A DNA Repair Pathway Can Regulate Transcriptional Noise to Promote Cell Fate Transitions

Stochastic fluctuations in gene expression (‘noise’) are often considered detrimental but, in many disciplines, fluctuations are exploited for benefit (e.g., dither). We show here that DNA base-excision repair amplifies transcriptional noise to facilitate cellular reprogramming. Specifically, the DNA-repair protein Apex1, which recognizes both naturally occurring and unnatural base modifications, amplifies expression noise while homeostatically maintaining mean-expression levels. This amplified expression noise originates from shorter duration, higher intensity, transcriptional bursts generated by Apex1-mediated DNA supercoiling. The remodeling of DNA topology first impedes and then accelerates transcription to maintain mean levels and this mechanism, which we term Discordant Transcription through Repair (DiThR), potentiates cellular reprogramming and differentiation. Our study reveals a potential functional role for transcriptional fluctuations mediated by DNA base modifications in embryonic development and disease. We set out to determine the effects of nucleotide base analogues on transcriptional noise and mean gene expression levels. Specifically, we tested a pyrimidine analogue, 5’-iodo-2’-deoxyuridine (IdU) in mouse embryonic stem cells (mESCs), and mouse embryonic fibroblasts (MEFs) during reprogramming. We performed single-cell RNA-seq in mESCs treated with 10uM IdU or DMSO control to analyze gene expression noise. And we also performed bulk RNA-seq in mESCs treated with 5uM IdU, 10uM IdU, and DMSO in triplicates to analyze gene expression changes in response to IdU. Further we analyzed Day 2 and Day 5 reprogramming MEFs treated with 4uM IdU and DMSO in duplicates using bulk RNA-seq to assess the effects of noise enhancer (IdU) on cell-fate transitions.