Diagenode

>>>   Click for Diagenode’s approach to COVID-19

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction


Inoue Fumitaka, Kreimer Anat, Ashuach Tal, Ahituv Nadav, Yosef Nir

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.

Tags
LowCell ChIP kit
IPure kit

Share this article

Published
November, 2019

Source

Products used in this publication

  • ChIP kit icon
    C01010072
    LowCell# ChIP kit protein A
  • default alt
    C03010015
    IPure kit v2

       Site map   |   Contact us   |   Conditions of sales   |   Conditions of purchase   |   Privacy policy   |   Diagenode Diagnostics