Differential context-specific impact of individual core promoter elements on transcriptional dynamics

Hendy, Oliver; Campbell, John A.; Weissman, Jocelyn D.; Larson, Daniel R.; Singer, Dinah S.

doi:10.1091/mbc.e17-06-0408

Cited by 30 publications

(31 citation statements)

References 38 publications

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“…Typically, the in vivo molecular mechanism of transcription factor action is inferred from measurements of transcriptional noise obtained through snapshots of dead and fixed embryos or cells using theoretical models (Zenklusen et al, 2008; So et al, 2011; Little et al, 2013; Jones et al, 2014; Senecal et al, 2014; Xu et al, 2015; Padovan-Merhar et al, 2015; Skinner et al, 2016; Bart-man et al, 2016; Zoller et al, 2018; Hendy et al, 2017). In contrast, MS2-based live imaging can directly inform on the dynamics of transcriptional bursting in real time.…”

Section: Resultsmentioning

confidence: 99%

Multimodal transcriptional control of pattern formation in embryonic development

Lammers

Galstyan

Reimer

et al. 2018

Preprint

110

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Predicting developmental outcomes from regulatory DNA sequence and transcription 17 factor patterns remains an open challenge in physical biology. Using stripe 2 of the even-skipped 18 gene in Drosophila embryos as a case study, we dissect the regulatory forces underpinning a key 19 step along the developmental decision-making cascade: the generation of cytoplasmic mRNA 20 patterns via the control of transcription in individual cells. Using live imaging and computational 21 approaches, we found that the transcriptional burst frequency is modulated across the stripe to 22 control the mRNA production rate. However, we discovered that bursting alone cannot 23 quantitatively recapitulate the formation of the stripe, and that control of the window of time over 24 which each nucleus transcribes even-skipped plays a critical role in stripe formation. Theoretical 25 modeling revealed that these regulatory strategies-bursting and the time window-obey different 26 kinds of regulatory logic, suggesting that the stripe is shaped by the interplay of two distinct 27 underlying molecular processes. 28 29 35the regulatory logic of the enhancer elements that dictate the behavior of these networks, the 36 precise prediction of how gene expression patterns and developmental outcomes are driven by 37 transcription factor concentrations remains a central challenge in the field (Vincent et al., 2016). 38 Predicting developmental outcomes demands a quantitative understanding of the flow of 39 information along the central dogma: how input transcription factors dictate the output rate of 40 1 of 69 Manuscript submitted to bioRxiv mRNA production, how this rate of mRNA production dictates cytoplasmic patterns of mRNA, 41 and how these mRNA patterns lead to protein patterns that feed back into the gene regulatory 42 network. While the connection between transcription factor concentration and output mRNA 43 production rate has been the subject of active research over the last three decades (Lawrence 44 et al.connection between this output rate and 47 In order to uncover the quantitative contribution of these three regulatory strategies to pattern 62 formation, and to determine whether other regulatory strategies are at play, it is necessary to 63 measure the rate of RNA polymerase loading in individual nuclei, in real time, in a living embryo. 64 2 of 69 Manuscript submitted to bioRxiv However, to date, most studies have relied on fixed-tissue techniques such as mRNA FISH and 65 immunofluorescence in order to obtain snapshots of the cytoplasmic distributions of mRNA and 66 protein as development progresses (Jaeger et al., 2004; Fakhouri et al., 2010; Parker et al., 2011; 67 Estrada et al., 2016; Crocker et al., 2016; Verd et al., 2017; Park et al., 2018). Such techniques 68 are virtually silent regarding the regulation of single-cell gene expression over time, and are thus 69 ill-suited to the study of how spatiotemporal variations in transcriptional dynamics give rise to 70 patterns of cytoplasmic mRNA. 71...

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Section: Resultsmentioning

confidence: 99%

Multimodal transcriptional control of pattern formation in embryonic development

Lammers

Galstyan

Reimer

et al. 2018

Preprint

110

View full text Add to dashboard Cite

show abstract

“…For instance, variation in r could indicate that transcription factors play an active role in the recruitment of RNAP to the promoter or in the release of RNAP from promoter-proximal pausing (38). Typically, the in vivo molecular mechanism of transcription factor action is inferred from measurements of transcriptional noise obtained through snapshots of dead and fixed embryos or cells using theoretical models (26,(31)(32)(33)(39)(40)(41)(42)(43)(44)(45)(46)(47). In contrast, MS2-based live imaging can directly inform on the dynamics of transcriptional bursting in real time.…”

Section: Mean Transcription Rate Is Dictated By Bursting Through Modumentioning

confidence: 99%

Multimodal transcriptional control of pattern formation in embryonic development

Lammers

Galstyan

Reimer

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

101

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Predicting how interactions between transcription factors and regulatory DNA sequence dictate rates of transcription and, ultimately, drive developmental outcomes remains an open challenge in physical biology. Using stripe 2 of the even-skipped gene in Drosophila embryos as a case study, we dissect the regulatory forces underpinning a key step along the developmental decision-making cascade: the generation of cytoplasmic mRNA patterns via the control of transcription in individual cells. Using live imaging and computational approaches, we found that the transcriptional burst frequency is modulated across the stripe to control the mRNA production rate. However, we discovered that bursting alone cannot quantitatively recapitulate the formation of the stripe and that control of the window of time over which each nucleus transcribes even-skipped plays a critical role in stripe formation. Theoretical modeling revealed that these regulatory strategies (bursting and the time window) respond in different ways to input transcription factor concentrations, suggesting that the stripe is shaped by the interplay of 2 distinct underlying molecular processes.

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“…Recent studies have shown that enhancers control burst fraction in Drosophila embryos (16) and mammalian erythrocytes (17). Individual core promoter elements of a major histocompatibility complex class I gene promoter contribute to burst frequency, size, or both in response to ␥-interferon stimulation (18). The transcription factor concentration, after MAPK induction, also modulates the c-Fos burst fraction in cultured cells (19).…”

mentioning

confidence: 99%

Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process

Limi

Senecal²,

Coleman³

et al. 2018

Journal of Biological Chemistry

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Genes are transcribed in irregular pulses of activity termed transcriptional bursts. Cellular differentiation requires coordinated gene expression; however, it is unknown whether the burst fraction ( the number of active phases of transcription) or size/intensity (the number of RNA molecules produced within a burst) changes during cell differentiation. In the ocular lens, the positions of lens fiber cells correlate precisely with their differentiation status, and the most advanced cells degrade their nuclei. Here, we examined the transcriptional parameters of the β-actin and lens differentiation-specific α-, β-, and γ-crystallin genes by RNA fluorescent hybridization (FISH) in the lenses of embryonic day (E) E12.5, E14.5, and E16.5 mouse embryos and newborns. We found that cellular differentiation dramatically alters the burst fraction in synchronized waves across the lens fiber cell compartment with less dramatic changes in burst intensity. Surprisingly, we observed nascent transcription of multiple genes in nuclei just before nuclear destruction. Nuclear condensation was accompanied by transfer of nuclear proteins, including histone and nonhistone proteins, to the cytoplasm. Although lens-specific deletion of the chromatin remodeler SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (Smarca5/Snf2h) interfered with denucleation, persisting nuclei remained transcriptionally competent and exhibited changes in both burst intensity and fraction depending on the gene examined. Our results uncover the mechanisms of nascent transcriptional control during differentiation and chromatin remodeling, confirm the burst fraction as the major factor adjusting gene expression levels, and reveal transcriptional competence of fiber cell nuclei even as they approach disintegration.

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Differential context-specific impact of individual core promoter elements on transcriptional dynamics

Cited by 30 publications

References 38 publications

Multimodal transcriptional control of pattern formation in embryonic development

Multimodal transcriptional control of pattern formation in embryonic development

Multimodal transcriptional control of pattern formation in embryonic development

Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process

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