Genome-wide analysis of effects of ARID1A depletion in mouse embryonic stem cells

A degron system is used to deplete ARID1A a subunit of the SWI/SNF complex in mouse embryonic stem cells. Genome wide analysis of chromatin accessibility (ATAC-seq), nucleosome posistioning (MNase-seq), nascent transcription (TT-seq), binding to EP300 and presence of histone H3 K27acetylation (ChIP-seq) amd histone H3K27 tria-methylation (ChIP-seq) allowed us to identify two different pathways responsible for the up and downregulation of transcription following the loss of ARID1A. The rapid depletion of ARID1A generates mini domains of nucleomes at pluripotency transcription factor binding sites. Loss of ARID1A also results in the redistribution of the co-activator EP300. Locations of co-incident EP300 dissociation and lost chromatin accessibility occur adjacent to rapidly downregulated genes. Promoter proximal regions that gain EP300 are linked to genes that are transcriptionally upregulated. Our findings illustrate the importance of both direct and indirect effects in causing rapid changes to gene expression. Only a few genes are directly affected after ARID1A depletion and contribute to pathways associated with cancer and pluripotency establishing the loss of ARID1A phenotype. We performed a time course (0h, 2h, 6h, 18, 54h, 162h) for the depletion of the ARID1A subunit of the SWI/SNF complex using the TIR1/Auxin-inducible-degron system in mouse embryonic stem cells (E14). Genome wide analysis was performed for the change in chromatin accessibility (ATAC-seq, 3 replicates per time point), nucleosome positioning (MNase-seq, 6 replicates for time point 0h and 2h), nascent transcription (Transient Transcriptome TT-seq, 4 replicates per time point), binding to EP300 (ChIP-seq, 4 replicates for time point) and presence of histone H3 K27acetylation (ChIP-seq, 4 replicates per time point) and histone H3K27 tri-methylation before and after ARID1A depletion. In addition TT-seq and ATAC-seq also performed for the untagged control cell lines ET905 (time points 0h, 2h, 18h) and the knock out ARID1A cell line.