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Updated: Dec 23, 2025

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues
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REPIC: a database for exploring the N6-methyladenosine methylome.

Shun Liu1,2,3, Allen Zhu2,3,4, Chuan He2,3,5

  • 1Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.

Genome Biology
|April 30, 2020
PubMed
Summary
This summary is machine-generated.

The REPIC database provides a comprehensive collection of N6-methyladenosine (m6A) modification sites, integrating millions of peaks from m6A-seq and MeRIP-seq data. This resource enables detailed exploration of m6A methylation across various cell types and organisms.

Keywords:
DatabaseGenome browserTissue specificitym6A modification

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Bioinformatics

Background:

  • N6-methyladenosine (m6A) is a crucial RNA modification involved in gene regulation.
  • Existing databases lack a unified and comprehensive collection of m6A modification sites.
  • Publicly available m6A-seq and MeRIP-seq data are fragmented and challenging to analyze collectively.

Purpose of the Study:

  • To establish the REPIC (RNA EPItranscriptome Collection) database, a centralized resource for m6A modification data.
  • To provide a unified pipeline for calling m6A peaks from diverse sequencing datasets.
  • To integrate m6A data with epigenetic marks and chromatin accessibility information.

Main Methods:

  • Collected and processed approximately 10 million m6A peaks from 672 samples across 49 studies.
  • Utilized a unified bioinformatics pipeline for consistent peak calling from m6A-seq and MeRIP-seq data.
  • Integrated REPIC data with 1418 histone ChIP-seq and 118 DNase-seq tracks from the ENCODE project.

Main Results:

  • REPIC database contains ~10 million m6A peaks from 61 cell lines/tissues in 11 organisms.
  • The database allows querying m6A sites by specific cell lines or tissue types.
  • Integrated genome browser visualizes m6A sites alongside histone modifications and chromatin accessibility.

Conclusions:

  • REPIC offers a valuable, comprehensive resource for studying RNA m6A modifications.
  • The integration of multiple epigenomic data types provides a holistic view of m6A regulation.
  • REPIC facilitates research into the functional roles of m6A in gene expression and cellular processes.