1
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Mondal S, Becskei A. Gene choice in cancer cells is exclusive in ion transport but concurrent in DNA replication. Comput Struct Biotechnol J 2024; 23:2534-2547. [PMID: 38974885 PMCID: PMC11226983 DOI: 10.1016/j.csbj.2024.06.004] [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: 02/29/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024] Open
Abstract
Cancers share common cellular and physiological features. Little is known about whether distinctive gene expression patterns can be displayed at the single-cell level by gene families in cancer cells. The expression of gene homologs within a family can exhibit concurrence and exclusivity. Concurrence can promote all-or-none expression patterns of related genes and underlie alternative physiological states. Conversely, exclusive gene families express the same or similar number of homologs in each cell, allowing a broad repertoire of cell identities to be generated. We show that gene families involved in the cell-cycle and antigen presentation are expressed concurrently. Concurrence in the DNA replication complex MCM reflects the replicative status of cells, including cell lines and cancer-derived organoids. Exclusive expression requires precise regulatory mechanism, but cancer cells retain this form of control for ion homeostasis and extend it to gene families involved in cell migration. Thus, the cell adhesion-based identity of healthy cells is transformed to an identity based on migration in the population of cancer cells, reminiscent of epithelial-mesenchymal transition.
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Affiliation(s)
- Samuel Mondal
- Biozentrum, University of Basel, Spitalstrasse 41, Basel 4056, Switzerland
| | - Attila Becskei
- Biozentrum, University of Basel, Spitalstrasse 41, Basel 4056, Switzerland
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2
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Hong CKY, Ramu A, Zhao S, Cohen BA. Effect of genomic and cellular environments on gene expression noise. Genome Biol 2024; 25:137. [PMID: 38790076 PMCID: PMC11127367 DOI: 10.1186/s13059-024-03277-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Individual cells from isogenic populations often display large cell-to-cell differences in gene expression. This "noise" in expression derives from several sources, including the genomic and cellular environment in which a gene resides. Large-scale maps of genomic environments have revealed the effects of epigenetic modifications and transcription factor occupancy on mean expression levels, but leveraging such maps to explain expression noise will require new methods to assay how expression noise changes at locations across the genome. RESULTS To address this gap, we present Single-cell Analysis of Reporter Gene Expression Noise and Transcriptome (SARGENT), a method that simultaneously measures the noisiness of reporter genes integrated throughout the genome and the global mRNA profiles of individual reporter-gene-containing cells. Using SARGENT, we perform the first comprehensive genome-wide survey of how genomic locations impact gene expression noise. We find that the mean and noise of expression correlate with different histone modifications. We quantify the intrinsic and extrinsic components of reporter gene noise and, using the associated mRNA profiles, assign the extrinsic component to differences between the CD24+ "stem-like" substate and the more "differentiated" substate. SARGENT also reveals the effects of transgene integrations on endogenous gene expression, which will help guide the search for "safe-harbor" loci. CONCLUSIONS Taken together, we show that SARGENT is a powerful tool to measure both the mean and noise of gene expression at locations across the genome and that the data generatd by SARGENT reveals important insights into the regulation of gene expression noise genome-wide.
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Affiliation(s)
- Clarice K Y Hong
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Avinash Ramu
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Siqi Zhao
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA
| | - Barak A Cohen
- The Edison Family Center for Genome Sciences and Systems Biology, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA.
- Department of Genetics, School of Medicine, Washington University in St. Louis, Saint Louis, MO, 63110, USA.
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3
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Boocock J, Alexander N, Tapia LA, Walter-McNeill L, Munugala C, Bloom JS, Kruglyak L. Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570640. [PMID: 38106186 PMCID: PMC10723400 DOI: 10.1101/2023.12.07.570640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in Saccharomyces cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to over 100,000 single cells from three crosses. We used scRNA-seq data to genotype each cell, measure gene expression, and classify the cells by cell-cycle stage. We mapped thousands of local and distant eQTLs and identified interactions between eQTL effects and cell-cycle stages. We took advantage of single-cell expression information to identify hundreds of genes with allele-specific effects on expression noise. We used cell-cycle stage classification to map 20 loci that influence cell-cycle progression. One of these loci influenced the expression of genes involved in the mating response. We showed that the effects of this locus arise from a common variant (W82R) in the gene GPA1, which encodes a signaling protein that negatively regulates the mating pathway. The 82R allele increases mating efficiency at the cost of slower cell-cycle progression and is associated with a higher rate of outcrossing in nature. Our results provide a more granular picture of the effects of genetic variants on gene expression and downstream traits.
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Affiliation(s)
- James Boocock
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Noah Alexander
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Leslie Alamo Tapia
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Laura Walter-McNeill
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Chetan Munugala
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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4
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Silkwood K, Dollinger E, Gervin J, Atwood S, Nie Q, Lander AD. Leveraging gene correlations in single cell transcriptomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532643. [PMID: 36993765 PMCID: PMC10055147 DOI: 10.1101/2023.03.14.532643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
BACKGROUND Many approaches have been developed to overcome technical noise in single cell RNA-sequencing (scRNAseq). As researchers dig deeper into data-looking for rare cell types, subtleties of cell states, and details of gene regulatory networks-there is a growing need for algorithms with controllable accuracy and fewer ad hoc parameters and thresholds. Impeding this goal is the fact that an appropriate null distribution for scRNAseq cannot simply be extracted from data when ground truth about biological variation is unknown (i.e., usually). RESULTS We approach this problem analytically, assuming that scRNAseq data reflect only cell heterogeneity (what we seek to characterize), transcriptional noise (temporal fluctuations randomly distributed across cells), and sampling error (i.e., Poisson noise). We analyze scRNAseq data without normalization-a step that skews distributions, particularly for sparse data-and calculate p-values associated with key statistics. We develop an improved method for selecting features for cell clustering and identifying gene-gene correlations, both positive and negative. Using simulated data, we show that this method, which we call BigSur (Basic Informatics and Gene Statistics from Unnormalized Reads), captures even weak yet significant correlation structures in scRNAseq data. Applying BigSur to data from a clonal human melanoma cell line, we identify thousands of correlations that, when clustered without supervision into gene communities, align with known cellular components and biological processes, and highlight potentially novel cell biological relationships. CONCLUSIONS New insights into functionally relevant gene regulatory networks can be obtained using a statistically grounded approach to the identification of gene-gene correlations.
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Affiliation(s)
- Kai Silkwood
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
| | - Emmanuel Dollinger
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
- Department of Mathematics, University of California, Irvine, Irvine CA
| | - Josh Gervin
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
| | - Scott Atwood
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
| | - Qing Nie
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
- Department of Mathematics, University of California, Irvine, Irvine CA
| | - Arthur D. Lander
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
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5
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Su Y, Xu C, Shea J, DeStephanis D, Su Z. Transcriptomic changes in single yeast cells under various stress conditions. BMC Genomics 2023; 24:88. [PMID: 36829151 PMCID: PMC9960639 DOI: 10.1186/s12864-023-09184-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The stress response of Saccharomyces cerevisiae has been extensively studied in the past decade. However, with the advent of recent technology in single-cell transcriptome profiling, there is a new opportunity to expand and further understanding of the yeast stress response with greater resolution on a system level. To understand transcriptomic changes in baker's yeast S. cerevisiae cells under stress conditions, we sequenced 117 yeast cells under three stress treatments (hypotonic condition, glucose starvation and amino acid starvation) using a full-length single-cell RNA-Seq method. RESULTS We found that though single cells from the same treatment showed varying degrees of uniformity, technical noise and batch effects can confound results significantly. However, upon careful selection of samples to reduce technical artifacts and account for batch-effects, we were able to capture distinct transcriptomic signatures for different stress conditions as well as putative regulatory relationships between transcription factors and target genes. CONCLUSION Our results show that a full-length single-cell based transcriptomic analysis of the yeast may help paint a clearer picture of how the model organism responds to stress than do bulk cell population-based methods.
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Affiliation(s)
- Yangqi Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Chen Xu
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Jonathan Shea
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Darla DeStephanis
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA.
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6
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Foo S, Cazenave-Gassiot A, Wenk MR, Oliferenko S. Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis. J Cell Sci 2023; 136:286881. [PMID: 36695178 DOI: 10.1242/jcs.260568] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/22/2022] [Indexed: 01/26/2023] Open
Abstract
Nuclear envelope (NE) expansion must be controlled to maintain nuclear shape and function. The nuclear membrane expands massively during closed mitosis, enabling chromosome segregation within an intact NE. Phosphatidic acid (PA) and diacylglycerol (DG) can both serve as biosynthetic precursors for membrane lipid synthesis. How they are regulated in time and space and what the implications are of changes in their flux for mitotic fidelity are largely unknown. Using genetically encoded PA and DG probes, we show that DG is depleted from the inner nuclear membrane during mitosis in the fission yeast Schizosaccharomyces pombe, but PA does not accumulate, indicating that it is rerouted to membrane synthesis. We demonstrate that DG-to-PA conversion catalyzed by the diacylglycerol kinase Dgk1 (also known as Ptp4) and direct glycerophospholipid synthesis from DG by diacylglycerol cholinephosphotransferase/ethanolaminephosphotransferase Ept1 reinforce NE expansion. We conclude that DG consumption through both the de novo pathway and the Kennedy pathway fuels a spike in glycerophospholipid biosynthesis, controlling NE expansion and, ultimately, mitotic fidelity.
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Affiliation(s)
- Sherman Foo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Amaury Cazenave-Gassiot
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, 117596 Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, 117596 Singapore
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
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7
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Gorin G, Vastola JJ, Fang M, Pachter L. Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments. Nat Commun 2022; 13:7620. [PMID: 36494337 PMCID: PMC9734650 DOI: 10.1038/s41467-022-34857-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
The question of how cell-to-cell differences in transcription rate affect RNA count distributions is fundamental for understanding biological processes underlying transcription. Answering this question requires quantitative models that are both interpretable (describing concrete biophysical phenomena) and tractable (amenable to mathematical analysis). This enables the identification of experiments which best discriminate between competing hypotheses. As a proof of principle, we introduce a simple but flexible class of models involving a continuous stochastic transcription rate driving a discrete RNA transcription and splicing process, and compare and contrast two biologically plausible hypotheses about transcription rate variation. One assumes variation is due to DNA experiencing mechanical strain, while the other assumes it is due to regulator number fluctuations. We introduce a framework for numerically and analytically studying such models, and apply Bayesian model selection to identify candidate genes that show signatures of each model in single-cell transcriptomic data from mouse glutamatergic neurons.
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Affiliation(s)
- Gennady Gorin
- grid.20861.3d0000000107068890Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - John J. Vastola
- grid.38142.3c000000041936754XDepartment of Neurobiology, Harvard Medical School, Boston, MA 02115 USA
| | - Meichen Fang
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Lior Pachter
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA ,grid.20861.3d0000000107068890Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125 USA
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8
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Palenchar PM, DeStefanis T. Transcriptional noise adjusted for expression levels reveals genes with high transcriptional noise that are highly expressed, functionally related, and co-regulated in yeast. Curr Genet 2022; 68:675-686. [PMID: 36245041 DOI: 10.1007/s00294-022-01255-x] [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] [Received: 08/21/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/26/2022]
Abstract
Understanding the relationship between variability in single-cell and non-single-cell gene expression studies will aid in understanding the role of and mechanisms that lead to variability in biological systems. Studies on the variation of gene expression levels in yeast normally focus on single cells and use the coefficient of variance (CV) as a measure of noise. The CV is typically negatively correlated with gene expression levels, so most of the studies using yeast find that genes with high transcriptional noise are lowly expressed. We find adjusting noise for expression levels using linear/natural log polynomial, and local fits and analyzing many non-single-cell RNA-seq sets identifies genes with high median transcriptional noise that are different than those that have high median CVs. Interestingly, these genes are heavily regulated by transcription factors that are related to variability and stochastic processes based on single-cell studies, including Msn2p, Msn4p, Hsf1p, and Crz1p but are not associated with genes with high median CVs based on non-single-cell gene expression data. In addition, adjusting noise for expression levels in a single-cell RNA-seq data set adds value by finding genes that have noisy gene expression levels and their associated transcription factors that are not found to be associated with genes with high CVs in the single-cell expression data or a comparable non-single-cell gene expression data. Lastly, S. cerevisiae genes with noisy expression tend to have orthologs with noisy gene expression in C. albicans, indicating transcriptional noise is evolutionarily conserved.
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9
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Gupta A, Martin-Rufino JD, Jones TR, Subramanian V, Qiu X, Grody EI, Bloemendal A, Weng C, Niu SY, Min KH, Mehta A, Zhang K, Siraj L, Al' Khafaji A, Sankaran VG, Raychaudhuri S, Cleary B, Grossman S, Lander ES. Inferring gene regulation from stochastic transcriptional variation across single cells at steady state. Proc Natl Acad Sci U S A 2022; 119:e2207392119. [PMID: 35969771 PMCID: PMC9407670 DOI: 10.1073/pnas.2207392119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022] Open
Abstract
Regulatory relationships between transcription factors (TFs) and their target genes lie at the heart of cellular identity and function; however, uncovering these relationships is often labor-intensive and requires perturbations. Here, we propose a principled framework to systematically infer gene regulation for all TFs simultaneously in cells at steady state by leveraging the intrinsic variation in the transcriptional abundance across single cells. Through modeling and simulations, we characterize how transcriptional bursts of a TF gene are propagated to its target genes, including the expected ranges of time delay and magnitude of maximum covariation. We distinguish these temporal trends from the time-invariant covariation arising from cell states, and we delineate the experimental and technical requirements for leveraging these small but meaningful cofluctuations in the presence of measurement noise. While current technology does not yet allow adequate power for definitively detecting regulatory relationships for all TFs simultaneously in cells at steady state, we investigate a small-scale dataset to inform future experimental design. This study supports the potential value of mapping regulatory connections through stochastic variation, and it motivates further technological development to achieve its full potential.
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Affiliation(s)
- Anika Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
| | - Jorge D. Martin-Rufino
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115
- Dana-Farber Cancer Institute, Boston, MA 02215
| | | | | | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | | | - Chen Weng
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115
- Dana-Farber Cancer Institute, Boston, MA 02215
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | | | - Kyung Hoi Min
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Kaite Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Layla Siraj
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Vijay G. Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115
- Dana-Farber Cancer Institute, Boston, MA 02215
| | - Soumya Raychaudhuri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA 02115
| | - Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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10
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Malcı K, Watts E, Roberts TM, Auxillos JY, Nowrouzi B, Boll HO, Nascimento CZSD, Andreou A, Vegh P, Donovan S, Fragkoudis R, Panke S, Wallace E, Elfick A, Rios-Solis L. Standardization of Synthetic Biology Tools and Assembly Methods for Saccharomyces cerevisiae and Emerging Yeast Species. ACS Synth Biol 2022; 11:2527-2547. [PMID: 35939789 PMCID: PMC9396660 DOI: 10.1021/acssynbio.1c00442] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
As redesigning organisms using engineering principles
is one of
the purposes of synthetic biology (SynBio), the standardization of
experimental methods and DNA parts is becoming increasingly a necessity.
The synthetic biology community focusing on the engineering of Saccharomyces cerevisiae has been in the foreground in this
area, conceiving several well-characterized SynBio toolkits widely
adopted by the community. In this review, the molecular methods and
toolkits developed for S. cerevisiae are discussed
in terms of their contributions to the required standardization efforts.
In addition, the toolkits designed for emerging nonconventional yeast
species including Yarrowia lipolytica, Komagataella
phaffii, and Kluyveromyces marxianus are
also reviewed. Without a doubt, the characterized DNA parts combined
with the standardized assembly strategies highlighted in these toolkits
have greatly contributed to the rapid development of many metabolic
engineering and diagnostics applications among others. Despite the
growing capacity in deploying synthetic biology for common yeast genome
engineering works, the yeast community has a long journey to go to
exploit it in more sophisticated and delicate applications like bioautomation.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Emma Watts
- School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3JW Edinburgh, United Kingdom
| | | | - Jamie Yam Auxillos
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Heloísa Oss Boll
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília, Federal District 70910-900, Brazil
| | | | - Andreas Andreou
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Peter Vegh
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sophie Donovan
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Rennos Fragkoudis
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Edward Wallace
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Alistair Elfick
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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11
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Hansberg W. A critical analysis on the conception of "Pre-existent gene expression programs" for cell differentiation and development. Differentiation 2022; 125:1-8. [DOI: 10.1016/j.diff.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 11/15/2022]
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12
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13
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Zhao X, Hu J, Li Y, Guo M. Volumetric compression develops noise-driven single-cell heterogeneity. Proc Natl Acad Sci U S A 2021; 118:e2110550118. [PMID: 34916290 PMCID: PMC8713786 DOI: 10.1073/pnas.2110550118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 10/19/2022] Open
Abstract
Recent studies have revealed that extensive heterogeneity of biological systems arises through various routes ranging from intracellular chromosome segregation to spatiotemporally varying biochemical stimulations. However, the contribution of physical microenvironments to single-cell heterogeneity remains largely unexplored. Here, we show that a homogeneous population of non-small-cell lung carcinoma develops into heterogeneous subpopulations upon application of a homogeneous physical compression, as shown by single-cell transcriptome profiling. The generated subpopulations stochastically gain the signature genes associated with epithelial-mesenchymal transition (EMT; VIM, CDH1, EPCAM, ZEB1, and ZEB2) and cancer stem cells (MKI67, BIRC5, and KLF4), respectively. Trajectory analysis revealed two bifurcated paths as cells evolving upon the physical compression, along each path the corresponding signature genes (epithelial or mesenchymal) gradually increase. Furthermore, we show that compression increases gene expression noise, which interplays with regulatory network architecture and thus generates differential cell-fate outcomes. The experimental observations of both single-cell sequencing and single-molecule fluorescent in situ hybridization agrees well with our computational modeling of regulatory network in the EMT process. These results demonstrate a paradigm of how mechanical stimulations impact cell-fate determination by altering transcription dynamics; moreover, we show a distinct path that the ecology and evolution of cancer interplay with their physical microenvironments from the view of mechanobiology and systems biology, with insight into the origin of single-cell heterogeneity.
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Affiliation(s)
- Xing Zhao
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jiliang Hu
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Yiwei Li
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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14
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Wen Y, Zhao J, He H, Zhao Q, Liu Z. Multiplexed Single-Cell Plasmonic Immunoassay of Intracellular Signaling Proteins Enables Non-Destructive Monitoring of Cell Fate. Anal Chem 2021; 93:14204-14213. [PMID: 34648273 DOI: 10.1021/acs.analchem.1c03062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It is of significant importance in cancer biology to identify signaling pathways that play key roles in cell fate determination. Dissecting cellular signaling pathways requires the measurement of a large number of signaling proteins. However, tools for simultaneously monitoring multiple signaling pathway components in single living cells remain limited at present. Herein, we describe an approach, termed multiplexed single-cell plasmonic immunosandwich assay (mxscPISA), for simultaneous detection of multiple signaling proteins in individual living cells. This approach enabled simultaneous non-destructive monitoring of multiple (up to five, currently the highest multiplexing capacity in living cells) cytoplasmic and nucleus signaling proteins in individual cells with ultrahigh detection sensitivity. As a proof of principle, the epidermal growth factor receptor (EGFR) pathway, which plays a central role in cell fate determination, was investigated using this approach in this study. We found that there were differential attenuation rate of pro-survival and accumulation rate of pro-death signaling protein of the EGFR pathway in response to EGFR inactivation. These findings implicate that, after EGFR inactivation, a transient imbalance between survival and apoptotic signaling outputs contributed to the final cell fate of death. The mxscPISA approach can be a promising tool to reveal a signaling dynamic pattern at the single-cell level and to identify key components of signaling pathways that contribute to the final cell fate using only a limited number of cells.
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Affiliation(s)
- Yanrong Wen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jialing Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hui He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Quan Zhao
- School of Life Science, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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15
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Ogundipe VML, Groen AH, Hosper N, Nagle PWK, Hess J, Faber H, Jellema AL, Baanstra M, Links TP, Unger K, Plukker JTM, Coppes RP. Generation and Differentiation of Adult Tissue-Derived Human Thyroid Organoids. Stem Cell Reports 2021; 16:913-925. [PMID: 33711265 PMCID: PMC8072035 DOI: 10.1016/j.stemcr.2021.02.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/21/2023] Open
Abstract
Total thyroidectomy as part of thyroid cancer treatment results in hypothyroidism requiring lifelong daily thyroid hormone replacement. Unbalanced hormone levels result in persistent complaints such as fatigue, constipation, and weight increase. Therefore, we aimed to investigate a patient-derived thyroid organoid model with the potential to regenerate the thyroid gland. Murine and human thyroid-derived cells were cultured as organoids capable of self-renewal and which expressed proliferation and putative stem cell and thyroid characteristics, without a change in the expression of thyroid tumor-related genes. These organoids formed thyroid-tissue-resembling structures in culture. (Xeno-)transplantation of 600,000 dispersed organoid cells underneath the kidney capsule of a hypothyroid mouse model resulted in the generation of hormone-producing thyroid-resembling follicles. This study provides evidence that thyroid-lineage-specific cells can form organoids that are able to self-renew and differentiate into functional thyroid tissue. Subsequent (xeno-)transplantation of these thyroid organoids demonstrates a proof of principle for functional miniature gland formation.
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Affiliation(s)
- Vivian M L Ogundipe
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands; Department of Radiation Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Andries H Groen
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands; Department of Surgical Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Nynke Hosper
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands; Department of Radiation Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Peter W K Nagle
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands; Department of Surgical Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands; Department of Radiation Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg 85764, Germany; Department of Radiation Oncology, University Hospital, LMU Munich, Munich 81377, Germany
| | - Hette Faber
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands; Department of Radiation Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Anne L Jellema
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Mirjam Baanstra
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands; Department of Radiation Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Thera P Links
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg 85764, Germany; Department of Radiation Oncology, University Hospital, LMU Munich, Munich 81377, Germany
| | - John T M Plukker
- Department of Surgical Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Rob P Coppes
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands; Department of Radiation Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands.
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16
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Cavallaro M, Walsh MD, Jones M, Teahan J, Tiberi S, Finkenstädt B, Hebenstreit D. 3 '-5 ' crosstalk contributes to transcriptional bursting. Genome Biol 2021; 22:56. [PMID: 33541397 PMCID: PMC7860045 DOI: 10.1186/s13059-020-02227-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3 ' and 5 ' ends of a gene that enable reinitiation of transcription upon termination. RESULTS Using Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment. CONCLUSIONS Interactions between the 3 ' and 5 ' ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.
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Affiliation(s)
- Massimo Cavallaro
- School of Life Sciences, University of Warwick, Coventry, UK.
- Mathematics Institute and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK.
- Department of Statistics, University of Warwick, Coventry, UK.
| | - Mark D Walsh
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Matt Jones
- School of Life Sciences, University of Warwick, Coventry, UK
| | - James Teahan
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Simone Tiberi
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
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17
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Cruz DF, De Meyer S, Ampe J, Sprenger H, Herman D, Van Hautegem T, De Block J, Inzé D, Nelissen H, Maere S. Using single-plant-omics in the field to link maize genes to functions and phenotypes. Mol Syst Biol 2020; 16:e9667. [PMID: 33346944 PMCID: PMC7751767 DOI: 10.15252/msb.20209667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/29/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.
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Affiliation(s)
- Daniel Felipe Cruz
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Sam De Meyer
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Joke Ampe
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Heike Sprenger
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dorota Herman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Tom Van Hautegem
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Jolien De Block
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Steven Maere
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
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18
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Rocabert C, Beslon G, Knibbe C, Bernard S. Phenotypic noise and the cost of complexity. Evolution 2020; 74:2221-2237. [PMID: 32820537 DOI: 10.1111/evo.14083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 08/13/2020] [Indexed: 11/28/2022]
Abstract
Experimental studies demonstrate the existence of phenotypic diversity despite constant genotype and environment. Theoretical models based on a single phenotypic character predict that during an adaptation event, phenotypic noise should be positively selected far from the fitness optimum because it increases the fitness of the genotype, and then be selected against when the population reaches the optimum. It is suggested that because of this fitness gain, phenotypic noise should promote adaptive evolution. However, it is unclear how the selective advantage of phenotypic noise is linked to the rate of evolution, and whether any advantage would hold for more realistic, multidimensional phenotypes. Indeed, complex organisms suffer a cost of complexity, where beneficial mutations become rarer as the number of phenotypic characters increases. Using a quantitative genetics approach, we first show that for a one-dimensional phenotype, phenotypic noise promotes adaptive evolution on plateaus of positive fitness, independently from the direct selective advantage on fitness. Second, we show that for multidimensional phenotypes, phenotypic noise evolves to a low-dimensional configuration, with elevated noise in the direction of the fitness optimum. Such a dimensionality reduction of the phenotypic noise promotes adaptive evolution and numerical simulations show that it reduces the cost of complexity.
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Affiliation(s)
- Charles Rocabert
- Inria, 78150 Rocquencourt, France.,Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary
| | - Guillaume Beslon
- Inria, 78150 Rocquencourt, France.,LIRIS, University of Lyon, INSA-Lyon, UMR5205, Lyon, F-69621, France
| | - Carole Knibbe
- Inria, 78150 Rocquencourt, France.,CarMeN Laboratory, University of Lyon, INSA-Lyon, INSERM U1060, Lyon, F-69621, France
| | - Samuel Bernard
- Inria, 78150 Rocquencourt, France.,Institut Camille Jordan, CNRS, University of Lyon, UMR5208, Lyon, F-69622, France
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19
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Sun M, Zhang J. Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises. Nucleic Acids Res 2020; 48:533-547. [PMID: 31799601 PMCID: PMC6954418 DOI: 10.1093/nar/gkz1134] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/19/2019] [Accepted: 11/20/2019] [Indexed: 01/13/2023] Open
Abstract
Gene expression noise refers to the variation of the expression level of a gene among isogenic cells in the same environment, and has two sources: extrinsic noise arising from the disparity of the cell state and intrinsic noise arising from the stochastic process of gene expression in the same cell state. Due to the low throughput of the existing method for measuring the two noise components, the architectures of intrinsic and extrinsic expression noises remain elusive. Using allele-specific single-cell RNA sequencing, we here estimate the two noise components of 3975 genes in mouse fibroblast cells. Our analyses verify predicted influences of several factors such as the TATA-box and microRNA targeting on intrinsic or extrinsic noises and reveal gene function-associated noise trends implicating the action of natural selection. These findings unravel differential regulations, optimizations, and biological consequences of intrinsic and extrinsic noises and can aid the construction of desired synthetic circuits.
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Affiliation(s)
- Mengyi Sun
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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20
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Foreman R, Wollman R. Mammalian gene expression variability is explained by underlying cell state. Mol Syst Biol 2020; 16:e9146. [PMID: 32043799 PMCID: PMC7011657 DOI: 10.15252/msb.20199146] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/04/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Gene expression variability in mammalian systems plays an important role in physiological and pathophysiological conditions. This variability can come from differential regulation related to cell state (extrinsic) and allele-specific transcriptional bursting (intrinsic). Yet, the relative contribution of these two distinct sources is unknown. Here, we exploit the qualitative difference in the patterns of covariance between these two sources to quantify their relative contributions to expression variance in mammalian cells. Using multiplexed error robust RNA fluorescent in situ hybridization (MERFISH), we measured the multivariate gene expression distribution of 150 genes related to Ca2+ signaling coupled with the dynamic Ca2+ response of live cells to ATP. We show that after controlling for cellular phenotypic states such as size, cell cycle stage, and Ca2+ response to ATP, the remaining variability is effectively at the Poisson limit for most genes. These findings demonstrate that the majority of expression variability results from cell state differences and that the contribution of transcriptional bursting is relatively minimal.
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Affiliation(s)
- Robert Foreman
- Institute for Quantitative and Computational BiosciencesUniversity of California, Los AngelesLos AngelesCAUSA
- Program in Bioinformatics and Systems BiologyUniversity of California, San DiegoSan DiegoCAUSA
| | - Roy Wollman
- Institute for Quantitative and Computational BiosciencesUniversity of California, Los AngelesLos AngelesCAUSA
- Program in Bioinformatics and Systems BiologyUniversity of California, San DiegoSan DiegoCAUSA
- Department of Integrative Biology and PhysiologyDepartment of Chemistry and BiochemistryUniversity of California, Los AngelesLos AngelesCAUSA
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21
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Finn EH, Misteli T. Molecular basis and biological function of variability in spatial genome organization. Science 2019; 365:365/6457/eaaw9498. [PMID: 31488662 DOI: 10.1126/science.aaw9498] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/22/2019] [Indexed: 12/14/2022]
Abstract
The complex three-dimensional organization of genomes in the cell nucleus arises from a wide range of architectural features including DNA loops, chromatin domains, and higher-order compartments. Although these features are universally present in most cell types and tissues, recent single-cell biochemistry and imaging approaches have demonstrated stochasticity in transcription and high variability of chromatin architecture in individual cells. We review the occurrence, mechanistic basis, and functional implications of stochasticity in genome organization. We summarize recent observations on cell- and allele-specific variability of genome architecture, discuss the nature of extrinsic and intrinsic sources of variability in genome organization, and highlight potential implications of structural heterogeneity for genome function.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, Bethesda, MD 20892, USA.
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22
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You ST, Jhou YT, Kao CF, Leu JY. Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering. PLoS Biol 2019; 17:e3000433. [PMID: 31613873 PMCID: PMC6814240 DOI: 10.1371/journal.pbio.3000433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/25/2019] [Accepted: 09/27/2019] [Indexed: 11/19/2022] Open
Abstract
Cell-to-cell heterogeneity within an isogenic population has been observed in prokaryotic and eukaryotic cells. Such heterogeneity often manifests at the level of individual protein abundance and may have evolutionary benefits, especially for organisms in fluctuating environments. Although general features and the origins of cellular noise have been revealed, details of the molecular pathways underlying noise regulation remain elusive. Here, we used experimental evolution of Saccharomyces cerevisiae to select for mutations that increase reporter protein noise. By combining bulk segregant analysis and CRISPR/Cas9-based reconstitution, we identified the methyltransferase Hmt1 as a general regulator of noise buffering. Hmt1 methylation activity is critical for the evolved phenotype, and we also show that two of the Hmt1 methylation targets can suppress noise. Hmt1 functions as an environmental sensor to adjust noise levels in response to environmental cues. Moreover, Hmt1-mediated noise buffering is conserved in an evolutionarily distant yeast species, suggesting broad significance of noise regulation. Experimental evolution in yeast reveals that the methyltransferase Hmt1 functions as a mediator connecting environmental stimuli to cellular noise; Hmt1-mediated noise buffering is conserved in an evolutionarily distant yeast.
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Affiliation(s)
- Shu-Ting You
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Jhou
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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23
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Hsf1 Phosphorylation Generates Cell-to-Cell Variation in Hsp90 Levels and Promotes Phenotypic Plasticity. Cell Rep 2019; 22:3099-3106. [PMID: 29562166 PMCID: PMC5893160 DOI: 10.1016/j.celrep.2018.02.083] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/11/2017] [Accepted: 02/22/2018] [Indexed: 01/07/2023] Open
Abstract
Clonal populations of cells exhibit cell-to-cell variation in the transcription of individual genes. In addition to this noise in gene expression, heterogeneity in the proteome and the proteostasis network expands the phenotypic diversity of a population. Heat shock factor 1 (Hsf1) regulates chaperone gene expression, thereby coupling transcriptional noise to proteostasis. Here we show that cell-to-cell variation in Hsf1 activity is an important determinant of phenotypic plasticity. Budding yeast cells with high Hsf1 activity were enriched for the ability to acquire resistance to an antifungal drug, and this enrichment depended on Hsp90, a known phenotypic capacitor and canonical Hsf1 target. We show that Hsf1 phosphorylation promotes cell-to-cell variation, and this variation, rather than absolute Hsf1 activity, promotes antifungal resistance. We propose that Hsf1 phosphorylation enables differential tuning of the proteostasis network in individual cells, allowing populations to access a range of phenotypic states.
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24
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Sun M, Zhang J. Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. PLoS Genet 2019; 15:e1008389. [PMID: 31525198 PMCID: PMC6762216 DOI: 10.1371/journal.pgen.1008389] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/26/2019] [Accepted: 08/28/2019] [Indexed: 12/31/2022] Open
Abstract
Gene expression is subject to stochastic noise, but to what extent and by which means such stochastic variations are coordinated among different genes are unclear. We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics, and verify it at the genomic scale using allele-specific single-cell RNA-sequencing data of mouse cells. Unexpectedly, the co-fluctuation extends to genes that are over 60 million bases apart. We provide evidence that this long-range effect arises in part from chromatin co-accessibilities of linked loci attributable to three-dimensional proximity, which is much closer intra-chromosomally than inter-chromosomally. We further show that genes encoding components of the same protein complex tend to be chromosomally linked, likely resulting from natural selection for intracellular among-component dosage balance. These findings have implications for both the evolution of genome organization and optimal design of synthetic genomes in the face of gene expression noise.
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Affiliation(s)
- Mengyi Sun
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
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25
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Abstract
Biochemical reactions are intrinsically stochastic, leading to variation in the production of mRNAs and proteins within cells. In the scientific literature, this source of variation is typically referred to as 'noise'. The observed variability in molecular phenotypes arises from a combination of processes that amplify and attenuate noise. Our ability to quantify cell-to-cell variability in numerous biological contexts has been revolutionized by recent advances in single-cell technology, from imaging approaches through to 'omics' strategies. However, defining, accurately measuring and disentangling the stochastic and deterministic components of cell-to-cell variability is challenging. In this Review, we discuss the sources, impact and function of molecular phenotypic variability and highlight future directions to understand its role.
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Affiliation(s)
- Nils Eling
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, UK.
| | | | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
- Wellcome Sanger Institute, Welcome Genome Campus, Hinxton, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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26
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Schmiedel JM, Carey LB, Lehner B. Empirical mean-noise fitness landscapes reveal the fitness impact of gene expression noise. Nat Commun 2019; 10:3180. [PMID: 31320634 PMCID: PMC6639414 DOI: 10.1038/s41467-019-11116-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/21/2019] [Indexed: 12/23/2022] Open
Abstract
The effects of cell-to-cell variation (noise) in gene expression have proven difficult to quantify because of the mechanistic coupling of noise to mean expression. To independently quantify the effects of changes in mean expression and noise we determine the fitness landscapes in mean-noise expression space for 33 genes in yeast. For most genes, short-lived (noise) deviations away from the expression optimum are nearly as detrimental as sustained (mean) deviations. Fitness landscapes can be classified by a combination of each gene’s sensitivity to protein shortage or surplus. We use this classification to explore evolutionary scenarios for gene expression and find that certain landscape topologies can break the mechanistic coupling of mean and noise, thus promoting independent optimization of both properties. These results demonstrate that noise is detrimental for many genes and reveal non-trivial consequences of mean-noise-fitness topologies for the evolution of gene expression systems. Quantifying the effects of noise in gene expression is difficult since noise and mean expression are coupled. Here the authors determine fitness landscapes in mean-noise expression space to uncouple these two parameters and show that changes in noise and mean expression are similarly detrimental to fitness.
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Affiliation(s)
- Jörn M Schmiedel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003, Barcelona, Spain.
| | - Lucas B Carey
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003, Barcelona, Spain.,Center for Quantitative Biology and Peking-Tsinghua Center for the Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. .,ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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27
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Hansen MMK, Weinberger LS. Post-Transcriptional Noise Control. Bioessays 2019; 41:e1900044. [PMID: 31222776 PMCID: PMC6637019 DOI: 10.1002/bies.201900044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/22/2019] [Indexed: 01/01/2023]
Abstract
Recent evidence indicates that transcriptional bursts are intrinsically amplified by messenger RNA cytoplasmic processing to generate large stochastic fluctuations in protein levels. These fluctuations can be exploited by cells to enable probabilistic bet-hedging decisions. But large fluctuations in gene expression can also destabilize cell-fate commitment. Thus, it is unclear if cells temporally switch from high to low noise, and what mechanisms enable this switch. Here, the discovery of a post-transcriptional mechanism that attenuates noise in HIV is reviewed. Early in its life cycle, HIV amplifies transcriptional fluctuations to probabilistically select alternate fates, whereas at late times, HIV utilizes a post-transcriptional feedback mechanism to commit to a specific fate. Reanalyzing various reported post-transcriptional negative feedback architectures reveals that they attenuate noise more efficiently than classic transcriptional autorepression, leading to the derivation of an assay to detect post-transcriptional motifs. It is hypothesized that coupling transcriptional and post-transcriptional autoregulation enables efficient temporal noise control to benefit developmental bet-hedging decisions.
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Affiliation(s)
- Maike M. K. Hansen
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Leor S. Weinberger
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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28
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Tye BW, Commins N, Ryazanova LV, Wühr M, Springer M, Pincus D, Churchman LS. Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness. eLife 2019; 8:43002. [PMID: 30843788 PMCID: PMC6453566 DOI: 10.7554/elife.43002] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/06/2019] [Indexed: 12/31/2022] Open
Abstract
To achieve maximal growth, cells must manage a massive economy of ribosomal proteins (r-proteins) and RNAs (rRNAs) to produce thousands of ribosomes every minute. Although ribosomes are essential in all cells, natural disruptions to ribosome biogenesis lead to heterogeneous phenotypes. Here, we model these perturbations in Saccharomyces cerevisiae and show that challenges to ribosome biogenesis result in acute loss of proteostasis. Imbalances in the synthesis of r-proteins and rRNAs lead to the rapid aggregation of newly synthesized orphan r-proteins and compromise essential cellular processes, which cells alleviate by activating proteostasis genes. Exogenously bolstering the proteostasis network increases cellular fitness in the face of challenges to ribosome assembly, demonstrating the direct contribution of orphan r-proteins to cellular phenotypes. We propose that ribosome assembly is a key vulnerability of proteostasis maintenance in proliferating cells that may be compromised by diverse genetic, environmental, and xenobiotic perturbations that generate orphan r-proteins. Cells are made up of thousands of different proteins that perform unique roles required for life. To create all of these proteins, cells use machines called ribosomes that are partly formed of elements known as r-proteins. When cells grow and divide, the ribosomes have to make copies of themselves through a process called ribosome biogenesis. Although all cells need ribosomes, certain types of cells are especially sensitive to events that interfere with ribosome biogenesis. For example, patients that have mutations in genes needed for ribosome biogenesis produce fewer red blood cells, but their other cells and tissues are mostly healthy. It is not clear why some cells are more sensitive than others. Ribosome biogenesis is very similar between different organisms, so researchers often use budding yeast as a model to study the process. Here, Tye et al. used genetic and chemical tools to interfere with ribosome biogenesis on short time scales, which made it possible to detect early on what was going wrong in the cells. The experiments found that when ribosome biogenesis was disrupted, r-proteins that were waiting to be assembled into ribosomes quickly stuck to one another and formed clumps that reduced the ability of the yeast cells to grow. The cells responded by switching on a protein called Hsf1, which restored their ability to grow. Yeast cells that were growing quickly, and therefore making more ribosomes, were more sensitive to abnormal ribosome biogenesis than slow-growing cells. These results indicate that how actively a cell is growing, and its ability to cope with r-proteins sticking together, may in part explain why certain cells are more vulnerable to events that interfere with ribosome biogenesis. Since human cells also have Hsf1, future experiments could investigate whether turning it on might also protect fast-growing human cells from such events.
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Affiliation(s)
- Blake W Tye
- Department of Genetics, Harvard Medical School, Boston, United States.,Program in Chemical Biology, Harvard University, Cambridge, United States
| | - Nicoletta Commins
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Lillia V Ryazanova
- Department of Molecular Biology, Princeton University, Princeton, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, United States.,Center for Physics of Evolving Systems, University of Chicago, Chicago, United States
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29
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Mitosch K, Rieckh G, Bollenbach T. Temporal order and precision of complex stress responses in individual bacteria. Mol Syst Biol 2019; 15:e8470. [PMID: 30765425 PMCID: PMC6375286 DOI: 10.15252/msb.20188470] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 12/28/2018] [Accepted: 01/22/2019] [Indexed: 01/27/2023] Open
Abstract
Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time-lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate-limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses.
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Affiliation(s)
- Karin Mitosch
- IST Austria, Klosterneuburg, Austria
- EMBL Heidelberg, Heidelberg, Germany
| | - Georg Rieckh
- IST Austria, Klosterneuburg, Austria
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA
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30
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Li S, Giardina DM, Siegal ML. Control of nongenetic heterogeneity in growth rate and stress tolerance of Saccharomyces cerevisiae by cyclic AMP-regulated transcription factors. PLoS Genet 2018; 14:e1007744. [PMID: 30388117 PMCID: PMC6241136 DOI: 10.1371/journal.pgen.1007744] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 11/14/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023] Open
Abstract
Genetically identical cells exhibit extensive phenotypic variation even under constant and benign conditions. This so-called nongenetic heterogeneity has important clinical implications: within tumors and microbial infections, cells show nongenetic heterogeneity in growth rate and in susceptibility to drugs or stress. The budding yeast, Saccharomyces cerevisiae, shows a similar form of nongenetic heterogeneity in which growth rate correlates positively with susceptibility to acute heat stress at the single-cell level. Using genetic and chemical perturbations, combined with high-throughput single-cell assays of yeast growth and gene expression, we show here that heterogeneity in intracellular cyclic AMP (cAMP) levels acting through the conserved Ras/cAMP/protein kinase A (PKA) pathway and its target transcription factors, Msn2 and Msn4, underlies this nongenetic heterogeneity. Lower levels of cAMP correspond to slower growth, as shown by direct comparison of cAMP concentration in subpopulations enriched for slower vs. faster growing cells. Concordantly, an endogenous reporter of this pathway’s activity correlates with growth in individual cells. The paralogs Msn2 and Msn4 differ in their roles in nongenetic heterogeneity in a way that demonstrates slow growth and stress tolerance are not inevitably linked. Heterogeneity in growth rate requires each, whereas only Msn2 is required for heterogeneity in expression of Tsl1, a subunit of trehalose synthase that contributes to acute-stress tolerance. Perturbing nongenetic heterogeneity by mutating genes in this pathway, or by culturing wild-type cells with the cell-permeable cAMP analog 8-bromo-cAMP or the PKA inhibitor H89, significantly impacts survival of acute heat stress. Perturbations that increase intracellular cAMP levels reduce the slower-growing subpopulation and increase susceptibility to acute heat stress, whereas PKA inhibition slows growth and decreases susceptibility to acute heat stress. Loss of Msn2 reduces, but does not completely eliminate, the correlation in individual cells between growth rate and acute-stress survival, suggesting a major role for the Msn2 pathway in nongenetic heterogeneity but also a residual benefit of slow growth. Our results shed light on the genetic control of nongenetic heterogeneity and suggest a possible means of defeating bet-hedging pathogens or tumor cells by making them more uniformly susceptible to treatment. Nongenetic heterogeneity exists when a trait differs among individuals that have identical genotypes and environments. A clonal population can maximize its long-term success in an uncertain environment by diversifying its phenotypes via nongenetic heterogeneity: the currently unfavored ones may become the favored ones when conditions change. Nongenetic heterogeneity has clinical relevance. For example, populations of tumor cells or infectious microbes show cell-to-cell differences in growth and in drug or stress tolerance. This heterogeneity hampers efficient treatment and can potentiate harmful evolution of a tumor or pathogen. We show that in budding yeast, heterogeneity in intracellular cyclic AMP levels acting through the conserved Ras/cAMP/protein kinase A (PKA) pathway and its target transcription factors, Msn2 and Msn4, underlies the nongenetic heterogeneity of both single-cell growth rate and acute heat-stress tolerance. Perturbations of this pathway significantly affect population survival upon acute heat stress. These results illuminate a mechanism of nongenetic heterogeneity and suggest the potential value of antitumor or antifungal treatment strategies that target nongenetic heterogeneity to render the tumor or pathogen population more uniformly susceptible to a second drug that aims to kill.
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Affiliation(s)
- Shuang Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Daniella M. Giardina
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Mark L. Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- * E-mail:
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31
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Levy E, Slavov N. Single cell protein analysis for systems biology. Essays Biochem 2018; 62:595-605. [PMID: 30072488 PMCID: PMC6204083 DOI: 10.1042/ebc20180014] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/01/2018] [Accepted: 07/12/2018] [Indexed: 01/14/2023]
Abstract
The cellular abundance of proteins can vary even between isogenic single cells. This variability between single-cell protein levels can have regulatory roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review examples connecting protein levels and their dynamics in single cells to cellular functions. Such findings were made possible by the introduction of antibodies, and subsequently fluorescent proteins, for tracking protein levels in single cells. However, in heterogeneous cell populations, such as tumors or differentiating stem cells, cellular decisions are controlled by hundreds, even thousands of proteins acting in concert. Characterizing such complex systems demands measurements of thousands of proteins across thousands of single cells. This demand has inspired the development of new methods for single-cell protein analysis, and we discuss their trade-offs, with an emphasis on their specificity and coverage. We finish by highlighting the potential of emerging mass-spec methods to enable systems-level measurement of single-cell proteomes with unprecedented coverage and specificity. Combining such methods with methods for quantitating the transcriptomes and metabolomes of single cells will provide essential data for advancing quantitative systems biology.
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Affiliation(s)
- Ezra Levy
- Department of Biology, Northeastern University, Boston, MA 02115, U.S.A
| | - Nikolai Slavov
- Department of Biology, Northeastern University, Boston, MA 02115, U.S.A.
- Department of Bioengineering, Northeastern University, Boston, MA 02115, U.S.A
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32
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Kucharavy A, Rubinstein B, Zhu J, Li R. Robustness and evolvability of heterogeneous cell populations. Mol Biol Cell 2018; 29:1400-1409. [PMID: 29851566 PMCID: PMC5994894 DOI: 10.1091/mbc.e18-01-0070] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/27/2018] [Indexed: 01/02/2023] Open
Abstract
Biological systems are endowed with two fundamental but seemingly contradictory properties: robustness, the ability to withstand environmental fluctuations and genetic variability; and evolvability, the ability to acquire selectable and heritable phenotypic changes. Cell populations with heterogeneous genetic makeup, such as those of infectious microbial organisms or cancer, rely on their inherent robustness to maintain viability and fitness, but when encountering environmental insults, such as drug treatment, these populations are also poised for rapid adaptation through evolutionary selection. In this study, we develop a general mathematical model that allows us to explain and quantify this fundamental relationship between robustness and evolvability of heterogeneous cell populations. Our model predicts that robustness is, in fact, essential for evolvability, especially for more adverse environments, a trend we observe in aneuploid budding yeast and breast cancer cells. Robustness also compensates for the negative impact of the systems' complexity on their evolvability. Our model also provides a mathematical means to estimate the number of independent processes underlying a system's performance and identify the most generally adapted subpopulation, which may resemble the multi-drug-resistant "persister" cells observed in cancer.
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Affiliation(s)
- Andrei Kucharavy
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
- UMR 7238 CNRS, Université Pierre et Marie Curie, Paris 75006, France
| | | | - Jin Zhu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Rong Li
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
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33
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Kovary KM, Taylor B, Zhao ML, Teruel MN. Expression variation and covariation impair analog and enable binary signaling control. Mol Syst Biol 2018; 14:e7997. [PMID: 29759982 PMCID: PMC5951153 DOI: 10.15252/msb.20177997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 03/26/2018] [Accepted: 04/05/2018] [Indexed: 11/09/2022] Open
Abstract
Due to noise in the synthesis and degradation of proteins, the concentrations of individual vertebrate signaling proteins were estimated to vary with a coefficient of variation (CV) of approximately 25% between cells. Such high variation is beneficial for population-level regulation of cell functions but abolishes accurate single-cell signal transmission. Here, we measure cell-to-cell variability of relative protein abundance using quantitative proteomics of individual Xenopus laevis eggs and cultured human cells and show that variation is typically much lower, in the range of 5-15%, compatible with accurate single-cell transmission. Focusing on bimodal ERK signaling, we show that variation and covariation in MEK and ERK expression improves controllability of the percentage of activated cells, demonstrating how variation and covariation in expression enables population-level control of binary cell-fate decisions. Together, our study argues for a control principle whereby low expression variation enables accurate control of analog single-cell signaling, while increased variation, covariation, and numbers of pathway components are required to widen the stimulus range over which external inputs regulate binary cell activation to enable precise control of the fraction of activated cells in a population.
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Affiliation(s)
- Kyle M Kovary
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Brooks Taylor
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Michael L Zhao
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Mary N Teruel
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
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34
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Nicolas D, Phillips NE, Naef F. What shapes eukaryotic transcriptional bursting? MOLECULAR BIOSYSTEMS 2018; 13:1280-1290. [PMID: 28573295 DOI: 10.1039/c7mb00154a] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promoters that leads to the discontinuous production of mRNA. The diversity in bursting patterns displayed by different genes suggests the existence of a connection between bursting and gene regulation. Experimental strategies such as single-molecule RNA FISH, MS2-GFP or short-lived protein reporters allow the quantification of transcriptional bursting and the comparison of bursting kinetics between conditions, allowing therefore the identification of molecular mechanisms modulating transcriptional bursting. In this review we recapitulate the impact on transcriptional bursting of different molecular aspects of transcription such as the chromatin environment, nucleosome occupancy, histone modifications, the number and affinity of regulatory elements, DNA looping and transcription factor availability. More specifically, we examine their role in tuning the burst size or the burst frequency. While some molecular mechanisms involved in transcription such as histone marks can affect every aspect of bursting, others predominantly influence the burst size (e.g. the number and affinity of cis-regulatory elements) or frequency (e.g. transcription factor availability).
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Affiliation(s)
- Damien Nicolas
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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35
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Fritzsch C, Baumgärtner S, Kuban M, Steinshorn D, Reid G, Legewie S. Estrogen-dependent control and cell-to-cell variability of transcriptional bursting. Mol Syst Biol 2018; 14:e7678. [PMID: 29476006 PMCID: PMC5825209 DOI: 10.15252/msb.20177678] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 01/16/2018] [Accepted: 01/26/2018] [Indexed: 01/14/2023] Open
Abstract
Cellular decision-making and environmental adaptation are dependent upon a heterogeneous response of gene expression to external cues. Heterogeneity arises in transcription from random switching between transcriptionally active and inactive states, resulting in bursts of RNA synthesis. Furthermore, the cellular state influences the competency of transcription, thereby globally affecting gene expression in a cell-specific manner. We determined how external stimuli interplay with cellular state to modulate the kinetics of bursting. To this end, single-cell dynamics of nascent transcripts were monitored at the endogenous estrogen-responsive GREB1 locus. Stochastic modeling of gene expression implicated a two-state promoter model in which the estrogen stimulus modulates the frequency of transcriptional bursting. The cellular state affects transcriptional dynamics by altering initiation and elongation kinetics and acts globally, as GREB1 alleles in the same cell correlate in their transcriptional output. Our results suggest that cellular state strongly affects the first step of the central dogma of gene expression, to promote heterogeneity in the transcriptional output of isogenic cells.
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Affiliation(s)
| | | | | | | | - George Reid
- Institute of Molecular Biology, Mainz, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
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36
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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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37
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 DOI: 10.1101/121202] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 05/28/2023] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Ewan Birney
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Ian Dunham
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Enard
- Department of Biology II, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Andrew Farmer
- Takara Bio United States, Inc., Mountain View, United States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, United States
- Massachusetts General Hospital Cancer Center, Boston, United States
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of Medicine, Stanford University School of Medicine, Stanford, United States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Genetics, Stanford University, Stanford, United States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, United States
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, United States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of Bioengineering, Stanford University, Stanford, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Rahul Satija
- Department of Biology, New York University, New York, United States
- New York Genome Center, New York University, New York, United States
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alex Shalek
- Broad Institute of MIT and Harvard, Cambridge, United States
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer Center, University of Texas, Houston, United States
| | - Jay W Shin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Oliver Stegle
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Fabian J Theis
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of Proteomics, KTH Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, United States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
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38
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 PMCID: PMC5762154 DOI: 10.7554/elife.27041] [Citation(s) in RCA: 1214] [Impact Index Per Article: 173.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 12/12/2022] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric S Lander
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Ido Amit
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
| | - Ewan Birney
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
| | - Ian Dunham
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
| | - Wolfgang Enard
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
| | - Andrew Farmer
- Takara Bio United States, Inc.Mountain ViewUnited States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
| | - Berthold Göttgens
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and HarvardCambridgeUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Muzlifah Haniffa
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Emma Lundberg
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
| | - Garry Nolan
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
| | - Dana Pe'er
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
| | - Rahul Satija
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
| | - Ton N Schumacher
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Alex Shalek
- Broad Institute of MIT and HarvardCambridgeUnited States
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Jay W Shin
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Oliver Stegle
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | - Fabian J Theis
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Barbara Wold
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Ramnik Xavier
- Broad Institute of MIT and HarvardCambridgeUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Human Cell Atlas Meeting Participants
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
- Takara Bio United States, Inc.Mountain ViewUnited States
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Massachusetts General Hospital Cancer CenterBostonUnited States
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Allen Institute for Brain ScienceSeattleUnited States
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
- National Institute of Biomedical GenomicsKalyaniIndia
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
- Hubrecht Institute and University Medical Center UtrechtUtrechtThe Netherlands
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
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39
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Dacheux E, Malys N, Meng X, Ramachandran V, Mendes P, McCarthy JEG. Translation initiation events on structured eukaryotic mRNAs generate gene expression noise. Nucleic Acids Res 2017; 45:6981-6992. [PMID: 28521011 PMCID: PMC5499741 DOI: 10.1093/nar/gkx430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/10/2017] [Indexed: 11/14/2022] Open
Abstract
Gene expression stochasticity plays a major role in biology, creating non-genetic cellular individuality and influencing multiple processes, including differentiation and stress responses. We have addressed the lack of knowledge about posttranscriptional contributions to noise by determining cell-to-cell variations in the abundance of mRNA and reporter protein in yeast. Two types of structural element, a stem–loop and a poly(G) motif, not only inhibit translation initiation when inserted into an mRNA 5΄ untranslated region, but also generate noise. The noise-enhancing effect of the stem–loop structure also remains operational when combined with an upstream open reading frame. This has broad significance, since these elements are known to modulate the expression of a diversity of eukaryotic genes. Our findings suggest a mechanism for posttranscriptional noise generation that will contribute to understanding of the generally poor correlation between protein-level stochasticity and transcriptional bursting. We propose that posttranscriptional stochasticity can be linked to cycles of folding/unfolding of a stem–loop structure, or to interconversion between higher-order structural conformations of a G-rich motif, and have created a correspondingly configured computational model that generates fits to the experimental data. Stochastic events occurring during the ribosomal scanning process can therefore feature alongside transcriptional bursting as a source of noise.
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Affiliation(s)
- Estelle Dacheux
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Naglis Malys
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Xiang Meng
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Vinoy Ramachandran
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Pedro Mendes
- Center for Quantitative Medicine, UConn Health, 263 Farmington Avenue, CT 06030-6033, USA
| | - John E G McCarthy
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
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40
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Faure AJ, Schmiedel JM, Lehner B. Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells. Cell Syst 2017; 5:471-484.e4. [DOI: 10.1016/j.cels.2017.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/06/2017] [Accepted: 10/02/2017] [Indexed: 01/23/2023]
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41
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Zaidi H, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT. Second-generation method for analysis of chromatin binding with formaldehyde-cross-linking kinetics. J Biol Chem 2017; 292:19338-19355. [PMID: 28972159 DOI: 10.1074/jbc.m117.796441] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/21/2017] [Indexed: 11/06/2022] Open
Abstract
Formaldehyde-cross-linking underpins many of the most commonly used experimental approaches in the chromatin field, especially in capturing site-specific protein-DNA interactions. Extending such assays to assess the stability and binding kinetics of protein-DNA interactions is more challenging, requiring absolute measurements with a relatively high degree of physical precision. We previously described an experimental framework called the cross-linking kinetics (CLK) assay, which uses time-dependent formaldehyde-cross-linking data to extract kinetic parameters of chromatin binding. Many aspects of formaldehyde behavior in cells are unknown or undocumented, however, and could potentially affect CLK data analyses. Here, we report biochemical results that better define the properties of formaldehyde-cross-linking in budding yeast cells. These results have the potential to inform interpretations of "standard" chromatin assays, including chromatin immunoprecipitation. Moreover, the chemical complexity we uncovered resulted in the development of an improved method for measuring binding kinetics with the CLK approach. Optimum conditions included an increased formaldehyde concentration and more robust glycine-quench conditions. Notably, we observed that formaldehyde-cross-linking rates can vary dramatically for different protein-DNA interactions in vivo Some interactions were cross-linked much faster than the in vivo macromolecular interactions, making them suitable for kinetic analysis. For other interactions, we found the cross-linking reaction occurred on the same time scale or slower than binding dynamics; for these interactions, it was sometimes possible to compute the in vivo equilibrium-binding constant but not binding on- and off-rates. This improved method yields more accurate in vivo binding kinetics estimates on the minute time scale.
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Affiliation(s)
- Hussain Zaidi
- From the School of Medicine Research Computing, University of Virginia and
| | - Elizabeth A Hoffman
- the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Savera J Shetty
- the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Stefan Bekiranov
- the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - David T Auble
- the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
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42
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Information Theoretical Study of Cross-Talk Mediated Signal Transduction in MAPK Pathways. ENTROPY 2017. [DOI: 10.3390/e19090469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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Boross G, Papp B. No Evidence That Protein Noise-Induced Epigenetic Epistasis Constrains Gene Expression Evolution. Mol Biol Evol 2017; 34:380-390. [PMID: 28025271 DOI: 10.1093/molbev/msw236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Changes in gene expression can affect phenotypes and therefore both its level and stochastic variability are frequently under selection. It has recently been proposed that epistatic interactions influence gene expression evolution: gene pairs where simultaneous knockout is more deleterious than expected should evolve reduced expression noise to avoid concurrent low expression of both proteins. In apparent support, yeast genes with many epistatic partners have low expression variation both among isogenic individuals and between species. However, the specific predictions and basic assumptions of this verbal model remain untested. Using bioinformatics analysis, we first demonstrate that the model's predictions are unsupported by available large-scale data. Based on quantitative biochemical modeling, we then show that epistasis between expression reductions (epigenetic epistasis) is not expected to aggravate the fitness cost of stochastic expression, which is in sharp contrast to the verbal argument. This nonintuitive result can be readily explained by the typical diminishing return of fitness on gene activity and by the fact that expression noise not only decreases but also increases the abundance of proteins. Overall, we conclude that stochastic variation in epistatic partners is unlikely to drive noise minimization or constrain gene expression divergence on a genomic scale.
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Affiliation(s)
- Gábor Boross
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
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44
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Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol 2017; 34:1145-1160. [PMID: 27824854 DOI: 10.1038/nbt.3711] [Citation(s) in RCA: 370] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Single-cell genomics has now made it possible to create a comprehensive atlas of human cells. At the same time, it has reopened definitions of a cell's identity and of the ways in which identity is regulated by the cell's molecular circuitry. Emerging computational analysis methods, especially in single-cell RNA sequencing (scRNA-seq), have already begun to reveal, in a data-driven way, the diverse simultaneous facets of a cell's identity, from discrete cell types to continuous dynamic transitions and spatial locations. These developments will eventually allow a cell to be represented as a superposition of 'basis vectors', each determining a different (but possibly dependent) aspect of cellular organization and function. However, computational methods must also overcome considerable challenges-from handling technical noise and data scale to forming new abstractions of biology. As the scale of single-cell experiments continues to increase, new computational approaches will be essential for constructing and characterizing a reference map of cell identities.
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Affiliation(s)
- Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, California, USA
| | - Aviv Regev
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, California, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, Massachusetts, USA
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45
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Scaling single-cell genomics from phenomenology to mechanism. Nature 2017; 541:331-338. [PMID: 28102262 DOI: 10.1038/nature21350] [Citation(s) in RCA: 472] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/14/2016] [Indexed: 02/08/2023]
Abstract
Three of the most fundamental questions in biology are how individual cells differentiate to form tissues, how tissues function in a coordinated and flexible fashion and which gene regulatory mechanisms support these processes. Single-cell genomics is opening up new ways to tackle these questions by combining the comprehensive nature of genomics with the microscopic resolution that is required to describe complex multicellular systems. Initial single-cell genomic studies provided a remarkably rich phenomenology of heterogeneous cellular states, but transforming observational studies into models of dynamics and causal mechanisms in tissues poses fresh challenges and requires stronger integration of theoretical, computational and experimental frameworks.
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46
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Martins AJ, Narayanan M, Prüstel T, Fixsen B, Park K, Gottschalk RA, Lu Y, Andrews-Pfannkoch C, Lau WW, Wendelsdorf KV, Tsang JS. Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network. Cell Syst 2017; 4:379-392.e12. [PMID: 28365150 DOI: 10.1016/j.cels.2017.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/15/2016] [Accepted: 03/01/2017] [Indexed: 01/22/2023]
Abstract
Cell-to-cell variation in gene expression and the propagation of such variation (PoV or "noise propagation") from one gene to another in the gene network, as reflected by gene-gene correlation across single cells, are commonly observed in single-cell transcriptomic studies and can shape the phenotypic diversity of cell populations. While gene network "rewiring" is known to accompany cellular adaptation to different environments, how PoV changes between environments and its underlying regulatory mechanisms are less understood. Here, we systematically explored context-dependent PoV among genes in human macrophages, utilizing different cytokines as natural perturbations of multiple molecular parameters that may influence PoV. Our single-cell, epigenomic, computational, and stochastic simulation analyses reveal that environmental adaptation can tune PoV to potentially shape cellular heterogeneity by changing parameters such as the degree of phosphorylation and transcription factor-chromatin interactions. This quantitative tuning of PoV may be a widespread, yet underexplored, property of cellular adaptation to distinct environments.
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Affiliation(s)
- Andrew J Martins
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Manikandan Narayanan
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thorsten Prüstel
- Computational Biology Section, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bethany Fixsen
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyemyung Park
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA; Biophysics Program, University of Maryland-NIH Graduate Partnership Program, University of Maryland, College Park, MD 20742, USA
| | - Rachel A Gottschalk
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yong Lu
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cynthia Andrews-Pfannkoch
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - William W Lau
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine V Wendelsdorf
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - John S Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA; Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA.
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47
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Aranda-Díaz A, Mace K, Zuleta I, Harrigan P, El-Samad H. Robust Synthetic Circuits for Two-Dimensional Control of Gene Expression in Yeast. ACS Synth Biol 2017; 6:545-554. [PMID: 27930885 PMCID: PMC5507677 DOI: 10.1021/acssynbio.6b00251] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cellular phenotypes are the result of complex interactions between many components. Understanding and predicting the system level properties of the resulting networks requires the development of perturbation tools that can simultaneously and independently modulate multiple cellular variables. Here, we develop synthetic modules that use different arrangements of two transcriptional regulators to achieve either concurrent and independent control of the expression of two genes, or decoupled control of the mean and variance of a single gene. These modules constitute powerful tools to probe the quantitative attributes of network wiring and function.
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Affiliation(s)
- Andrés Aranda-Díaz
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Kieran Mace
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Ignacio Zuleta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Patrick Harrigan
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States
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48
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Determining the Limitations and Benefits of Noise in Gene Regulation and Signal Transduction through Single Cell, Microscopy-Based Analysis. J Mol Biol 2017; 429:1143-1154. [PMID: 28288800 DOI: 10.1016/j.jmb.2017.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022]
Abstract
Stochastic fluctuations, termed "noise," in the level of biological molecules can greatly impact cellular functions. While biological noise can sometimes be detrimental, recent studies have provided an increasing number of examples in which biological noise can be functionally beneficial. Rather than provide an exhaustive review of the growing literature in this field, in this review, we focus on single-cell studies based on quantitative microscopy that have generated a deeper understanding of the sources, characteristics, limitations, and benefits of biological noise. Specifically, we highlight studies showing how noise can help coordinate the expression of multiple downstream target genes, impact the channel capacity of signaling networks, and interact synergistically with oscillatory dynamics to enhance the sensitivity of signal processing. We conclude with a discussion of current challenges and future opportunities.
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49
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RNA synthesis is associated with multiple TBP-chromatin binding events. Sci Rep 2017; 7:39631. [PMID: 28051102 PMCID: PMC5209698 DOI: 10.1038/srep39631] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/25/2016] [Indexed: 01/12/2023] Open
Abstract
Competition ChIP is an experimental method that allows transcription factor (TF) chromatin turnover dynamics to be measured across a genome. We develop and apply a physical model of TF-chromatin competitive binding using chemical reaction rate theory and are able to derive the physical half-life or residence time for TATA-binding protein (TBP) across the yeast genome from competition ChIP data. Using our physical modeling approach where we explicitly include the induction profile of the competitor in the model, we are able to estimate yeast TBP-chromatin residence times as short as 1.3 minutes, demonstrating that competition ChIP is a relatively high temporal-resolution approach. Strikingly, we find a median value of ~5 TBP-chromatin binding events associated with the synthesis of one RNA molecule across Pol II genes, suggesting multiple rounds of pre-initiation complex assembly and disassembly before productive elongation of Pol II is achieved at most genes in the yeast genome.
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50
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Yaakov G, Lerner D, Bentele K, Steinberger J, Barkai N. Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress. Nat Ecol Evol 2017; 1:16. [PMID: 28812556 DOI: 10.1038/s41559-016-0016] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/13/2016] [Indexed: 12/30/2022]
Abstract
Mutation rate balances the need to protect genome integrity with the advantage of evolutionary innovations. Microorganisms increase their mutation rate when stressed, perhaps addressing the growing need for evolutionary innovation. Such a strategy, however, is only beneficial under moderate stresses that allow cells to divide and realize their mutagenic potential. In contrast, severe stresses rapidly kill the majority of the population with the exception of a small minority of cells that are in a phenotypically distinct state termed persistence. Although persisters were discovered many decades ago, the stochastic event triggering persistence is poorly understood. We report that spontaneous DNA damage triggers persistence in Saccharomyces cerevisiae by activating the general stress response, providing protection against a range of harsh stress and drug environments. We further show that the persister subpopulation carries an increased load of genetic variants in the form of insertions, deletions or large structural variations, which are unrelated to their stress survival. This coupling of DNA damage to phenotypic persistence may increase genetic diversity specifically in severe stress conditions, where diversity is beneficial but the ability to generate de novo mutations is limited.
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Affiliation(s)
- Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Lerner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kajetan Bentele
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Steinberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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