Scalable inference of transcriptional kinetic parameters from MS2 time series data

Bowles, Jonathan R.; Hoppe, Caroline; Ashe, Hilary L.; Rattray, Magnus

doi:10.1101/2020.12.04.412049

Cited by 3 publications

(1 citation statement)

References 34 publications

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“…However, such promising experimental techniques can only be as powerful as their underlying data-analysis infrastructure. For example, while initial studies using MS2 set the technological foundation for revealing transcriptional bursts in bacteria [ 20 ], single-celled eukaryotes [ 28 , 111 ], and animals [ 25 , 31 ], only recently did analysis techniques become available to reliably obtain parameters such as transcriptional burst frequency, duration, and amplitude [ 24 , 35 , 112 – 114 ].…”

Section: Discussionmentioning

confidence: 99%

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage

Liu

Hansen

Eck³

et al. 2021

PLoS Comput Biol

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The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.

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Section: Discussionmentioning

confidence: 99%

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage

Liu

Hansen

Eck³

et al. 2021

PLoS Comput Biol

View full text Add to dashboard Cite

show abstract

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage

Liu

Hansen

Eck³

et al. 2020

Preprint

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The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel computational technique to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters with high precision. These measurements, combined with theoretical modeling, reveal a significant variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.

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Modulation of transcription burst amplitude underpins dosage compensation in theDrosophilaembryo

Beadle¹,

Zhou²,

Rattray³

et al. 2023

Preprint

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Dosage compensation, the balancing of X linked gene expression between sexes and to the autosomes, is critical to an organism's fitness and survival. In Drosophila, dosage compensation involves hypertranscription of the male X chromosome. Here we use quantitative live imaging and modelling at single-cell resolution to determine the mechanism underlying X chromosome dosage compensation in Drosophila. We show that the four X chromosome genes studied undergo transcriptional bursting in male and female embryos. Mechanistically our data reveal that transcriptional upregulation of male X chromosome genes is primarily mediated by a higher RNA polymerase II initiation rate and burst amplitude across the expression domain. In contrast, burst frequency is spatially modulated in nuclei within the expression domain in response to different transcription factor concentrations to tune the transcriptional response. Together, these data show how the local and global regulation of distinct burst parameters establish complex the transcriptional outputs underpinning developmental patterning.

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Scalable inference of transcriptional kinetic parameters from MS2 time series data

Cited by 3 publications

References 34 publications

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage

Modulation of transcription burst amplitude underpins dosage compensation in theDrosophilaembryo

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