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Updated: Jan 8, 2026

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Regulatory element modules as universal features for single-cell chromatin analysis.

Chrysania Lim1, Javen Tan Yih Ruay1,2, Tim Stuart1

  • 1Genome Institute of Singapore (GIS), Agency for Science Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore.

Biorxiv : the Preprint Server for Biology
|December 19, 2025
PubMed
Summary
This summary is machine-generated.

We developed DNA regulatory element modules (REMO) to standardize single-cell chromatin accessibility data analysis. REMO improves cell state separation, scalability, and automated cell type annotation, overcoming limitations of dataset-specific peak regions.

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Area of Science:

  • Genomics
  • Computational Biology
  • Epigenetics

Background:

  • Single-cell chromatin accessibility data offer insights into DNA regulatory element activity in various biological states.
  • Current analysis methods face challenges due to the absence of standardized features, leading to dataset-specific peak regions that hinder cross-study comparisons.

Purpose of the Study:

  • To develop a comprehensive set of DNA regulatory element modules (REMO) for the human genome.
  • To address the limitations in analyzing and comparing single-cell chromatin accessibility data across different studies.

Main Methods:

  • Development of a standardized set of DNA regulatory element modules (REMO) for the human genome.
  • Application of REMO to single-cell chromatin data for analysis.
  • Creation of memory-efficient and scalable software for quantifying single-cell chromatin accessibility data.

Main Results:

  • REMO application enables better separation of cell states in a low-dimensional space compared to traditional peak matrix quantification.
  • The REMO approach significantly improves the scalability of dimension reduction steps in data analysis.
  • Automated annotation of cell types is enabled through the use of REMO.

Conclusions:

  • REMO provides a standardized framework for analyzing single-cell chromatin accessibility data.
  • The developed REMO approach enhances data comparability, scalability, and cell type annotation accuracy.
  • New software facilitates efficient and scalable quantification of single-cell chromatin accessibility data.