p53 transcription factor mediates nuclear speckle association of target genes

Nuclear speckles are prominent nuclear bodies that contain a myriad of factors involved in gene expression. The role of nuclear speckles as activating transcriptional compartments is emerging. However, the extent that the association between speckles and DNA is regulatable, and the mechanisms that govern regulated speckle association are currently unclear. Using DNA- and RNA-FISH, we show that speckle association can be mediated by the p53 transcription factor, finding that p53 activation drives speckle association of specific p53 transcriptional targets. Analysis of a key p53 target, p21, revealed an increase in nascent transcripts at speckle-adjacent transcription sites, supporting a role for speckles in amplifying transcriptional output. Importantly, p53-regulated speckle association of p21 did not depend on transcriptional activation, demonstrating that speckle association is not merely a consequence of gene expression. In contrast, speckle association of p21 did require DNA binding functions of p53, providing a mechanism for the specificity by which speckle association is regulated. Beyond p21, a substantial subset of p53 targets have p53-regulated speckle association, while other p53 targets do not, and we find that genomic context is highly deterministic of which target genes have regulated speckle association. These findings reveal a novel means by which transcription factors may control gene expression and provide a mechanism for the specificity of regulated speckle association. IMR90 cells were treated with 5uM Nutlin3a or the equivalent volume of DMSO for 6 hours. DMSO- or Nutlin-treated cells were then harvested along for TSA-seq using an antibody against SON (SON TSA-seq). Untreated IMR90 cells were used for a no primary control. Each of the three conditions (DMSO SON TSA-seq, Nutlin SON TSA-seq, and No Primary TSA-seq) were perfomed in duplicate, and sequenced with their respective Input (chromatin before pulldown) controls.