Abstract
BackgroundTranscription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3 ′ and 5 ′ ends of a gene that enable reinitiation of transcription upon termination.ResultsUsing Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment.ConclusionsInteractions between the 3 ′ and 5 ′ ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.
Highlights
In many cellular systems, mRNAs appear to be produced in burst-like fashion
We focus on genome-wide 3 -5 interactions involved in transcription by means of polymerase II (PolII) ChIA-PET sequencing data, showing that they are related to the gene-expression parameters to the transgenes’ results
Cell lines as model systems for PolII recycling We utilised two HEK293 cell lines which contain on their genomes copies of the genes β-globin (HBB) [33] and a modified version of HIV-1-env [36], respectively, driven by inducible CMV promoters (Fig. 1a, b)
Summary
MRNAs appear to be produced in burst-like fashion This is directly observed in real-time experimental studies [1,2,3] and agrees with theoretical analyses of steady-state mRNA distributions among single cells [4, 5]. Various factors have been found to influence transcriptional dynamics, mostly by modulating bursting parameters such as the size or frequency of bursts [3, 5] These factors are often classified as either intrinsic or extrinsic, this distinction is blurred in many cases. Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. We focus on processes at the 3 and 5 ends of a gene that enable reinitiation of transcription upon termination
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