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Jones, Daniel
Publications (5 of 5) Show all publications
Jones, D. & Elf, J. (2018). Bursting onto the scene?: Exploring stochastic mRNA production in bacteria. Current Opinion in Microbiology, 45, 124-130
Open this publication in new window or tab >>Bursting onto the scene?: Exploring stochastic mRNA production in bacteria
2018 (English)In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 45, p. 124-130Article, review/survey (Refereed) Published
Abstract [en]

Recent large-scale measurements of gene expression variability (or noise) in E. coli have led to the unexpected conclusion that the variability is in large part dictated by and increasing with the mean level of expression. Here we review the evidence for this apparent universal trend in variability, as well as for the related idea that transcription is fundamentally bursty. We examine recently proposed mechanisms for burstiness and universality and argue that they do not explain important features of observed data. Finally, we discuss potential limitations and pitfalls in the interpretation of experimental measurements of cell-to-cell variability.

Place, publisher, year, edition, pages
CURRENT BIOLOGY LTD, 2018
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-375611 (URN)10.1016/j.mib.2018.04.001 (DOI)000454972700019 ()29705632 (PubMedID)
Funder
Swedish Research Council, VR 642-2013-7841Swedish Research Council, VR 621-2012-4027EU, European Research Council, ERC-2013-CoG/616047EU, Horizon 2020, MSCA-IF-2015-704206
Available from: 2019-01-31 Created: 2019-01-31 Last updated: 2019-01-31Bibliographically approved
Forcier, T. L., Ayaz, A., Gill, M. S., Jones, D., Phillips, R. & Kinney, J. B. (2018). Measuring cis-regulatory energetics in living cells using allelic manifolds. eLIFE, 7, Article ID e40618.
Open this publication in new window or tab >>Measuring cis-regulatory energetics in living cells using allelic manifolds
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2018 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 7, article id e40618Article in journal (Refereed) Published
Abstract [en]

Gene expression in all organisms is controlled by cooperative interactions between DNA-bound transcription factors (TFs), but quantitatively measuring TF-DNA and TF-TF interactions remains difficult. Here we introduce a strategy for precisely measuring the Gibbs free energy of such interactions in living cells. This strategy centers on the measurement and modeling of 'allelic manifolds', a multidimensional generalization of the classical genetics concept of allelic series. Allelic manifolds are measured using reporter assays performed on strategically designed cis-regulatory sequences. Quantitative biophysical models are then fit to the resulting data. We used this strategy to study regulation by two Escherichia coli TFs, CRP and sigma(70) RNA polymerase. Doing so, we consistently obtained energetic measurements precise to similar to 0.1 kcal/mol. We also obtained multiple results that deviate from the prior literature. Our strategy is compatible with massively parallel reporter assays in both prokaryotes and eukaryotes, and should therefore be highly scalable and broadly applicable.

Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that minor issues remain unresolved (see decision letter).

Place, publisher, year, edition, pages
ELIFE SCIENCES PUBLICATIONS LTD, 2018
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-372885 (URN)10.7554/eLife.40618 (DOI)000453818300001 ()30570483 (PubMedID)
Available from: 2019-01-09 Created: 2019-01-09 Last updated: 2019-01-09Bibliographically approved
Belliveau, N. M., Barnes, S. L., Ireland, W. T., Jones, D. L., Sweredoski, M. J., Moradian, A., . . . Phillips, R. (2018). Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 115(21), E4796-E4805
Open this publication in new window or tab >>Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 21, p. E4796-E4805Article in journal (Refereed) Published
Abstract [en]

Gene regulation is one of the most ubiquitous processes in biology. However, while the catalog of bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in these genomes are regulated. At present, characterizing the molecular mechanisms by which individual regulatory sequences operate requires focused efforts using low-throughput methods. Here, we take a first step toward multipromoter dissection and show how a combination of massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used to dissect multiple bacterial promoters in a systematic way. We show this approach on both well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all cases, we recover nucleotide-resolution models of promoter mechanism. For some promoters, including previously unannotated ones, the approach allowed us to further extract quantitative biophysical models describing input-output relationships. Given the generality of the approach presented here, it opens up the possibility of quantitatively dissecting the mechanisms of promoter function in E. coli and a wide range of other bacteria.

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2018
Keywords
gene regulation, massively parallel reporter assay, quantitative models, DNA affinity chromatography, mass spectrometry
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-357276 (URN)10.1073/pnas.1722055115 (DOI)000432663000011 ()29728462 (PubMedID)
Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-12-05Bibliographically approved
Jones, D., Unoson, C., Leroy, P., Curic, V. & Elf, J. (2017). Kinetics of dCas9 Target Search in Escherichia Coli. Paper presented at 58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA. Biophysical Journal, 112(3), 314A-314A
Open this publication in new window or tab >>Kinetics of dCas9 Target Search in Escherichia Coli
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2017 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 314A-314AArticle in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
CELL PRESS, 2017
National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-332758 (URN)000402375600553 ()
Conference
58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA
Available from: 2017-11-06 Created: 2017-11-06 Last updated: 2017-11-06Bibliographically approved
Jones, D., Leroy, P., Unoson, C., Fange, D., Curic, V., Lawson, M. J. & Elf, J. (2017). Kinetics of dCas9 target search in Escherichia coli. Science, 357(6358), 1420-1423
Open this publication in new window or tab >>Kinetics of dCas9 target search in Escherichia coli
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2017 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 357, no 6358, p. 1420-1423Article in journal (Refereed) Published
Abstract [en]

How fast can a cell locate a specific chromosomal DNA sequence specified by a single-stranded oligonucleotide? To address this question, we investigate the intracellular search processes of the Cas9 protein, which can be programmed by a guide RNA to bind essentially any DNA sequence. This targeting flexibility requires Cas9 to unwind the DNA double helix to test for correct base pairing to the guide RNA. Here we study the search mechanisms of the catalytically inactive Cas9 (dCas9) in living Escherichia coli by combining single-molecule fluorescence microscopy and bulk restriction-protection assays. We find that it takes a single fluorescently labeled dCas9 6 hours to find the correct target sequence, which implies that each potential target is bound for less than 30 milliseconds. Once bound, dCas9 remains associated until replication. To achieve fast targeting, both Cas9 and its guide RNA have to be present at high concentrations.

Place, publisher, year, edition, pages
AMER ASSOC ADVANCEMENT SCIENCE, 2017
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-337092 (URN)10.1126/science.aah7084 (DOI)000411880800052 ()28963258 (PubMedID)
Funder
EU, European Research CouncilSwedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2018-01-25 Created: 2018-01-25 Last updated: 2018-01-25Bibliographically approved
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