Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity

Woo Jun Shim, Enakshi Sinniah, Jun Xu, Burcu Vitrinel, Michael Alexanian, Gaia Andreoletti, Sophie Shen, Yuliangzi Sun, Brad Balderson, Carles Boix, Guangdun Peng, Naihe Jing, Yuliang Wang, Manolis Kellis, Patrick P.L. Tam, Aaron Smith, Michael Piper, Lionel Christiaen, Quan Nguyen, Mikael BodénNathan J. Palpant

Research output: Contribution to journalArticlepeer-review

Abstract

Determining genes that orchestrate cell differentiation in development and disease remains a fundamental goal of cell biology. This study establishes a genome-wide metric based on the gene-repressive trimethylation of histone H3 at lysine 27 (H3K27me3) across hundreds of diverse cell types to identify genetic regulators of cell differentiation. We introduce a computational method, TRIAGE, which uses discordance between gene-repressive tendency and expression to identify genetic drivers of cell identity. We apply TRIAGE to millions of genome-wide single-cell transcriptomes, diverse omics platforms, and eukaryotic cells and tissue types. Using a wide range of data, we validate the performance of TRIAGE in identifying cell-type-specific regulatory factors across diverse species including human, mouse, boar, bird, fish, and tunicate. Using CRISPR gene editing, we use TRIAGE to experimentally validate RNF220 as a regulator of Ciona cardiopharyngeal development and SIX3 as required for differentiation of endoderm in human pluripotent stem cells. A record of this paper's transparent peer review process is included in the Supplemental Information. Perturbing genes controlling cell decisions have major implications in development or disease. However, identifying key regulatory genes from the thousands expressed in a cell is challenging. TRIAGE is a computational method that distills patterns of epigenetic repression across diverse cell types to infer regulatory genes using input gene expression data from any cell type. Demonstrating its utility, we combine single-cell RNA-seq and TRIAGE to identify and experimentally confirm novel regulators of heart development in evolutionarily distant species.

Original languageEnglish (US)
Pages (from-to)625-639.e13
JournalCell Systems
Volume11
Issue number6
DOIs
StatePublished - Dec 16 2020

Keywords

  • EpiMap
  • H3K27me3
  • TRIAGE
  • cell differentiation
  • computational method
  • epigenetic
  • pluripotent stem cell
  • predictions
  • single cell RNA-seq

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Histology
  • Cell Biology

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