1
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Sweeney K, Luffey EL, McClean MN. Protocol to probe how promoters decode TF dynamics in Saccharomyces cerevisiae by combining optogenetic control with microscopy. STAR Protoc 2024; 5:103002. [PMID: 39003745 DOI: 10.1016/j.xpro.2024.103002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 01/21/2024] [Accepted: 03/21/2024] [Indexed: 07/16/2024] Open
Abstract
Gene promoters filter transcription factor (TF) localization dynamics and changes in the DNA binding affinity of TFs. Here, we present a protocol to probe how promoters decode TF dynamics in Saccharomyces cerevisiae by combining optogenetic control with microscopy. We describe steps for preparing and characterizing a light delivery platform and light-controlled TF mutants. We then detail procedures for subjecting the TFs to light doses that generate defined patterns of localization while measuring fluorescent reporter gene activation via live-cell microscopy. For complete details on the use and execution of this protocol, please refer to Sweeney and McClean.1.
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Affiliation(s)
- Kieran Sweeney
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Emily L Luffey
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705, USA; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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2
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Roop BW, Parrell B, Lammert AC. A compressive sensing approach for inferring cognitive representations with reverse correlation. Behav Res Methods 2024; 56:3606-3618. [PMID: 38049576 PMCID: PMC11133035 DOI: 10.3758/s13428-023-02281-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
Uncovering cognitive representations is an elusive goal that is increasingly pursued using the reverse correlation method, wherein human subjects make judgments about ambiguous stimuli. Employing reverse correlation often entails collecting thousands of stimulus-response pairs, which severely limits the breadth of studies that are feasible using the method. Current techniques to improve efficiency bias the outcome. Here we show that this methodological barrier can be diminished using compressive sensing, an advanced signal processing technique designed to improve sampling efficiency. Simulations are performed to demonstrate that compressive sensing can improve the accuracy of reconstructed cognitive representations and dramatically reduce the required number of stimulus-response pairs. Additionally, compressive sensing is used on human subject data from a previous reverse correlation study, demonstrating a dramatic improvement in reconstruction quality. This work concludes by outlining the potential of compressive sensing to improve representation reconstruction throughout the fields of psychology, neuroscience, and beyond.
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Affiliation(s)
- Benjamin W Roop
- Program of Neuroscience, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Benjamin Parrell
- Department of Communication Sciences and Disorders, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam C Lammert
- Program of Neuroscience, Worcester Polytechnic Institute, Worcester, MA, USA.
- Biomedical Engineering Department, Worcester Polytechnic Institute, 100 Institute Rd, Worcester, MA, 01609, USA.
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3
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Deschênes-Simard X, Malleshaiah M, Ferbeyre G. Extracellular Signal-Regulated Kinases: One Pathway, Multiple Fates. Cancers (Basel) 2023; 16:95. [PMID: 38201521 PMCID: PMC10778234 DOI: 10.3390/cancers16010095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
This comprehensive review delves into the multifaceted aspects of ERK signaling and the intricate mechanisms underlying distinct cellular fates. ERK1 and ERK2 (ERK) govern proliferation, transformation, epithelial-mesenchymal transition, differentiation, senescence, or cell death, contingent upon activation strength, duration, and context. The biochemical mechanisms underlying these outcomes are inadequately understood, shaped by signaling feedback and the spatial localization of ERK activation. Generally, ERK activation aligns with the Goldilocks principle in cell fate determination. Inadequate or excessive ERK activity hinders cell proliferation, while balanced activation promotes both cell proliferation and survival. Unraveling the intricacies of how the degree of ERK activation dictates cell fate requires deciphering mechanisms encompassing protein stability, transcription factors downstream of ERK, and the chromatin landscape.
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Affiliation(s)
- Xavier Deschênes-Simard
- Montreal University Hospital Center (CHUM), Université de Montréal, Montréal, QC H3T 1J4, Canada;
| | - Mohan Malleshaiah
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada;
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Gerardo Ferbeyre
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Montreal Cancer Institute, CR-CHUM, Université de Montréal, Montréal, QC H3T 1J4, Canada
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4
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Liu Y, Zhang X, Zhang X, Liu X, Wang B, Zhang Q, Wei X. Temporal logic circuits implementation using a dual cross-inhibition mechanism based on DNA strand displacement. RSC Adv 2023; 13:27125-27134. [PMID: 37701285 PMCID: PMC10493850 DOI: 10.1039/d3ra03995a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
Molecular circuits crafted from DNA molecules harness the inherent programmability and biocompatibility of DNA to intelligently steer molecular machines in the execution of microscopic tasks. In comparison to combinational circuits, DNA-based temporal circuits boast supplementary capabilities, allowing them to proficiently handle the omnipresent temporal information within biochemical systems and life sciences. However, the lack of temporal mechanisms and components proficient in comprehending and processing temporal information presents challenges in advancing DNA circuits that excel in complex tasks requiring temporal control and time perception. In this study, we engineered temporal logic circuits through the design and implementation of a dual cross-inhibition mechanism, which enables the acceptance and processing of temporal information, serving as a fundamental building block for constructing temporal circuits. By incorporating the dual cross-inhibition mechanism, the temporal logic gates are endowed with cascading capabilities, significantly enhancing the inhibitory effect compared to a cross-inhibitor. Furthermore, we have introduced the annihilation mechanism into the circuit to further augment the inhibition effect. As a result, the circuit demonstrates sensitive time response characteristics, leading to a fundamental improvement in circuit performance. This architecture provides a means to efficiently process temporal signals in DNA strand displacement circuits. We anticipate that our findings will contribute to the design of complex temporal logic circuits and the advancement of molecular programming.
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Affiliation(s)
- Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University Dalian 116622 China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
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5
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Huang W, Lin W, Chen B, Zhang J, Gao P, Fan Y, Lin Y, Wei P. NFAT and NF-κB dynamically co-regulate TCR and CAR signaling responses in human T cells. Cell Rep 2023; 42:112663. [PMID: 37347664 DOI: 10.1016/j.celrep.2023.112663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 04/02/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
While it has been established that the responses of T cells to antigens are combinatorially regulated by multiple signaling pathways, it remains elusive what mechanisms cells utilize to quantitatively modulate T cell responses during pathway integration. Here, we show that two key pathways in T cell signaling, calcium/nuclear factor of activated T cells (NFAT) and protein kinase C (PKC)/nuclear factor κB (NF-κB), integrate through a dynamic and combinatorial strategy to fine-tune T cell response genes. At the cis-regulatory level, the two pathways integrate through co-binding of NFAT and NF-κB to immune response genes. Pathway integration is further regulated temporally, where T cell receptor (TCR) and chimeric antigen receptor (CAR) activation signals modulate the temporal relationships between the nuclear localization dynamics of NFAT and NF-κB. Such physical and temporal integrations together contribute to distinct modes of expression modulation for genes. Thus, the temporal relationships between regulators can be modulated to affect their co-targets during immune responses, underscoring the importance of dynamic combinatorial regulation in cellular signaling.
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Affiliation(s)
- Wen Huang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Lin
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Baoqiang Chen
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianhan Zhang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Peifen Gao
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yingying Fan
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yihan Lin
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Ping Wei
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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6
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Sweeney K, McClean MN. Transcription factor localization dynamics and DNA binding drive distinct promoter interpretations. Cell Rep 2023; 42:112426. [PMID: 37087734 DOI: 10.1016/j.celrep.2023.112426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/17/2023] [Accepted: 04/07/2023] [Indexed: 04/24/2023] Open
Abstract
Environmental information may be encoded in the temporal dynamics of transcription factor (TF) activation and subsequently decoded by gene promoters to enact stimulus-specific gene expression programs. Previous studies of this behavior focused on the encoding and decoding of information in TF nuclear localization dynamics, yet cells control the activity of TFs in myriad ways, including by regulating their ability to bind DNA. Here, we use light-controlled mutants of the yeast TF Msn2 as a model system to investigate how promoter decoding of TF localization dynamics is affected by changes in the ability of the TF to bind DNA. We find that yeast promoters directly decode the light-controlled localization dynamics of Msn2 and that the effects of changing Msn2 affinity on that decoding behavior are highly promoter dependent, illustrating how cells could regulate TF localization dynamics and DNA binding in concert for improved control of gene expression.
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Affiliation(s)
- Kieran Sweeney
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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7
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Zhao S, Liu Y, Zhang X, Qin R, Wang B, Zhang Q. Mapping Temporally Ordered Inputs to Binary Message Outputs with a DNA Temporal Logic Circuit. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:903. [PMID: 36903782 PMCID: PMC10005157 DOI: 10.3390/nano13050903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Molecular circuits and devices with temporal signal processing capability are of great significance for the analysis of complex biological processes. Mapping temporal inputs to binary messages is a process of history-dependent signal responses, which can help understand the signal-processing behavior of organisms. Here, we propose a DNA temporal logic circuit based on DNA strand displacement reactions, which can map temporally ordered inputs to corresponding binary message outputs. The presence or absence of the output signal is determined by the type of substrate reaction with the input so that different orders of inputs correspond to different binary outputs. We demonstrate that a circuit can be generalized to more complex temporal logic circuits by increasing or decreasing the number of substrates or inputs. We also show that our circuit had excellent responsiveness to temporally ordered inputs, flexibility, and expansibility in the case of symmetrically encrypted communications. We envision that our scheme can provide some new ideas for future molecular encryption, information processing, and neural networks.
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Affiliation(s)
- Shuai Zhao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Rui Qin
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
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8
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Abstract
![]()
Molecular circuits
capable of processing temporal information are
essential for complex decision making in response to both the presence
and history of a molecular environment. A particular type of temporal
information that has been recognized to be important is the relative
timing of signals. Here we demonstrate the strategy of temporal memory
combined with logic computation in DNA strand-displacement circuits
capable of making decisions based on specific combinations of inputs
as well as their relative timing. The circuit encodes the timing information
on inputs in a set of memory strands, which allows for the construction
of logic gates that act on current and historical signals. We show
that mismatches can be employed to reduce the complexity of circuit
design and that shortening specific toeholds can be useful for improving
the robustness of circuit behavior. We also show that a detailed model
can provide critical insights for guiding certain aspects of experimental
investigations that an abstract model cannot. We envision that the
design principles explored in this study can be generalized to more
complex temporal logic circuits and incorporated into other types
of circuit architectures, including DNA-based neural networks, enabling
the implementation of timing-dependent learning rules and opening
up new opportunities for embedding intelligent behaviors into artificial
molecular machines.
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Affiliation(s)
- Anna P Lapteva
- Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Namita Sarraf
- Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Lulu Qian
- Bioengineering, California Institute of Technology, Pasadena, California 91125, United States.,Computer Science, California Institute of Technology, Pasadena, California 91125, United States
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9
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Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression. Cell Syst 2022; 13:353-364.e6. [PMID: 35298924 DOI: 10.1016/j.cels.2022.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 11/18/2021] [Accepted: 02/17/2022] [Indexed: 12/27/2022]
Abstract
Cells live in constantly changing environments and employ dynamic signaling pathways to transduce information about the signals they encounter. However, the mechanisms by which dynamic signals are decoded into appropriate gene expression patterns remain poorly understood. Here, we devise networked optogenetic pathways that achieve dynamic signal processing functions that recapitulate cellular information processing. Exploiting light-responsive transcriptional regulators with differing response kinetics, we build a falling edge pulse detector and show that this circuit can be employed to demultiplex dynamically encoded signals. We combine this demultiplexer with dCas9-based gene networks to construct pulsatile signal filters and decoders. Applying information theory, we show that dynamic multiplexing significantly increases the information transmission capacity from signal to gene expression state. Finally, we use dynamic multiplexing for precise multidimensional regulation of a heterologous metabolic pathway. Our results elucidate design principles of dynamic information processing and provide original synthetic systems capable of decoding complex signals for biotechnological applications.
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10
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11
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Chen L, Wang Y, Liu J, Wang H. Coloured noise induces phenotypic diversity with energy dissipation. Biosystems 2022; 214:104648. [PMID: 35218875 DOI: 10.1016/j.biosystems.2022.104648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 11/02/2022]
Abstract
Genes integrate many different sources of noise to adapt their survival strategy with energy costs, but how this noise impacts gene phenotype switching is not fully understood. Here, we refine a mechanistic model with multiplicative and additive coloured noise and analyse the influence of noise strength (NS) and autocorrelation time (AT) on gene phenotypic diversity. Different from white noise, we found that in the autocorrelation time-scale plane, increasing the multiplicative noise will broaden the bimodal region of the gene product, and additive noise will induce bimodal region drift from the lower level to the higher level, while the AT will promote this transition. Specifically, the effect of AT on gene expression is similar to a feedback loop; that is, the AT of multiplicative noise will elongate the mean first passage time (MFPT) from the low stable state to the high stable state, but it will reduce the MFPT from the high stable state to the low stable state, and the opposite is true for additive noise. Moreover, these transitions will violate the detailed equilibrium and then consume energy. By effective topology network reconstruction, we found that when the NS is small, the more obvious the bimodality is, the lower the energy dissipation; however, when the NS is large, it will consume more energy with a tendency for bimodality. The overall analysis implies that living organisms will utilize noise strength and its autocorrelation time for better survival in complex and fluctuating environments.
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Affiliation(s)
- Leiyan Chen
- School of Sciences, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Yan Wang
- Department of Neurology, The First Affiliated Hospital, University of South China, HengYang, 421001, Hunan, People's Republic of China
| | - Jinrong Liu
- School of Sciences, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Haohua Wang
- School of Sciences, Hainan University, Haikou, 570228, Hainan, People's Republic of China; Hainan University, Coll Forestry, Key Laboratory of Genetics & Germplasm Innovation Tropical Special Fo, Ministry of Education, Haikou, 570228, Hainan, People's Republic of China; Hainan University, Key Laboratory of Engineering Modeling and Statistical Computation of Hainan Province, Haikou, 570228, Hainan, People's Republic of China.
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12
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Mukund A, Bintu L. Temporal signaling, population control, and information processing through chromatin-mediated gene regulation. J Theor Biol 2022; 535:110977. [PMID: 34919934 PMCID: PMC8757591 DOI: 10.1016/j.jtbi.2021.110977] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/03/2021] [Accepted: 12/05/2021] [Indexed: 01/02/2023]
Abstract
Chromatin regulation is a key pathway cells use to regulate gene expression in response to temporal stimuli, and is becoming widely used as a platform for synthetic biology applications. Here, we build a mathematical framework for analyzing the response of genetic circuits containing chromatin regulators to temporal signals in mammalian cell populations. Chromatin regulators can silence genes in an all-or-none fashion at the single-cell level, with individual cells stochastically transitioning between active, reversibly silent, and irreversibly silent gene states at constant rates over time. We integrate this mode of regulation with classical gene regulatory motifs, such as autoregulatory and incoherent feedforward loops, to determine the types of responses achievable with duration-dependent signaling. We demonstrate that repressive regulators without long-term epigenetic memory can filter out high frequency noise, and as part of an autoregulatory loop can precisely tune the fraction of cells in a population that expresses a gene of interest. Additionally, we find that repressive regulators with epigenetic memory can sum up and encode the total duration of their recruitment in the fraction of cells irreversibly silenced and, when included in a feed forward loop, enable perfect adaptation. Last, we use an information theoretic approach to show that all-or-none stochastic silencing can be used by populations to transmit information reliably and with high fidelity even in very simple genetic circuits. Altogether, we show that chromatin-mediated gene control enables a repertoire of complex cell population responses to temporal signals and can transmit higher information levels than previously measured in gene regulation.
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Affiliation(s)
- Adi Mukund
- Biophysics Program, Stanford University, Stanford, CA 94305, USA.
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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13
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Chowdhury D, Wang C, Lu A, Zhu H. Cis-Regulatory Logic Produces Gene-Expression Noise Describing Phenotypic Heterogeneity in Bacteria. Front Genet 2021; 12:698910. [PMID: 34650591 PMCID: PMC8506120 DOI: 10.3389/fgene.2021.698910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/31/2021] [Indexed: 12/04/2022] Open
Abstract
Gene transcriptional process is random. It occurs in bursts and follows single-molecular kinetics. Intermittent bursts are measured based on their frequency and size. They influence temporal fluctuations in the abundance of total mRNA and proteins by generating distinct transcriptional variations referred to as “noise”. Noisy expression induces uncertainty because the association between transcriptional variation and the extent of gene expression fluctuation is ambiguous. The promoter architecture and remote interference of different cis-regulatory elements are the crucial determinants of noise, which is reflected in phenotypic heterogeneity. An alternative perspective considers that cellular parameters dictating genome-wide transcriptional kinetics follow a universal pattern. Research on noise and systematic perturbations of promoter sequences reinforces that both gene-specific and genome-wide regulation occur across species ranging from bacteria and yeast to animal cells. Thus, deciphering gene-expression noise is essential across different genomics applications. Amidst the mounting conflict, it is imperative to reconsider the scope, progression, and rational construction of diversified viewpoints underlying the origin of the noise. Here, we have established an indication connecting noise, gene expression variations, and bacterial phenotypic variability. This review will enhance the understanding of gene-expression noise in various scientific contexts and applications.
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Affiliation(s)
- Debajyoti Chowdhury
- HKBU Institute for Research and Continuing Education, Shenzhen, China.,Computational Medicine Lab, Hong Kong Baptist University, Hong Kong, China.,Institute of Integrated Bioinformedicine and Translational Sciences, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Chao Wang
- HKBU Institute for Research and Continuing Education, Shenzhen, China.,Institute of Integrated Bioinformedicine and Translational Sciences, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Aiping Lu
- Computational Medicine Lab, Hong Kong Baptist University, Hong Kong, China.,Institute of Integrated Bioinformedicine and Translational Sciences, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Hailong Zhu
- HKBU Institute for Research and Continuing Education, Shenzhen, China.,Computational Medicine Lab, Hong Kong Baptist University, Hong Kong, China.,Institute of Integrated Bioinformedicine and Translational Sciences, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
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14
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Hsu IS, Strome B, Lash E, Robbins N, Cowen LE, Moses AM. A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling. PLoS Genet 2021; 17:e1009629. [PMID: 34506483 PMCID: PMC8457507 DOI: 10.1371/journal.pgen.1009629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/22/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
Stochastic signaling dynamics expand living cells' information processing capabilities. An increasing number of studies report that regulators encode information in their pulsatile dynamics. The evolutionary mechanisms that lead to complex signaling dynamics remain uncharacterized, perhaps because key interactions of signaling proteins are encoded in intrinsically disordered regions (IDRs), whose evolution is difficult to analyze. Here we focused on the IDR that controls the stochastic pulsing dynamics of Crz1, a transcription factor in fungi downstream of the widely conserved calcium signaling pathway. We find that Crz1 IDRs from anciently diverged fungi can all respond transiently to calcium stress; however, only Crz1 IDRs from the Saccharomyces clade support pulsatility, encode extra information, and rescue fitness in competition assays, while the Crz1 IDRs from distantly related fungi do none of the three. On the other hand, we find that Crz1 pulsing is conserved in the distantly related fungi, consistent with the evolutionary model of stabilizing selection on the signaling phenotype. Further, we show that a calcineurin docking site in a specific part of the IDRs appears to be sufficient for pulsing and show evidence for a beneficial increase in the relative calcineurin affinity of this docking site. We propose that evolutionary flexibility of functionally divergent IDRs underlies the conservation of stochastic signaling by stabilizing selection.
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Affiliation(s)
- Ian S. Hsu
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Bob Strome
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Emma Lash
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alan M. Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- * E-mail:
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15
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Gene Expression at a Single Molecule Level: Implications for MDS and AML. Blood 2021; 138:625-636. [PMID: 34157070 DOI: 10.1182/blood.2019004261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Non-genetic heterogeneity, or gene expression stochasticity, is an important source of variability in biological systems. With the advent and improvement of single molecule resolution technologies, it has been shown that transcription dynamics and resultant transcript number fluctuations generate significant cell-to-cell variability that has important biological effects and may contribute substantially to both tissue homeostasis and disease. In this respect, the pathophysiology of stem cell-derived malignancies such as AML and MDS, which has historically been studied at the ensemble level, may require re-evaluation. To that end, it is our aim in this review to highlight the results of recent single-molecule, biophysical, and systems studies of gene expression dynamics, with the explicit purpose of demonstrating how the insights from these basic science studies may help inform and progress the field of leukemia biology and, ultimately, research into novel therapies.
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16
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Biddle JW, Martinez-Corral R, Wong F, Gunawardena J. Allosteric conformational ensembles have unlimited capacity for integrating information. eLife 2021; 10:e65498. [PMID: 34106049 PMCID: PMC8189718 DOI: 10.7554/elife.65498] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
Integration of binding information by macromolecular entities is fundamental to cellular functionality. Recent work has shown that such integration cannot be explained by pairwise cooperativities, in which binding is modulated by binding at another site. Higher-order cooperativities (HOCs), in which binding is collectively modulated by multiple other binding events, appear to be necessary but an appropriate mechanism has been lacking. We show here that HOCs arise through allostery, in which effective cooperativity emerges indirectly from an ensemble of dynamically interchanging conformations. Conformational ensembles play important roles in many cellular processes but their integrative capabilities remain poorly understood. We show that sufficiently complex ensembles can implement any form of information integration achievable without energy expenditure, including all patterns of HOCs. Our results provide a rigorous biophysical foundation for analysing the integration of binding information through allostery. We discuss the implications for eukaryotic gene regulation, where complex conformational dynamics accompanies widespread information integration.
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Affiliation(s)
- John W Biddle
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | | | - Felix Wong
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Infectious Disease and Microbiome Program, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
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17
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Shi X. A Hill type equation can predict target gene expression driven by p53 pulsing. FEBS Open Bio 2021; 11:1799-1808. [PMID: 33955710 PMCID: PMC8167869 DOI: 10.1002/2211-5463.13179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 11/27/2022] Open
Abstract
Many factors determine target gene expression dynamics under p53 pulsing. In this study, I sought to determine the mechanism by which duration, frequency, binding affinity and maximal transcription rate affect the expression dynamics of target genes. Using an analytical method to solve a simple model, I found that the fold change of target gene expression increases relative to the number of p53 pulses, and the optimal frequency, 0.18 h-1 , from two real p53 pulses drives the maximal fold change with a decay rate of 0.18 h-1 . Moreover, p53 pulses may also lead to a higher fold change than sustained p53. Finally, I discovered that a Hill-type equation, including these effect factors, can characterise target gene expression. The average error between the theoretical predictions and experiments was 23%. Collectively, this equation advances the understanding of transcription factor dynamics, where duration and frequency play a significant role in the fine regulation of target gene expression with higher binding affinity.
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Affiliation(s)
- Xiaomin Shi
- Department of Mathematics and International Center for Quantum and Molecular StructuresShanghai UniversityChina
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18
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Wu Y, Wu J, Deng M, Lin Y. Yeast cell fate control by temporal redundancy modulation of transcription factor paralogs. Nat Commun 2021; 12:3145. [PMID: 34035307 PMCID: PMC8149833 DOI: 10.1038/s41467-021-23425-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 04/28/2021] [Indexed: 11/19/2022] Open
Abstract
Recent single-cell studies have revealed that yeast stress response involves transcription factors that are activated in pulses. However, it remains unclear whether and how these dynamic transcription factors temporally interact to regulate stress survival. Here we show that budding yeast cells can exploit the temporal relationship between paralogous general stress regulators, Msn2 and Msn4, during stress response. We find that individual pulses of Msn2 and Msn4 are largely redundant, and cells can enhance the expression of their shared targets by increasing their temporal divergence. Thus, functional redundancy between these two paralogs is modulated in a dynamic manner to confer fitness advantages for yeast cells, which might feed back to promote the preservation of their redundancy. This evolutionary implication is supported by evidence from Msn2/Msn4 orthologs and analyses of other transcription factor paralogs. Together, we show a cell fate control mechanism through temporal redundancy modulation in yeast, which may represent an evolutionarily important strategy for maintaining functional redundancy between gene duplicates.
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Affiliation(s)
- Yan Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Jiaqi Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Minghua Deng
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences, Peking University, Beijing, China
- Center for Statistical Science, Peking University, Beijing, China
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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19
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Stress-induced growth rate reduction restricts metabolic resource utilization to modulate osmo-adaptation time. Cell Rep 2021; 34:108854. [PMID: 33730573 DOI: 10.1016/j.celrep.2021.108854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/09/2021] [Accepted: 02/18/2021] [Indexed: 01/15/2023] Open
Abstract
A near-constant feature of stress responses is a downregulation or arrest of the cell cycle, resulting in transient growth slowdown. To investigate the role of growth slowdown in the hyperosmotic shock response of S. cerevisiae, we perturbed the G1/S checkpoint protein Sic1 to enable osmo-stress response activation with diminished growth slowdown. We document that in this mutant, adaptation to stress is accelerated rather than delayed. This accelerated recovery of the mutant proceeds by liquidation of internal glycogen stores, which are then shunted into the osmo-shock response. Therefore, osmo-adaptation in wild-type cells is delayed because growth slowdown prevents full accessibility to cellular glycogen stores. However, faster adaptation comes at the cost of acute sensitivity to subsequent osmo-stresses. We suggest that stress-induced growth slowdown acts as an arbiter to regulate the resources devoted to osmo-shock, balancing short-term adaptation with long-term robustness.
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20
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Laidlaw KME, Bisinski DD, Shashkova S, Paine KM, Veillon MA, Leake MC, MacDonald C. A glucose-starvation response governs endocytic trafficking and eisosomal retention of surface cargoes in budding yeast. J Cell Sci 2021; 134:jcs257733. [PMID: 33443082 PMCID: PMC7860119 DOI: 10.1242/jcs.257733] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic cells adapt their metabolism to the extracellular environment. Downregulation of surface cargo proteins in response to nutrient stress reduces the burden of anabolic processes whilst elevating catabolic production in the lysosome. We show that glucose starvation in yeast triggers a transcriptional response that increases internalisation from the plasma membrane. Nuclear export of the Mig1 transcriptional repressor in response to glucose starvation increases levels of the Yap1801 and Yap1802 clathrin adaptors, which is sufficient to increase cargo internalisation. Beyond this, we show that glucose starvation results in Mig1-independent transcriptional upregulation of various eisosomal factors. These factors serve to sequester a portion of nutrient transporters at existing eisosomes, through the presence of Ygr130c and biochemical and biophysical changes in Pil1, allowing cells to persist throughout the starvation period and maximise nutrient uptake upon return to replete conditions. This provides a physiological benefit for cells to rapidly recover from glucose starvation. Collectively, this remodelling of the surface protein landscape during glucose starvation calibrates metabolism to available nutrients.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Kamilla M E Laidlaw
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Daniel D Bisinski
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Sviatlana Shashkova
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
- Department of Physics, University of York, York YO10 5DD, UK
| | - Katherine M Paine
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Malaury A Veillon
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Mark C Leake
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
- Department of Physics, University of York, York YO10 5DD, UK
| | - Chris MacDonald
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
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21
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Chowdhury D, Wang C, Lu A, Zhu H. Identifying Transcription Factor Combinations to Modulate Circadian Rhythms by Leveraging Virtual Knockouts on Transcription Networks. iScience 2020; 23:101490. [PMID: 32920484 PMCID: PMC7492989 DOI: 10.1016/j.isci.2020.101490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/24/2020] [Accepted: 08/19/2020] [Indexed: 02/02/2023] Open
Abstract
The mammalian circadian systems consist of indigenous, self-sustained 24-h rhythm generators. They comprise many genes, molecules, and regulators. To decode their systematic controls, a robust computational approach was employed. It integrates transcription-factor-occupancy and time-series gene-expression data as input. The model equations were constructed and solved to determine the transcriptional regulatory logics in the mouse transcriptome network. This hypothesizes to explore the underlying mechanisms of combinatorial transcriptional regulations for circadian rhythms in mouse. We reconstructed the quantitative transcriptional-regulatory networks for circadian gene regulation at a dynamic scale. Transcriptional-simulations with virtually knocked-out mutants were performed to estimate their influence on networks. The potential transcriptional-regulators-combinations modulating the circadian rhythms were identified. Of them, CLOCK/CRY1 double knockout preserves the highest modulating capacity. Our quantitative framework offers a quick, robust, and physiologically relevant way to characterize the druggable targets to modulate the circadian rhythms at a dynamic scale effectively.
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Affiliation(s)
- Debajyoti Chowdhury
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chao Wang
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Aiping Lu
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Hailong Zhu
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
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22
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Schmidt GW, Welkenhuysen N, Ye T, Cvijovic M, Hohmann S. Mig1 localization exhibits biphasic behavior which is controlled by both metabolic and regulatory roles of the sugar kinases. Mol Genet Genomics 2020; 295:1489-1500. [PMID: 32948893 PMCID: PMC7524853 DOI: 10.1007/s00438-020-01715-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/20/2020] [Indexed: 12/01/2022]
Abstract
Glucose, fructose and mannose are the preferred carbon/energy sources for the yeast Saccharomyces cerevisiae. Absence of preferred energy sources activates glucose derepression, which is regulated by the kinase Snf1. Snf1 phosphorylates the transcriptional repressor Mig1, which results in its exit from the nucleus and subsequent derepression of genes. In contrast, Snf1 is inactive when preferred carbon sources are available, which leads to dephosphorylation of Mig1 and its translocation to the nucleus where Mig1 acts as a transcription repressor. Here we revisit the role of the three hexose kinases, Hxk1, Hxk2 and Glk1, in glucose de/repression. We demonstrate that all three sugar kinases initially affect Mig1 nuclear localization upon addition of glucose, fructose and mannose. This initial import of Mig1 into the nucleus was temporary; for continuous nucleocytoplasmic shuttling of Mig1, Hxk2 is required in the presence of glucose and mannose and in the presence of fructose Hxk2 or Hxk1 is required. Our data suggest that Mig1 import following exposure to preferred energy sources is controlled via two different pathways, where (1) the initial import is regulated by signals derived from metabolism and (2) continuous shuttling is regulated by the Hxk2 and Hxk1 proteins. Mig1 nucleocytoplasmic shuttling appears to be important for the maintenance of the repressed state in which Hxk1/2 seems to play an essential role.
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Affiliation(s)
- Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Niek Welkenhuysen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.,Department of Mathematical Sciences, University of Gothenburg and Chalmers University of Technology, Göteborg, Sweden
| | - Tian Ye
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg and Chalmers University of Technology, Göteborg, Sweden
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden. .,Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
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23
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Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa. Sci Rep 2020; 10:15168. [PMID: 32938998 PMCID: PMC7495483 DOI: 10.1038/s41598-020-72213-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/25/2020] [Indexed: 11/09/2022] Open
Abstract
Stochastic networks for the clock were identified by ensemble methods using genetic algorithms that captured the amplitude and period variation in single cell oscillators of Neurospora crassa. The genetic algorithms were at least an order of magnitude faster than ensemble methods using parallel tempering and appeared to provide a globally optimum solution from a random start in the initial guess of model parameters (i.e., rate constants and initial counts of molecules in a cell). The resulting goodness of fit [Formula: see text] was roughly halved versus solutions produced by ensemble methods using parallel tempering, and the resulting [Formula: see text] per data point was only [Formula: see text] = 2,708.05/953 = 2.84. The fitted model ensemble was robust to variation in proxies for "cell size". The fitted neutral models without cellular communication between single cells isolated by microfluidics provided evidence for only one Stochastic Resonance at one common level of stochastic intracellular noise across days from 6 to 36 h of light/dark (L/D) or in a D/D experiment. When the light-driven phase synchronization was strong as measured by the Kuramoto (K), there was degradation in the single cell oscillations away from the stochastic resonance. The rate constants for the stochastic clock network are consistent with those determined on a macroscopic scale of 107 cells.
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24
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Persson S, Welkenhuysen N, Shashkova S, Cvijovic M. Fine-Tuning of Energy Levels Regulates SUC2 via a SNF1-Dependent Feedback Loop. Front Physiol 2020; 11:954. [PMID: 32922308 PMCID: PMC7456839 DOI: 10.3389/fphys.2020.00954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/15/2020] [Indexed: 11/22/2022] Open
Abstract
Nutrient sensing pathways are playing an important role in cellular response to different energy levels. In budding yeast, Saccharomyces cerevisiae, the sucrose non-fermenting protein kinase complex SNF1 is a master regulator of energy homeostasis. It is affected by multiple inputs, among which energy levels is the most prominent. Cells which are exposed to a switch in carbon source availability display a change in the gene expression machinery. It has been shown that the magnitude of the change varies from cell to cell. In a glucose rich environment Snf1/Mig1 pathway represses the expression of its downstream target, such as SUC2. However, upon glucose depletion SNF1 is activated which leads to an increase in SUC2 expression. Our single cell experiments indicate that upon starvation, gene expression pattern of SUC2 shows rapid increase followed by a decrease to initial state with high cell-to-cell variability. The mechanism behind this behavior is currently unknown. In this work we study the long-term behavior of the Snf1/Mig1 pathway upon glucose starvation with a microfluidics and non-linear mixed effect modeling approach. We show a negative feedback mechanism, involving Snf1 and Reg1, which reduces SUC2 expression after the initial strong activation. Snf1 kinase activity plays a key role in this feedback mechanism. Our systems biology approach proposes a negative feedback mechanism that works through the SNF1 complex and is controlled by energy levels. We further show that Reg1 likely is involved in the negative feedback mechanism.
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Affiliation(s)
- Sebastian Persson
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Niek Welkenhuysen
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Sviatlana Shashkova
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
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25
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Su Y, Ko ME, Cheng H, Zhu R, Xue M, Wang J, Lee JW, Frankiw L, Xu A, Wong S, Robert L, Takata K, Yuan D, Lu Y, Huang S, Ribas A, Levine R, Nolan GP, Wei W, Plevritis SK, Li G, Baltimore D, Heath JR. Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line. Nat Commun 2020; 11:2345. [PMID: 32393797 PMCID: PMC7214418 DOI: 10.1038/s41467-020-15956-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/02/2020] [Indexed: 12/12/2022] Open
Abstract
The determination of individual cell trajectories through a high-dimensional cell-state space is an outstanding challenge for understanding biological changes ranging from cellular differentiation to epigenetic responses of diseased cells upon drugging. We integrate experiments and theory to determine the trajectories that single BRAFV600E mutant melanoma cancer cells take between drug-naive and drug-tolerant states. Although single-cell omics tools can yield snapshots of the cell-state landscape, the determination of individual cell trajectories through that space can be confounded by stochastic cell-state switching. We assayed for a panel of signaling, phenotypic, and metabolic regulators at points across 5 days of drug treatment to uncover a cell-state landscape with two paths connecting drug-naive and drug-tolerant states. The trajectory a given cell takes depends upon the drug-naive level of a lineage-restricted transcription factor. Each trajectory exhibits unique druggable susceptibilities, thus updating the paradigm of adaptive resistance development in an isogenic cell population.
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Affiliation(s)
- Yapeng Su
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Institute for Systems Biology, Seattle, Washington, USA
| | - Melissa E Ko
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, USA
| | - Hanjun Cheng
- Institute for Systems Biology, Seattle, Washington, USA
| | - Ronghui Zhu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Min Xue
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Jessica Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Jihoon W Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Luke Frankiw
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Alexander Xu
- Institute for Systems Biology, Seattle, Washington, USA
| | - Stephanie Wong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Lidia Robert
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Kaitlyn Takata
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, Washington, USA
| | - Yue Lu
- Institute for Systems Biology, Seattle, Washington, USA
| | - Sui Huang
- Institute for Systems Biology, Seattle, Washington, USA
| | - Antoni Ribas
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California, USA
- Department of Surgery, UCLA, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
| | - Raphael Levine
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
- The Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Wei Wei
- Institute for Systems Biology, Seattle, Washington, USA
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
| | | | - Guideng Li
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Suzhou Institute of Systems Medicine, Suzhou, China.
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
- Institute for Systems Biology, Seattle, Washington, USA.
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA.
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26
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Qiu B, Zhou T, Zhang J. Stochastic fluctuations in apoptotic threshold of tumour cells can enhance apoptosis and combat fractional killing. ROYAL SOCIETY OPEN SCIENCE 2020; 7:190462. [PMID: 32257298 PMCID: PMC7062090 DOI: 10.1098/rsos.190462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 01/20/2020] [Indexed: 06/11/2023]
Abstract
Fractional killing, which is a significant impediment to successful chemotherapy, is observed even in a population of genetically identical cancer cells exposed to apoptosis-inducing agents. This phenomenon arises not from genetic mutation but from cell-to-cell variation in the activation timing and level of the proteins that regulates apoptosis. To understand the mechanism behind the phenomenon, we formulate complex fractional killing processes as a first-passage time (FPT) problem with a stochastically fluctuating boundary. Analytical calculations are performed for the FPT distribution in a toy model of stochastic p53 gene expression, where the cancer cell is killed only when the p53 expression level crosses an active apoptotic threshold. Counterintuitively, we find that threshold fluctuations can effectively enhance cellular killing by significantly decreasing the mean time that the p53 protein reaches the threshold level for the first time. Moreover, faster fluctuations lead to the killing of more cells. These qualitative results imply that fluctuations in threshold are a non-negligible stochastic source, and can be taken as a strategy for combating fractional killing of cancer cells.
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Affiliation(s)
- Baohua Qiu
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
- Key Laboratory of Computational Mathematics, Guangzhou, Guangdong Province, People's Republic of China
| | - Tianshou Zhou
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
- Key Laboratory of Computational Mathematics, Guangzhou, Guangdong Province, People's Republic of China
| | - Jiajun Zhang
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
- Key Laboratory of Computational Mathematics, Guangzhou, Guangdong Province, People's Republic of China
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27
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Cao M, Qiu B, Zhou T, Zhang J. Control strategies for the timing of intracellular events. Phys Rev E 2020; 100:062401. [PMID: 31962487 DOI: 10.1103/physreve.100.062401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 11/07/2022]
Abstract
While the timing of intracellular events is essential for many cellular processes, gene expression inside a single cell can exhibit substantial cell-to-cell variability, raising the question of how cells ensure precision in event timing despite such stochasticity. We address this question by analyzing a biologically reasonable model of gene expression in the context of first passage time (FPT), focusing on two experimentally measurable statistics: mean FPT (MFPT) and timing variability (TV). We show that (1) transcriptional burst size (BS) and burst frequency (BF) can minimize the TV; (2) translational BS monotonically reduces the MFPT to a nonzero low bound; (3) the timescale of promoter kinetics can minimize both the MFPT and the TV, depending on the ratio of the on-switching rate over the off-switching rate; and (4) positive feedback regulation of any form can all minimize the TV, whereas negative feedback regulation of transcriptional BF or BS always enhances the TV. These control strategies can have broad implications for diverse cellular processes relying on precise temporal triggering of events.
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Affiliation(s)
- Mengfang Cao
- Key Laboratory of Computational Mathematics, Guangdong Province, School of Mathematics, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Baohua Qiu
- Key Laboratory of Computational Mathematics, Guangdong Province, School of Mathematics, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Tianshou Zhou
- Key Laboratory of Computational Mathematics, Guangdong Province, School of Mathematics, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jiajun Zhang
- Key Laboratory of Computational Mathematics, Guangdong Province, School of Mathematics, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
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28
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Chapal M, Mintzer S, Brodsky S, Carmi M, Barkai N. Resolving noise-control conflict by gene duplication. PLoS Biol 2019; 17:e3000289. [PMID: 31756183 PMCID: PMC6874299 DOI: 10.1371/journal.pbio.3000289] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/21/2019] [Indexed: 12/15/2022] Open
Abstract
Gene duplication promotes adaptive evolution in two main ways: allowing one duplicate to evolve a new function and splitting ancestral functions between the duplicates. The second scenario may resolve adaptive conflicts that can rise when one gene performs different functions. In an apparent departure from both scenarios, low-expressing transcription factor (TF) duplicates commonly bind to the same DNA motifs and act in overlapping conditions. To examine for possible benefits of this apparent redundancy, we examined the Msn2 and Msn4 duplicates in budding yeast. We show that Msn2,4 function as one unit by inducing the same set of target genes in overlapping conditions. Yet, the two-factor composition allows this unit's expression to be both environmentally responsive and with low noise, resolving an adaptive conflict that limits expression of single genes. We propose that duplication can provide adaptive benefit through cooperation rather than functional divergence, allowing two-factor dynamics with beneficial properties that cannot be achieved by a single gene.
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Affiliation(s)
- Michal Chapal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sefi Mintzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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29
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Brouwer I, Lenstra TL. Visualizing transcription: key to understanding gene expression dynamics. Curr Opin Chem Biol 2019; 51:122-129. [DOI: 10.1016/j.cbpa.2019.05.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 12/24/2022]
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30
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Abstract
A handful of core intercellular signaling pathways play pivotal roles in a broad variety of developmental processes. It has remained puzzling how so few pathways can provide the precision and specificity of cell-cell communication required for multicellular development. Solving this requires us to quantitatively understand how developmentally relevant signaling information is actively sensed, transformed and spatially distributed by signaling pathways. Recently, single cell analysis and cell-based reconstitution, among other approaches, have begun to reveal the 'communication codes' through which information is represented in the identities, concentrations, combinations and dynamics of extracellular ligands. They have also revealed how signaling pathways decipher these features and control the spatial distribution of signaling in multicellular contexts. Here, we review recent work reporting the discovery and analysis of communication codes and discuss their implications for diverse developmental processes.
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Affiliation(s)
- Pulin Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, Pasadena, CA 91125, USA
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31
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Activation-induced deaminase (AID) localizes to the nucleus in brief pulses. PLoS Genet 2019; 15:e1007968. [PMID: 30811383 PMCID: PMC6411215 DOI: 10.1371/journal.pgen.1007968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/11/2019] [Accepted: 01/16/2019] [Indexed: 11/19/2022] Open
Abstract
Activation-induced deaminase (AID) converts C to U and 5-methyl-C to T. These mutagenic activities are critical to immunoglobulin (Ig) gene diversification and epigenetic reprogramming, but they must be tightly controlled to prevent compromising cell fitness. AID acts in the nucleus but localizes predominately to the cytoplasm. To address this apparent paradox, we have carried out time-lapse imaging of AID in single living B cells and fibroblasts. We demonstrate that AID enters the nucleus in brief (30 min) pulses, evident in about 10% of cells in the course of a single cell cycle (24 hr imaging). Pulses do not depend on AID catalytic activity, but they are coordinated with nuclear accumulation of P53. Pulsing may protect cells from pathologic consequences of excess exposure to AID, or enable AID to synchronize its activity with transcription of genes that are AID targets or with nuclear entry of factors that act at sites of AID-catalyzed DNA deamination to promote Ig gene diversification or epigenetic reprogramming.
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32
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Roy A, Klumpp S. Simulating Genetic Circuits in Bacterial Populations with Growth Heterogeneity. Biophys J 2019; 114:484-492. [PMID: 29401445 DOI: 10.1016/j.bpj.2017.11.3745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/31/2017] [Accepted: 11/17/2017] [Indexed: 01/21/2023] Open
Abstract
We computationally study genetic circuits in bacterial populations with heterogeneities in the growth rate. To that end, we present a stochastic simulation method for gene circuits in populations of cells and propose an efficient implementation that we call the "Next Family Method". Within this approach, we implement different population setups, specifically Chemostat-type growth and growth in an ideal Mother Machine and show that the population structure and its statistics are different for the different setups whenever there is growth heterogeneity. Such dependence on the population setup is demonstrated, in the case of bistable systems with different growth rates in the stable states, to have distinctive signatures on quantities including the distributions of protein concentration and growth rates, and hysteresis curves. Applying this method to a bistable antibiotic resistance circuit, we find that as a result of the different statistics in different population setups, the estimated minimal inhibitory concentration of the antibiotic becomes dependent on the population setup in which it is measured.
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Affiliation(s)
- Anjan Roy
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany; Institute for Nonlinear Dynamics, University of Göttingen, Göttingen, Germany
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany; Institute for Nonlinear Dynamics, University of Göttingen, Göttingen, Germany.
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33
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A Noisy Analog-to-Digital Converter Connects Cytosolic Calcium Bursts to Transcription Factor Nuclear Localization Pulses in Yeast. G3-GENES GENOMES GENETICS 2019; 9:561-570. [PMID: 30573469 PMCID: PMC6385971 DOI: 10.1534/g3.118.200841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Several examples of transcription factors that show stochastic, unsynchronized pulses of nuclear localization have been described. Here we show that under constant calcium stress, nuclear localization pulses of the transcription factor Crz1 follow stochastic variations in cytosolic calcium concentration. We find that the size of the stochastic calcium bursts is positively correlated with the number of subsequent Crz1 pulses. Based on our observations, we propose a simple stochastic model of how the signaling pathway converts a constant external calcium concentration into a digital number of Crz1 pulses in the nucleus, due to the time delay from nuclear transport and the stochastic decoherence of individual Crz1 molecule dynamics. We find support for several additional predictions of the model and suggest that stochastic input to nuclear transport may produce noisy digital responses to analog signals in other signaling systems.
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34
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Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation. Cell 2019; 172:1079-1090.e12. [PMID: 29474908 PMCID: PMC5847172 DOI: 10.1016/j.cell.2018.01.026] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/26/2017] [Accepted: 01/18/2018] [Indexed: 12/22/2022]
Abstract
How signaling dynamics encode information is a central question in biology. During vertebrate development, dynamic Notch signaling oscillations control segmentation of the presomitic mesoderm (PSM). In mouse embryos, this molecular clock comprises signaling oscillations of several pathways, i.e., Notch, Wnt, and FGF signaling. Here, we directly address the role of the relative timing between Wnt and Notch signaling oscillations during PSM patterning. To this end, we developed a new experimental strategy using microfluidics-based entrainment that enables specific control of the rhythm of segmentation clock oscillations. Using this approach, we find that Wnt and Notch signaling are coupled at the level of their oscillation dynamics. Furthermore, we provide functional evidence that the oscillation phase shift between Wnt and Notch signaling is critical for PSM segmentation. Our work hence reveals that dynamic signaling, i.e., the relative timing between oscillatory signals, encodes essential information during multicellular development. Wnt and Notch signaling wave dynamics differ within segmenting mouse mesoderm Entraining oscillations by microfluidics allows external control of the dynamics Oscillatory Wnt and Notch signaling networks are coupled at the level of dynamics Relative timing of Wnt and Notch signaling oscillations is critical for segmentation
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35
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Martinez-Corral R, Raimundez E, Lin Y, Elowitz MB, Garcia-Ojalvo J. Self-Amplifying Pulsatile Protein Dynamics without Positive Feedback. Cell Syst 2018; 7:453-462.e1. [PMID: 30316816 DOI: 10.1016/j.cels.2018.08.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/27/2018] [Accepted: 08/23/2018] [Indexed: 01/20/2023]
Abstract
Many proteins exhibit dynamic activation patterns in the form of irregular pulses. Such behavior is typically attributed to a combination of positive and negative feedback loops in the underlying regulatory network. However, the presence of positive feedbacks is difficult to demonstrate unequivocally, raising the question of whether stochastic pulses can arise from negative feedback only. Here, we use the protein kinase A (PKA) system, a key regulator of the yeast pulsatile transcription factor Msn2, as a case example to show that irregular pulses of protein activity can arise from a negative feedback loop alone. Simplification to two variables reveals that a combination of zero-order ultrasensitivity, timescale separation between the activator and the repressor, and an effective delay in the feedback are sufficient to amplify a perturbation into a pulse. The same circuit topology can account for both activation and inactivation pulses, pointing toward a general mechanism of stochastic pulse generation.
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Affiliation(s)
- Rosa Martinez-Corral
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Elba Raimundez
- Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg 85764, Germany; Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching 85748, Germany
| | - Yihan Lin
- Center for Quantitative Biology and Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Michael B Elowitz
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Dr. Aiguader 88, Barcelona 08003, Spain.
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36
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Pfanzagl V, Görner W, Radolf M, Parich A, Schuhmacher R, Strauss J, Reiter W, Schüller C. A constitutive active allele of the transcription factor Msn2 mimicking low PKA activity dictates metabolic remodeling in yeast. Mol Biol Cell 2018; 29:2848-2862. [PMID: 30256697 PMCID: PMC6249869 DOI: 10.1091/mbc.e18-06-0389] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In yeast, protein kinase A (PKA) adjusts transcriptional profiles, metabolic rates, and cell growth in accord with carbon source availability. PKA affects gene expression mostly via the transcription factors Msn2 and Msn4, two key regulators of the environmental stress response. Here we analyze the role of the PKA-Msn2 signaling module using an Msn2 allele that harbors serine-to-alanine substitutions at six functionally important PKA motifs (Msn2A6) . Expression of Msn2A6 mimics low PKA activity, entails a transcription profile similar to that of respiring cells, and prevents formation of colonies on glucose-containing medium. Furthermore, Msn2A6 leads to high oxygen consumption and hence high respiratory activity. Substantially increased intracellular concentrations of several carbon metabolites, such as trehalose, point to a metabolic adjustment similar to diauxic shift. This partial metabolic switch is the likely cause for the slow-growth phenotype in the presence of glucose. Consistently, Msn2A6 expression does not interfere with growth on ethanol and tolerated is to a limited degree in deletion mutant strains with a gene expression signature corresponding to nonfermentative growth. We propose that the lethality observed in mutants with hampered PKA activity resides in metabolic reprogramming that is initiated by Msn2 hyperactivity.
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Affiliation(s)
- Vera Pfanzagl
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | - Wolfram Görner
- Department for Biochemistry, Max. F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Martin Radolf
- Management Scientific Service/EHS, Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Alexandra Parich
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences, 3430 Tulln, Austria
| | - Joseph Strauss
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | - Wolfgang Reiter
- Department for Biochemistry, Max. F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, 3430 Tulln, Austria
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37
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Wolff SC, Kedziora KM, Dumitru R, Dungee CD, Zikry TM, Beltran AS, Haggerty RA, Cheng J, Redick MA, Purvis JE. Inheritance of OCT4 predetermines fate choice in human embryonic stem cells. Mol Syst Biol 2018; 14:e8140. [PMID: 30177503 PMCID: PMC6120590 DOI: 10.15252/msb.20178140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 07/28/2018] [Accepted: 07/30/2018] [Indexed: 01/21/2023] Open
Abstract
It is well known that clonal cells can make different fate decisions, but it is unclear whether these decisions are determined during, or before, a cell's own lifetime. Here, we engineered an endogenous fluorescent reporter for the pluripotency factor OCT4 to study the timing of differentiation decisions in human embryonic stem cells. By tracking single-cell OCT4 levels over multiple cell cycle generations, we found that the decision to differentiate is largely determined before the differentiation stimulus is presented and can be predicted by a cell's preexisting OCT4 signaling patterns. We further quantified how maternal OCT4 levels were transmitted to, and distributed between, daughter cells. As mother cells underwent division, newly established OCT4 levels in daughter cells rapidly became more predictive of final OCT4 expression status. These results imply that the choice between developmental cell fates can be largely predetermined at the time of cell birth through inheritance of a pluripotency factor.
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Affiliation(s)
- Samuel C Wolff
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Raluca Dumitru
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Cierra D Dungee
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Tarek M Zikry
- Department of Biostatistics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Adriana S Beltran
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Rachel A Haggerty
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - JrGang Cheng
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Margaret A Redick
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
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38
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Leake MC. Transcription factors in eukaryotic cells can functionally regulate gene expression by acting in oligomeric assemblies formed from an intrinsically disordered protein phase transition enabled by molecular crowding. Transcription 2018; 9:298-306. [PMID: 29895219 PMCID: PMC6150617 DOI: 10.1080/21541264.2018.1475806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
High-speed single-molecule fluorescence microscopy in vivo shows that transcription factors in eukaryotes can act in oligomeric clusters mediated by molecular crowding and intrinsically disordered protein. This finding impacts on the longstanding puzzle of how transcription factors find their gene targets so efficiently in the complex, heterogeneous environment of the cell. Abbreviations CDF - cumulative distribution function; FRAP - fluorescence recovery after photobleaching; GFP - Green fluorescent protein; STORM - stochastic optical reconstruction microscopy; TF - Transcription factor; YFP - Yellow fluorescent protein
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Affiliation(s)
- Mark C Leake
- a Departments of Physics and Biology , Biological Physical Sciences Institute, University of York , York , UK
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39
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Zinkgraf M, Gerttula S, Zhao S, Filkov V, Groover A. Transcriptional and temporal response of Populus stems to gravi-stimulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:578-590. [PMID: 29480544 DOI: 10.1111/jipb.12645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 02/24/2018] [Indexed: 05/12/2023]
Abstract
Plants modify development in response to external stimuli, to produce new growth that is appropriate for environmental conditions. For example, gravi-stimulation of leaning branches in angiosperm trees results in modifications of wood development, to produce tension wood that pulls leaning stems upright. Here, we use gravi-stimulation and tension wood response to dissect the temporal changes in gene expression underlying wood formation in Populus stems. Using time-series analysis of seven time points over a 14-d experiment, we identified 8,919 genes that were differentially expressed between tension wood (upper) and opposite wood (lower) sides of leaning stems. Clustering of differentially expressed genes showed four major transcriptional responses, including gene clusters whose transcript levels were associated with two types of tissue-specific impulse responses that peaked at about 24-48 h, and gene clusters with sustained changes in transcript levels that persisted until the end of the 14-d experiment. Functional enrichment analysis of those clusters suggests they reflect temporal changes in pathways associated with hormone regulation, protein localization, cell wall biosynthesis and epigenetic processes. Time-series analysis of gene expression is an underutilized approach for dissecting complex developmental responses in plants, and can reveal gene clusters and mechanisms influencing development.
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Affiliation(s)
- Matthew Zinkgraf
- USDA Forest Service, Pacific Southwest Research Station, 1731 Research Park Drive, Davis, CA 95618, USA
- Department of Computer Science, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Suzanne Gerttula
- USDA Forest Service, Pacific Southwest Research Station, 1731 Research Park Drive, Davis, CA 95618, USA
- Department of Computer Science, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Shutang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Vladimir Filkov
- Department of Computer Science, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Andrew Groover
- USDA Forest Service, Pacific Southwest Research Station, 1731 Research Park Drive, Davis, CA 95618, USA
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
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40
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Hannanta-anan P, Chow BY. Optogenetic Inhibition of Gα q Protein Signaling Reduces Calcium Oscillation Stochasticity. ACS Synth Biol 2018; 7:1488-1495. [PMID: 29792810 PMCID: PMC6311707 DOI: 10.1021/acssynbio.8b00065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As fast terminators of G-protein coupled receptor (GPCR) signaling, regulators of G-protein signaling (RGS) serve critical roles in fine-tuning second messenger levels and, consequently, cellular responses to external stimuli. Here, we report the creation of an optogenetic RGS2 (opto-RGS2) that suppresses agonist-evoked calcium oscillations by the inactivation of Gαq protein. In this system, cryptochrome-mediated heterodimerization of the catalytic RGS2-box with its N-terminal amphipathic helix reconstitutes a functional membrane-localized complex that can dynamically suppress store-operated release of calcium. Engineered opto-RGS2 cell lines were used to establish the role of RGS2 as a key inhibitory feedback regulator of the stochasticity of the Gαq-mediated calcium spike timing. RGS2 reduced the stochasticity of carbachol-stimulated calcium oscillations, and the feedback inhibition was coupled to the global calcium elevation by calmodulin/RGS2 interactions. The identification of a critical negative feedback circuit exemplifies the utility of optogenetic approaches for interrogating RGS/GPCR biology and calcium encoding principles through temporally precise molecular gain-of-function.
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Affiliation(s)
| | - Brian Y. Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
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41
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Sampattavanich S, Steiert B, Kramer BA, Gyori BM, Albeck JG, Sorger PK. Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases. Cell Syst 2018; 6:664-678.e9. [PMID: 29886111 DOI: 10.1016/j.cels.2018.05.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/19/2017] [Accepted: 05/04/2018] [Indexed: 02/05/2023]
Abstract
Extracellular growth factors signal to transcription factors via a limited number of cytoplasmic kinase cascades. It remains unclear how such cascades encode ligand identities and concentrations. In this paper, we use live-cell imaging and statistical modeling to study FOXO3, a transcription factor regulating diverse aspects of cellular physiology that is under combinatorial control. We show that FOXO3 nuclear-to-cytosolic translocation has two temporally distinct phases varying in magnitude with growth factor identity and cell type. These phases comprise synchronous translocation soon after ligand addition followed by an extended back-and-forth shuttling; this shuttling is pulsatile and does not have a characteristic frequency, unlike a simple oscillator. Early and late dynamics are differentially regulated by Akt and ERK and have low mutual information, potentially allowing the two phases to encode different information. In cancer cells in which ERK and Akt are dysregulated by oncogenic mutation, the diversity of states is lower.
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Affiliation(s)
- Somponnat Sampattavanich
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA; Siriraj Laboratory for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor Srisavarindhira Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand.
| | - Bernhard Steiert
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA; Institute of Physics, University of Freiburg, Freiburg, Germany; Freiburg Center for Systems Biology, University of Freiburg, Freiburg, Germany
| | - Bernhard A Kramer
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA; Division of Systems Biology of Signal Transduction, German Cancer Research Center, Heidelberg, Germany
| | - Benjamin M Gyori
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Peter K Sorger
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA.
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42
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Caranica C, Al-Omari A, Deng Z, Griffith J, Nilsen R, Mao L, Arnold J, Schüttler HB. Ensemble methods for stochastic networks with special reference to the biological clock of Neurospora crassa. PLoS One 2018; 13:e0196435. [PMID: 29768444 PMCID: PMC5955539 DOI: 10.1371/journal.pone.0196435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 11/18/2022] Open
Abstract
A major challenge in systems biology is to infer the parameters of regulatory networks that operate in a noisy environment, such as in a single cell. In a stochastic regime it is hard to distinguish noise from the real signal and to infer the noise contribution to the dynamical behavior. When the genetic network displays oscillatory dynamics, it is even harder to infer the parameters that produce the oscillations. To address this issue we introduce a new estimation method built on a combination of stochastic simulations, mass action kinetics and ensemble network simulations in which we match the average periodogram and phase of the model to that of the data. The method is relatively fast (compared to Metropolis-Hastings Monte Carlo Methods), easy to parallelize, applicable to large oscillatory networks and large (~2000 cells) single cell expression data sets, and it quantifies the noise impact on the observed dynamics. Standard errors of estimated rate coefficients are typically two orders of magnitude smaller than the mean from single cell experiments with on the order of ~1000 cells. We also provide a method to assess the goodness of fit of the stochastic network using the Hilbert phase of single cells. An analysis of phase departures from the null model with no communication between cells is consistent with a hypothesis of Stochastic Resonance describing single cell oscillators. Stochastic Resonance provides a physical mechanism whereby intracellular noise plays a positive role in establishing oscillatory behavior, but may require model parameters, such as rate coefficients, that differ substantially from those extracted at the macroscopic level from measurements on populations of millions of communicating, synchronized cells.
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Affiliation(s)
- C. Caranica
- Department of Statistics, University of Georgia, Athens, Georgia
| | - A. Al-Omari
- Department of Biomedical Systems and Informatics Engineering, Yarmouk University, Irbid, Jordan
| | - Z. Deng
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, Georgia
| | - J. Griffith
- Genetics Department, University of Georgia, Athens, Georgia
- College of Agricultural and Environmental Sciences, University of Georgia, Athens, Georgia
| | - R. Nilsen
- Genetics Department, University of Georgia, Athens, Georgia
| | - L. Mao
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, Georgia
| | - J. Arnold
- Genetics Department, University of Georgia, Athens, Georgia
- * E-mail:
| | - H.-B. Schüttler
- Department of Physics and Astronomy, University of Georgia, Athens, Georgia
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43
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Abstract
The noncoding portion of the genome, including microRNAs, has been fertile evolutionary soil for cortical development in primates. A major contribution to cortical expansion in primates is the generation of novel precursor cell populations. Because miRNA expression profiles track closely with cell identity, it is likely that numerous novel microRNAs have contributed to cellular diversity in the brain. The tools to determine the genomic context within which novel microRNAs emerge and how they become integrated into molecular circuitry are now in hand.
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Affiliation(s)
- Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - Tomasz Nowakowski
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California 94143, USA.,Department of Anatomy, University of California, San Francisco, California 94158, USA
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44
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Nikolaev EV, Rahi SJ, Sontag ED. Subharmonics and Chaos in Simple Periodically Forced Biomolecular Models. Biophys J 2018. [PMID: 29539408 DOI: 10.1016/j.bpj.2018.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This article uncovers a remarkable behavior in two biochemical systems that commonly appear as components of signal transduction pathways in systems biology. These systems have globally attracting steady states when unforced, so they might have been considered uninteresting from a dynamical standpoint. However, when subject to a periodic excitation, strange attractors arise via a period-doubling cascade. Quantitative analyses of the corresponding discrete chaotic trajectories are conducted numerically by computing largest Lyapunov exponents, power spectra, and autocorrelation functions. To gain insight into the geometry of the strange attractors, the phase portraits of the corresponding iterated maps are interpreted as scatter plots for which marginal distributions are additionally evaluated. The lack of entrainment to external oscillations, in even the simplest biochemical networks, represents a level of additional complexity in molecular biology, which has previously been insufficiently recognized but is plausibly biologically important.
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Affiliation(s)
- Evgeni V Nikolaev
- Center for Quantitative Biology, Rutgers University, Piscataway, New Jersey
| | - Sahand Jamal Rahi
- Department of Physics and Center for Brain Science, Harvard University, Cambridge, Massachusetts
| | - Eduardo D Sontag
- Center for Quantitative Biology, Rutgers University, Piscataway, New Jersey; Department of Electrical and Computer Engineering and Department of Bioengineering, Northeastern University, Boston, Massachusetts.
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45
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Abstract
Craniofacial surgery, since its inauguration, has been the culmination of collaborative efforts to solve complex congenital, dysplastic, oncological, and traumatic cranial bone defects. Now, 50 years on from the first craniofacial meeting, the collaborative efforts between surgeons, scientists, and bioengineers are further advancing craniofacial surgery with new discoveries in tissue regeneration. Recent advances in regenerative medicine and stem cell biology have transformed the authors' understanding of bone healing, the role of stem cells governing bone healing, and the effects of the niche environment and extracellular matrix on stem cell fate. This review aims at summarizing the advances within each of these fields.
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46
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Park J, Dies M, Lin Y, Hormoz S, Smith-Unna SE, Quinodoz S, Hernández-Jiménez MJ, Garcia-Ojalvo J, Locke JCW, Elowitz MB. Molecular Time Sharing through Dynamic Pulsing in Single Cells. Cell Syst 2018; 6:216-229.e15. [PMID: 29454936 PMCID: PMC6070344 DOI: 10.1016/j.cels.2018.01.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 09/04/2017] [Accepted: 01/10/2018] [Indexed: 11/19/2022]
Abstract
In cells, specific regulators often compete for limited amounts of a core enzymatic resource. It is typically assumed that competition leads to partitioning of core enzyme molecules among regulators at constant levels. Alternatively, however, different regulatory species could time share, or take turns utilizing, the core resource. Using quantitative time-lapse microscopy, we analyzed sigma factor activity dynamics, and their competition for RNA polymerase, in individual Bacillus subtilis cells under energy stress. Multiple alternative sigma factors were activated in ~1-hr pulses in stochastic and repetitive fashion. Pairwise analysis revealed that two sigma factors rarely pulse simultaneously and that some pairs are anti-correlated, indicating that RNAP utilization alternates among different sigma factors. Mathematical modeling revealed how stochastic time-sharing dynamics can emerge from pulse-generating sigma factor regulatory circuits actively competing for RNAP. Time sharing provides a mechanism for cells to dynamically control the distribution of cell states within a population. Since core molecular components are limiting in many other systems, time sharing may represent a general mode of regulation.
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Affiliation(s)
- Jin Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marta Dies
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain; Department of Physics and Nuclear Engineering, Universitat Politecnica de Catalunya, 08222 Terrassa, Spain; Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Yihan Lin
- Center for Quantitative Biology, and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Sahand Hormoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Sofia Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
| | - James C W Locke
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Microsoft Research, Cambridge, UK.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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47
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Abstract
Microfluidic systems in combination with microscopy (e.g., fluorescence) can be a powerful tool to study, at single-cell level, the behavior and morphology of biological cells after uptake of glucose. Here, we briefly discuss the advantages of using microfluidic systems. We further describe how microfluidic systems are fabricated and how they are utilized. Finally, we discuss how the large amount of data can be analyzed in a "semi-automatic" manner using custom-made software. In summary, we provide a guide to how to use microfluidic systems in single-cell studies.
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48
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Abstract
The last past decade has witnessed a revolution in our appreciation of transcriptome complexity and regulation. This remarkable expansion in our knowledge largely originates from the advent of high-throughput methodologies, and the consecutive discovery that up to 90% of eukaryotic genomes are transcribed, thus generating an unanticipated large range of noncoding RNAs (Hangauer et al., 15(4):112, 2014). Besides leading to the identification of new noncoding RNA species, transcriptome-wide studies have uncovered novel layers of posttranscriptional regulatory mechanisms controlling RNA processing, maturation or translation, and each contributing to the precise and dynamic regulation of gene expression. Remarkably, the development of systems-level studies has been accompanied by tremendous progress in the visualization of individual RNA molecules in single cells, such that it is now possible to image RNA species with a single-molecule resolution from birth to translation or decay. Monitoring quantitatively, with unprecedented spatiotemporal resolution, the fate of individual molecules has been key to understanding the molecular mechanisms underlying the different steps of RNA regulation. This has also revealed biologically relevant, intracellular and intercellular heterogeneities in RNA distribution or regulation. More recently, the convergence of imaging and high-throughput technologies has led to the emergence of spatially resolved transcriptomic techniques that provide a means to perform large-scale analyses while preserving spatial information. By generating transcriptome-wide data on single-cell RNA content, or even subcellular RNA distribution, these methodologies are opening avenues to a wide range of network-level studies at the cell and organ-level, and promise to strongly improve disease diagnostic and treatment.In this introductory chapter, we highlight how recently developed technologies aiming at detecting and visualizing RNA molecules have contributed to the emergence of entirely new research fields, and to dramatic progress in our understanding of gene expression regulation.
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Affiliation(s)
- Caroline Medioni
- Université Côte d'Azur, CNRS, Inserm, iBV, Parc Valrose, 06100, Nice, France
| | - Florence Besse
- Université Côte d'Azur, CNRS, Inserm, iBV, Parc Valrose, 06100, Nice, France.
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49
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Impact of Methods on the Measurement of mRNA Turnover. Int J Mol Sci 2017; 18:ijms18122723. [PMID: 29244760 PMCID: PMC5751324 DOI: 10.3390/ijms18122723] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/04/2017] [Accepted: 12/08/2017] [Indexed: 12/25/2022] Open
Abstract
The turnover of the RNA molecules is determined by the rates of transcription and RNA degradation. Several methods have been developed to study RNA turnover since the beginnings of molecular biology. Here we summarize the main methods to measure RNA half-life: transcription inhibition, gene control, and metabolic labelling. These methods were used to detect the cellular activity of the mRNAs degradation machinery, including the exo-ribonuclease Xrn1 and the exosome. On the other hand, the study of the differential stability of mature RNAs has been hampered by the fact that different methods have often yielded inconsistent results. Recent advances in the systematic comparison of different method variants in yeast have permitted the identification of the least invasive methodologies that reflect half-lives the most faithfully, which is expected to open the way for a consistent quantitative analysis of the determinants of mRNA stability.
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50
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Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol 2017; 15:e2004050. [PMID: 29240790 PMCID: PMC5746276 DOI: 10.1371/journal.pbio.2004050] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 11/17/2017] [Indexed: 02/01/2023] Open
Abstract
From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing to quantify transcript heterogeneity in single Saccharomyces cerevisiae cells treated with and without salt stress to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. We also discovered that a subset of cells appears to decouple expression of ribosomal protein genes from the environmental stress response in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results suggest that cells maintain a cellular filter against decoupled bursts of transcription factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells. Genetically identical cells growing in the same environment can vary in their cellular state and behavior. Such heterogeneity may explain why some cells in an isogenic population can survive sudden severe environmental stress whereas other cells succumb. Cell-to-cell variation in gene expression has been linked to variable stress survival, but how and why transcript levels vary across the transcriptome in single cells is only beginning to emerge. Here, we used single-cell RNA sequencing (scRNA-seq) to measure cell-to-cell heterogeneity in the transcriptome of budding yeast (Saccharomyces cerevisiae). We find surprising patterns of variation across known sets of transcription factor targets, indicating that cells vary in their transcriptome profile both before and after stress exposure. scRNA-seq analysis combined with live-cell imaging of transcription factor activation dynamics revealed some cells in which the stress response was coordinately activated and other cells in which the traditional response was decoupled, suggesting unrecognized regulatory nuances that expand our understanding of stress response and survival.
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Affiliation(s)
- Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Feiqiao Brian Yu
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Leah E. Escalante
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mike Place
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Rhonda Bacher
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Jad Kanbar
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Doina Ciobanu
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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