Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction

Cell Stem Cell. 2019 Nov 7;25(5):713-727.e10. doi: 10.1016/j.stem.2019.09.010. Epub 2019 Oct 17.


Epigenomic regulation and lineage-specific gene expression act in concert to drive cellular differentiation, but the temporal interplay between these processes is largely unknown. Using neural induction from human pluripotent stem cells (hPSCs) as a paradigm, we interrogated these dynamics by performing RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and assay for transposase accessible chromatin using sequencing (ATAC-seq) at seven time points during early neural differentiation. We found that changes in DNA accessibility precede H3K27ac, which is followed by gene expression changes. Using massively parallel reporter assays (MPRAs) to test the activity of 2,464 candidate regulatory sequences at all seven time points, we show that many of these sequences have temporal activity patterns that correlate with their respective cell-endogenous gene expression and chromatin changes. A prioritization method incorporating all genomic and MPRA data further identified key transcription factors involved in driving neural fate. These results provide a comprehensive resource of genes and regulatory elements that orchestrate neural induction and illuminate temporal frameworks during differentiation.

Keywords: ATAC-seq; ChIP-seq; RNA-seq; enhancer; functional genomics; genetic variation; massively parallel reporter assay; neural induction; stem cell differentiation; transcriptional regulation.

MeSH terms

  • Acetylation
  • Chromatin / metabolism*
  • Chromatin Immunoprecipitation Sequencing
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • Computational Biology
  • Enhancer Elements, Genetic*
  • Gene Expression Regulation, Developmental / genetics*
  • Histones / chemistry
  • Histones / metabolism*
  • Human Embryonic Stem Cells / drug effects
  • Human Embryonic Stem Cells / metabolism*
  • Humans
  • Mental Disorders / genetics
  • Mental Disorders / metabolism
  • Neurogenesis / drug effects
  • Neurogenesis / genetics*
  • RNA-Seq
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*


  • Chromatin
  • Histones
  • Transcription Factors