TY - JOUR
T1 - STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
AU - Peng, Tianran
AU - Zhai, Yanan
AU - Atlasi, Yaser
AU - ter Huurne, Menno
AU - Marks, Hendrik
AU - Stunnenberg, Hendrik G.
AU - Megchelenbrink, Wout
PY - 2020/9/10
Y1 - 2020/9/10
N2 - Background: Enhancers are distal regulators of gene expression that shape cell
identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the
pluripotency network is maintained by the function of a complex network of
enhancers, that are drastically altered upon differentiation. Genome-wide chromatin
accessibility and histone modification assays are commonly used as a proxy for
identifying putative enhancers and for describing their activity levels and dynamics.
Results: Here, we applied STARR-seq, a genome-wide plasmid-based assay, as a
read-out for the enhancer landscape in “ground-state” (2i+LIF; 2iL) and “metastable”
(serum+LIF; SL) mESCs. This analysis reveals that active STARR-seq loci show modest
overlap with enhancer locations derived from peak calling of ChIP-seq libraries for
common enhancer marks. We unveil ZIC3-bound loci with significant STARR-seq
activity in SL-ESCs. Knock-out of Zic3 removes STARR-seq activity only in SL-ESCs and
increases their propensity to differentiate towards the endodermal fate. STARR-seq
also reveals enhancers that are not accessible, masked by a repressive chromatin
signature. We describe a class of dormant, p53 bound enhancers that gain H3K27ac
under specific conditions, such as after treatment with Nocodazol, or transiently
during reprogramming from fibroblasts to pluripotency.
Conclusions: In conclusion, loci identified as active by STARR-seq often overlap with
those identified by chromatin accessibility and active epigenetic marking, yet a significant
fraction is epigenetically repressed or display condition-specific enhancer activity.
AB - Background: Enhancers are distal regulators of gene expression that shape cell
identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the
pluripotency network is maintained by the function of a complex network of
enhancers, that are drastically altered upon differentiation. Genome-wide chromatin
accessibility and histone modification assays are commonly used as a proxy for
identifying putative enhancers and for describing their activity levels and dynamics.
Results: Here, we applied STARR-seq, a genome-wide plasmid-based assay, as a
read-out for the enhancer landscape in “ground-state” (2i+LIF; 2iL) and “metastable”
(serum+LIF; SL) mESCs. This analysis reveals that active STARR-seq loci show modest
overlap with enhancer locations derived from peak calling of ChIP-seq libraries for
common enhancer marks. We unveil ZIC3-bound loci with significant STARR-seq
activity in SL-ESCs. Knock-out of Zic3 removes STARR-seq activity only in SL-ESCs and
increases their propensity to differentiate towards the endodermal fate. STARR-seq
also reveals enhancers that are not accessible, masked by a repressive chromatin
signature. We describe a class of dormant, p53 bound enhancers that gain H3K27ac
under specific conditions, such as after treatment with Nocodazol, or transiently
during reprogramming from fibroblasts to pluripotency.
Conclusions: In conclusion, loci identified as active by STARR-seq often overlap with
those identified by chromatin accessibility and active epigenetic marking, yet a significant
fraction is epigenetically repressed or display condition-specific enhancer activity.
U2 - 10.1186/s13059-020-02156-3
DO - 10.1186/s13059-020-02156-3
M3 - Article
VL - 21
JO - Genome biology
JF - Genome biology
SN - 1474-7596
M1 - 243
ER -