Pioneer activity distinguishes activating from non-activating pluripotency transcription factor binding sites

Abstract

Genome-wide transcriptional activity involves the binding of many transcription factors to thousands of sites in the genome. Determining which sites are directly driving transcription remains a challenge. Here we use acute protein depletion of the pioneer transcription factors OCT4 and SOX2 to establish their functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of pioneer factors. To understand the relationship with transcription we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to SOX2 binding sites that do not maintain accessibility. We use CRISPR-Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted largely at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation.

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

“…Although our results do not directly implicate ZFP143 in regulating pluripotency genes, we observed an up-regulation of differentiation genes after 24 hours of ZFP143 depletion. However, acute depletion of bona fide pluripotency transcription factors such as OCT4 or SOX2 109,110 leads to rapid changes in morphology and differentiation, which we did not observe for ZFP143 depletion. Paradoxically, loss of ZFP143 in the early stages of gastruloid development results in a failure to differentiate.…”

Distinct chromatin scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2

“…The SMT analysis of ectopically expressed FOXA1 in hepatic cells 19 could have been biased by conditioning of the chromatin environment due to the endogenous expression of FOXA1 and co-acting factors [26][27][28] . The cellular context in which transcription factors are studied can influence their activity 29 .…”

A universal molecular mechanism driving aging

“…We tested the interdependence of pioneer factor binding and G4 formation on pGQS by analyzing ATAC-seq and RNA-seq data from mouse cells with genetic perturbation of the pioneer factors Oct4, Nanog, Sox2 90 , and Zbtb7a 91 . ChIP-seq of these TFs revealed the expected enrichment of the pGQSpos gene TSS compared to the pGQSneg gene TSS (Extended Data Fig.…”