Study / S8R43UQUS2019-11-07

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction

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

Read publication Raw data (53)Download all raw data (ZIP)

About this study

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.

Full author list & citation

Fumitaka Inoue, Anat Kreimer, Tal Ashuach, Nadav Ahituv, Nir Yosef. Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction. 2019-11-07. https://doi.org/10.1016/j.stem.2019.09.010

Experiments 1

E0G2N0MYM

H1 hESC lentiMPRA neural-induction time course

A 171-bp lentiMPRA library containing 2,664 candidate, control, and scrambled regulatory elements, with 90 designed 15-bp barcodes per element, was integrated into H1 human embryonic stem cells. Nuclear RNA and genomic DNA barcode counts were collected from three replicate cultures at 0, 3, 6, 12, 24, 48, and 72 hours after neural induction to quantify temporal reporter activity.

Integrated lentiMPRAHumanhg19

Explore data

Raw source data 53 files

Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.

Download all 53 files (ZIP)1-s2.0-S1934590919304217-mmc1.pdf 1-s2.0-S1934590919304217-mmc4.xlsx 1-s2.0-S1934590919304217-mmc5.xlsx 1-s2.0-S1934590919304217-mmc6.xlsx 1-s2.0-S1934590919304217-mmc9.xlsx GSE115042_experimental_design.txt.gz GSE115042_index_rep1.lst.txt.gz GSE115042_index_rep2.lst.txt.gz GSE115042_index_rep3.lst.txt.gz GSE115042_MPRA.tar.gz GSE115042_plasmid_library_MPRA.fa.gz T0h_rep1_DNA.tsv.gz T0h_rep1_RNA.tsv.gz T0h_rep2_DNA.tsv.gz T0h_rep2_RNA.tsv.gz T0h_rep3_DNA.tsv.gz T0h_rep3_RNA.tsv.gz T12h_rep1_DNA.tsv.gz T12h_rep1_RNA.tsv.gz T12h_rep2_DNA.tsv.gz T12h_rep2_RNA.tsv.gz T12h_rep3_DNA.tsv.gz T12h_rep3_RNA.tsv.gz T24h_rep1_DNA.tsv.gz T24h_rep1_RNA.tsv.gz T24h_rep2_DNA.tsv.gz T24h_rep2_RNA.tsv.gz T24h_rep3_DNA.tsv.gz T24h_rep3_RNA.tsv.gz T3h_rep1_DNA.tsv.gz T3h_rep1_RNA.tsv.gz T3h_rep2_DNA.tsv.gz T3h_rep2_RNA.tsv.gz T3h_rep3_DNA.tsv.gz T3h_rep3_RNA.tsv.gz T48h_rep1_DNA.tsv.gz T48h_rep1_RNA.tsv.gz T48h_rep2_DNA.tsv.gz T48h_rep2_RNA.tsv.gz T48h_rep3_DNA.tsv.gz T48h_rep3_RNA.tsv.gz T6h_rep1_DNA.tsv.gz T6h_rep1_RNA.tsv.gz T6h_rep2_DNA.tsv.gz T6h_rep2_RNA.tsv.gz T6h_rep3_DNA.tsv.gz T6h_rep3_RNA.tsv.gz T72h_rep1_DNA.tsv.gz T72h_rep1_RNA.tsv.gz T72h_rep2_DNA.tsv.gz T72h_rep2_RNA.tsv.gz T72h_rep3_DNA.tsv.gz T72h_rep3_RNA.tsv.gz