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Computational workflow for integrative analyses of DNA replication timing, epigenomic, and transcriptomic data.

Fei Ji1, Capucine Van Rechem2, Johnathan R Whetstine3

  • 1Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.

STAR Protocols
|November 17, 2022
PubMed
Summary

This study presents a computational protocol to analyze DNA replication timing (RT) alongside chromatin data. It offers new insights into how chromatin influences RT across the cell cycle and upon experimental changes.

Keywords:
BioinformaticsChIPseqGenomicsRNAseqSequence analysisSequencing

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Area of Science:

  • Molecular Biology
  • Genomics
  • Computational Biology

Background:

  • DNA replication timing (RT) is crucial for genome stability and cell cycle progression.
  • Understanding the interplay between chromatin features and RT is essential for deciphering cell cycle regulation.

Purpose of the Study:

  • To describe a protocol for integrative computational analysis of multiple high-throughput sequencing datasets.
  • To investigate the causal relationships between chromatin modifications, accessibility, gene expression, and RT during the cell cycle.

Main Methods:

  • Integrative computational analysis of Repli-seq, ATAC-seq, RNA-seq, and ChIP-seq or CUT&RUN data.
  • Temporal profiling across various cell cycle time points.
  • Analysis of interrelationships upon experimental perturbations like gene knockdown or overexpression.

Main Results:

  • The protocol enables in-depth analysis of complex multi-omics data.
  • It facilitates the study of dynamic changes in chromatin and RT relationships.
  • Insights into regulatory mechanisms governing replication timing can be gained.

Conclusions:

  • This integrative computational approach provides a powerful framework for studying DNA replication timing.
  • It allows for a deeper understanding of the causal links between chromatin state and replication dynamics.
  • The protocol is valuable for investigating cell cycle regulation and responses to perturbations.