NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

Hailu Fu, Haizi Zheng, Xiaoting Chen, Matthew T. Weirauch, Louis J. Muglia, Li Wang, Yaping Liu

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Cis-regulatory elements are coordinated to regulate the expression of their targeted genes. However, the joint measurement of cis-regulatory elements’ activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single-nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.

Original languageEnglish
Article number50
JournalGenome Biology
Volume24
Issue number1
DOIs
StatePublished - Dec 2023
Externally publishedYes

Keywords

  • 3D genome
  • Chromatin accessibility
  • Chromosome conformation changes
  • Cis-regulatory elements
  • Coordinated GpC methyltransferase footprints
  • DNA methylation
  • GpC methyltransferase footprints
  • Joint profiling
  • Long-range allelic-specific CRE activity
  • transcriptome

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