Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

Abstract

The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-occupied sites, and that their cooperative binding is mostly mediated indirectly through regulation of chromatin accessibility. Controlled protein degradation strategies revealed that the uninterrupted presence of OCT4 is required for post-mitotic re-establishment and interphase maintenance of chromatin accessibility, and that highly OCT4-bound enhancers are particularly vulnerable to transient loss of OCT4 expression. Our study sheds light on the constant pioneer activity required to maintain the dynamic pluripotency regulatory landscape in an accessible state.

Base-resolution models of transcription factor binding reveal soft motif syntax

“…Friman et al 77 profiled chromatin accessibility via ATAC-seq in mESCs before and after (ON and OFF, respectively) induced depletion of Oct4 and Sox2. After profiling, they classified differentially accessible states via peak calling and differential enrichment analysis between the ON and OFF ATAC-seq experiments for Oct4 and Sox2, annotating regions as Oct4dependent (OD), Sox2-dependent (SD), or Co-dependent (CD).…”

“…F) Histogram of the number mapped motif instances in thousands (k) found per region. G) Evaluation of the mapped motifs using independent data: regions that lose ATAC-seq signal in response to either Oct4 or Sox2 depletion (but not both) as defined by Friman et al, 2019. BPNet motif instances of Oct4-Sox2 and Sox2 (ranked by contribution scores) outperformed those obtained by HOMER and MEME (ranked by PWM match scores).…”

“…ATAC-seq data processing Friman et al 77 profiled chromatin accessibility via ATAC-seq in mESCs before and after induced depletion of Oct4 and Sox2. We downloaded the corresponding paired-end ATACseq FASTQ files for both replicates of the Sox2 26h (ON & OFF) and the Oct4 S2iL (ON & OFF) from GSE134680 77 .…”

“…Motif validation using ATAC-seq data. A) Overlap of ranked Oct4-Sox2 and Sox2 motif instances (in thousands k) with regions that lose ATAC-seq signal in response to either Oct4 or Sox2 depletion as defined by 77 . In addition to the data shown in Figure 2G, the results for co-dependent regions are shown, in which ATAC-seq signal is lost in response to either Oct4 or Sox2 depletion.…”

Runx1 Shapes the Chromatin Landscape Via a Cascade of Direct and Indirect Targets

“…This raises the possibility that Runx1 may play an additional role in facilitating the loading of other TFs through the opening or maintaining of enhancer accessibility, to allow full transcriptional activation of its target genes, as has been described for other transcription factors (van Bakel, 2011). The integration of signaling pathways through control of chromatin accessibility in co-occupied regions, even in the absence of direct interactions, has been shown to be an important regulatory mechanism for other TFs, such as SOX2 and OCT4 (Friman et al, 2019). It will be interesting to determine whether Runx1 plays a generalized master-regulator role controlling the activity of other signaling pathways through the modulation of chromatin accessibility.…”