: 2070-2083.
3. Yan F, Powell D R, Curtis D J, et al. From reads to insight: a hitchhiker's guide to ATAC-seq data analysis. Genome biology, 2020, 21: 1-16.