A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions

Abstract

Stochastic fluctuations in gene expression (‘noise’) are often considered detrimental, but fluctuations can also be 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. This mechanism, which we term Discordant Transcription through Repair (DiThR; pronounced /’dither’/), 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.

DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes

“…However, we find that the inhibitory effect of negative supercoils is more dominant (Figure 5). In line with this, in mouse embryonic stem cells, a transient accumulation of negative supercoils during base excision repair was recently found to inhibit transcription and upon release, cause increased noise fluctuations (61). The level of negative supercoiling thus requires careful regulation by topoisomerase, since low levels of negative supercoils enhance transcription (4-6, 22, 43, 62), but hypernegative supercoiling is inhibitory (11,(63)(64)(65).…”

“…Even though mammalian genes are spaced much further apart than in yeast, supercoiling-dependent cohesin extrusion may cause supercoiling-effects from adjacent genes at a much larger distance. In higher eukaryotes, the accumulation of negative supercoils during nuclear processes, such as base excision repair ( 61 ), could influence the transcription of genes throughout the TAD. Overall, our single-cell live-cell approach highlights how efficient release of torsional stress is necessary to prevent inhibition of neighboring eukaryotic genes.…”

RNA velocity unraveled

“…We obtained ten datasets generated with the 10x Genomics scRNA-seq platform. Two were released as part of a study by Desai et al and used v2 chemistry [155]. Eight were released by 10x Genomics and used v3 chemistry.…”

“…The datasets analyzed for Section 3.1, as outlined in Section 6.1, are listed in Table 1. The datasets released by Desai et al were collated from the Sequence Read Archive (runs SRR14713295 for dmso and SRR14713295 for idu) [155]. The datasets released by 10x Genomics were obtained from https://support.10xgenomics.com/single-cell-gene-expression/datasets.…”

Single cell biology—a Keystone Symposia report

“…118,119 Understanding how the structure of genetic programs designed to promote reprogramming integrates into the chromatin structure will be key to ensuring their function. 120,121 The meeting ended with talks highlighting unpublished work on understanding cell fate and differentiation. Michael Ratz from Jonas Frisén's lab at the Karolinska Institute presented unpublished work on combining in vivo clonal tracking and scRNA-seq to understand neurogenesis in the mouse brain.…”