1
|
Sivaramakrishnan P, Watkins C, Murray JI. Transcript accumulation rates in the early Caenorhabditis elegans embryo. SCIENCE ADVANCES 2023; 9:eadi1270. [PMID: 37611097 PMCID: PMC10446496 DOI: 10.1126/sciadv.adi1270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
Dynamic transcriptional changes are widespread in rapidly dividing developing embryos when cell fate decisions are made quickly. The Caenorhabditis elegans embryo overcomes these constraints partly through the rapid production of high levels of transcription factor mRNAs. Transcript accumulation rates for some developmental genes are known at single-cell resolution, but genome-scale measurements are lacking. We estimate zygotic mRNA accumulation rates from single-cell RNA sequencing data calibrated with single-molecule transcript imaging. Rapid transcription is common in the early C. elegans embryo with rates highest soon after zygotic transcription begins. High-rate genes are enriched for recently duplicated cell-fate regulators and share common genomic features. We identify core promoter elements associated with high rate and measure their contributions for two early endomesodermal genes, ceh-51 and sdz-31. Individual motifs modestly affect accumulation rates, suggesting multifactorial control. These results are a step toward estimating absolute transcription kinetics and understanding how transcript dosage drives developmental decisions.
Collapse
Affiliation(s)
- Priya Sivaramakrishnan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Cameron Watkins
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | |
Collapse
|
2
|
Forbes Beadle L, Love JC, Shapovalova Y, Artemev A, Rattray M, Ashe HL. Combined modelling of mRNA decay dynamics and single-molecule imaging in the Drosophila embryo uncovers a role for P-bodies in 5' to 3' degradation. PLoS Biol 2023; 21:e3001956. [PMID: 36649329 PMCID: PMC9882958 DOI: 10.1371/journal.pbio.3001956] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 01/27/2023] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
Regulation of mRNA degradation is critical for a diverse array of cellular processes and developmental cell fate decisions. Many methods for determining mRNA half-lives rely on transcriptional inhibition or metabolic labelling. Here, we use a non-invasive method for estimating half-lives for hundreds of mRNAs in the early Drosophila embryo. This approach uses the intronic and exonic reads from a total RNA-seq time series and Gaussian process regression to model the dynamics of premature and mature mRNAs. We show how regulation of mRNA stability is used to establish a range of mature mRNA dynamics during embryogenesis, despite shared transcription profiles. Using single-molecule imaging, we provide evidence that, for the mRNAs tested, there is a correlation between short half-life and mRNA association with P-bodies. Moreover, we detect an enrichment of mRNA 3' ends in P-bodies in the early embryo, consistent with 5' to 3' degradation occurring in P-bodies for at least a subset of mRNAs. We discuss our findings in relation to recently published data suggesting that the primary function of P-bodies in other biological contexts is mRNA storage.
Collapse
Affiliation(s)
- Lauren Forbes Beadle
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jennifer C. Love
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Yuliya Shapovalova
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Artem Artemev
- Department of Computing, Imperial College London, London, United Kingdom
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- * E-mail: (MR); (HLA)
| | - Hilary L. Ashe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- * E-mail: (MR); (HLA)
| |
Collapse
|
3
|
Casey MJ, Call AM, Thorpe AV, Jette CA, Engel ME, Stewart RA. The scaffolding function of LSD1/KDM1A reinforces a negative feedback loop to repress stem cell gene expression during primitive hematopoiesis. iScience 2022; 26:105737. [PMID: 36594016 PMCID: PMC9803847 DOI: 10.1016/j.isci.2022.105737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/15/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Lsd1/Kdm1a functions both as a histone demethylase enzyme and as a scaffold for assembling chromatin modifier and transcription factor complexes to regulate gene expression. The relative contributions of Lsd1's demethylase and scaffolding functions during embryogenesis are not known. Here, we analyze two independent zebrafish lsd1/kdm1a mutant lines and show Lsd1 is required to repress primitive hematopoietic stem cell gene expression. Lsd1 rescue constructs containing point mutations that selectively abrogate its demethylase or scaffolding capacity demonstrate the scaffolding function of Lsd1, not its demethylase activity, is required for repression of gene expression in vivo. Lsd1's SNAG-binding domain mediates its scaffolding function and reinforces a negative feedback loop to repress the expression of SNAG-domain-containing genes during embryogenesis, including gfi1 and snai1/2. Our findings reveal a model in which the SNAG-binding and scaffolding function of Lsd1, and its associated negative feedback loop, provide transient and reversible regulation of gene expression during hematopoietic development.
Collapse
Affiliation(s)
- Mattie J. Casey
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Alexandra M. Call
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Annika V. Thorpe
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Cicely A. Jette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Michael E. Engel
- Department of Pediatric Hematology/Oncology, Emily Couric Cancer Center, University of Virginia, Charlottesville, VA 22903, USA,Corresponding author
| | - Rodney A. Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA,Corresponding author
| |
Collapse
|
4
|
Ghosh S, Lehner CF. Incorporation of CENP-A/CID into centromeres during early Drosophila embryogenesis does not require RNA polymerase II-mediated transcription. Chromosoma 2022; 131:1-17. [PMID: 35015118 PMCID: PMC9079035 DOI: 10.1007/s00412-022-00767-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 11/24/2022]
Abstract
In many species, centromere identity is specified epigenetically by special nucleosomes containing a centromere-specific histone H3 variant, designated as CENP-A in humans and CID in Drosophila melanogaster. After partitioning of centromere-specific nucleosomes onto newly replicated sister centromeres, loading of additional CENP-A/CID into centromeric chromatin is required for centromere maintenance in proliferating cells. Analyses with cultured cells have indicated that transcription of centromeric DNA by RNA polymerase II is required for deposition of new CID into centromere chromatin. However, a dependence of centromeric CID loading on transcription is difficult to reconcile with the notion that the initial embryonic stages appear to proceed in the absence of transcription in Drosophila, as also in many other animal species. To address the role of RNA polymerase II–mediated transcription for CID loading in early Drosophila embryos, we have quantified the effects of alpha-amanitin and triptolide on centromeric CID-EGFP levels. Our analyses demonstrate that microinjection of these two potent inhibitors of RNA polymerase II–mediated transcription has at most a marginal effect on centromeric CID deposition during progression through the early embryonic cleavage cycles. Thus, we conclude that at least during early Drosophila embryogenesis, incorporation of CID into centromeres does not depend on RNA polymerase II–mediated transcription.
Collapse
Affiliation(s)
- Samadri Ghosh
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Christian F Lehner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
5
|
Lin TA, Lin WS, Chou YC, Nagabhushanam K, Ho CT, Pan MH. Oxyresveratrol inhibits human colon cancer cell migration through regulating epithelial-mesenchymal transition and microRNA. Food Funct 2021; 12:9658-9668. [PMID: 34664597 DOI: 10.1039/d1fo01920a] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The major cause of death in colorectal cancer (CRC) patients is metastasis. Moreover, lots of studies have emphasized that the epithelial-mesenchymal transition (EMT) is a pivotal step in metastasis. Both transforming growth factor beta (TGF-β) and dysregulation of microRNAs (miRNAs) can induce or regulate EMT, promoting the loss of intercellular adhesion and increased motility of cancer cells. Therefore, it is necessary to prevent or inhibit the metastasis of colorectal cancer. Relatively little is known about the anti-metastatic effect of oxyresveratrol (OXY), a natural derivative of resveratrol (RES), compared to RES. Accordingly, RES was used as the positive control to investigate the effects of OXY on colon cancer cell migration. The results showed that OXY could significantly inhibit cell migration (67.17% ± 0.04, 64.89% ± 0.04) compared to RES (84.6% ± 0.07, 76.34% ± 0.08) in HCT116 cells and TGF-β-induced HT-29 cells, respectively, via Snail/E-cadherin expression. In addition, OXY improved EMT-related miRNA expression through, for example, lowering the levels of miR-3687 and miR-301a-3p while upregulating miR-3612 in TGF-β-induced HT-29 cells. In conclusion, OXY inhibits human colon cancer cell migration by regulating EMT and miRNAs. Based on these findings, it can be stated that OXY promotes anti-metastatic properties in CRC.
Collapse
Affiliation(s)
- Ting-Ann Lin
- Institute of Food Sciences and Technology, National Taiwan University, Taipei 10617, Taiwan.
| | - Wei-Sheng Lin
- Institute of Food Sciences and Technology, National Taiwan University, Taipei 10617, Taiwan.
| | - Ya-Chun Chou
- Institute of Food Sciences and Technology, National Taiwan University, Taipei 10617, Taiwan.
| | | | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, New Jersey 08901, USA
| | - Min-Hisung Pan
- Institute of Food Sciences and Technology, National Taiwan University, Taipei 10617, Taiwan. .,Department of Health and Nutrition Biotechnology, Asia University, Taichung 41354, Taiwan.,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| |
Collapse
|
6
|
Pimmett VL, Dejean M, Fernandez C, Trullo A, Bertrand E, Radulescu O, Lagha M. Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics. Nat Commun 2021; 12:4504. [PMID: 34301936 PMCID: PMC8302612 DOI: 10.1038/s41467-021-24461-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/31/2021] [Indexed: 11/09/2022] Open
Abstract
Genes are expressed in stochastic transcriptional bursts linked to alternating active and inactive promoter states. A major challenge in transcription is understanding how promoter composition dictates bursting, particularly in multicellular organisms. We investigate two key Drosophila developmental promoter motifs, the TATA box (TATA) and the Initiator (INR). Using live imaging in Drosophila embryos and new computational methods, we demonstrate that bursting occurs on multiple timescales ranging from seconds to minutes. TATA-containing promoters and INR-containing promoters exhibit distinct dynamics, with one or two separate rate-limiting steps respectively. A TATA box is associated with long active states, high rates of polymerase initiation, and short-lived, infrequent inactive states. In contrast, the INR motif leads to two inactive states, one of which relates to promoter-proximal polymerase pausing. Surprisingly, the model suggests pausing is not obligatory, but occurs stochastically for a subset of polymerases. Overall, our results provide a rationale for promoter switching during zygotic genome activation.
Collapse
Affiliation(s)
- Virginia L Pimmett
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Matthieu Dejean
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Carola Fernandez
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Antonio Trullo
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
- Institut de Génétique Humaine, Univ Montpellier, CNRS, Montpellier, France
| | - Ovidiu Radulescu
- Laboratory of Pathogen Host Interactions, Univ Montpellier, CNRS, Montpellier, France
| | - Mounia Lagha
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
| |
Collapse
|
7
|
Fukaya T. Dynamic regulation of anterior-posterior patterning genes in living Drosophila embryos. Curr Biol 2021; 31:2227-2236.e6. [PMID: 33761316 DOI: 10.1016/j.cub.2021.02.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/27/2021] [Accepted: 02/18/2021] [Indexed: 10/21/2022]
Abstract
Expression of the gap and pair-rule genes plays an essential role in body segmentation during Drosophila embryogenesis.1-5 However, it remains unclear how precise expression patterns of these key developmental genes arise from stochastic transcriptional activation at the single-cell level. Here, I employed genome-editing and live-imaging approaches to comprehensively visualize regulation of the gap and pair-rule genes at the endogenous loci. Quantitative image analysis revealed that the total duration of active transcription (transcription period) is a major determinant of spatial patterning of gene expression in early embryos. The length of the transcription period is determined by the continuity of bursting activities in individual nuclei, with the core expression domain producing more bursts than boundary regions. Each gene exhibits a distinct rate of nascent RNA production during transcriptional bursting, which contributes to gene-to-gene variability in the total output. I also provide evidence for "enhancer interference," wherein a distal weak enhancer interferes with transcriptional activation by a strong proximal enhancer to downregulate the length of the transcription period without changing the transcription rate. Analysis of the endogenous hunchback (hb) locus revealed that the removal of the distal shadow enhancer induces strong ectopic transcriptional activation, which suppresses refinement of the initial broad expression domain into narrower stripe patterns at the anterior part of embryos. This study provides key insights into the link between transcriptional bursting, enhancer-promoter interaction, and spatiotemporal patterning of gene expression during animal development.
Collapse
Affiliation(s)
- Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| |
Collapse
|
8
|
Liu J, Hansen D, Eck E, Kim YJ, Turner M, Alamos S, Garcia HG. Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. PLoS Comput Biol 2021; 17:e1008999. [PMID: 34003867 PMCID: PMC8162642 DOI: 10.1371/journal.pcbi.1008999] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/28/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022] Open
Abstract
The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.
Collapse
Affiliation(s)
- Jonathan Liu
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
| | - Donald Hansen
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Elizabeth Eck
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Meghan Turner
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, United States of America
| | - Hernan G. Garcia
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, United States of America
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California, United States of America
| |
Collapse
|
9
|
Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. Nat Protoc 2021; 16:1647-1713. [PMID: 33619390 PMCID: PMC8525907 DOI: 10.1038/s41596-020-00478-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/26/2020] [Indexed: 01/31/2023]
Abstract
Chromatin conformation capture (3C) methods and fluorescent in situ hybridization (FISH) microscopy have been used to investigate the spatial organization of the genome. Although powerful, both techniques have limitations. Hi-C is challenging for low cell numbers and requires very deep sequencing to achieve its high resolution. In contrast, FISH can be done on small cell numbers and capture rare cell populations, but typically targets pairs of loci at a lower resolution. Here we detail a protocol for optical reconstruction of chromatin architecture (ORCA), a microscopy approach to trace the 3D DNA path within the nuclei of fixed tissues and cultured cells with a genomic resolution as fine as 2 kb and a throughput of ~10,000 cells per experiment. ORCA can identify structural features with comparable resolution to Hi-C while providing single-cell resolution and multimodal measurements characteristic of microscopy. We describe how to use this DNA labeling in parallel with multiplexed labeling of dozens of RNAs to relate chromatin structure and gene expression in the same cells. Oligopaint probe design, primary probe making, sample collection, cryosectioning and RNA/DNA primary probe hybridization can be completed in 1.5 weeks, while automated RNA/DNA barcode hybridization and RNA/DNA imaging typically takes 2-6 d for data collection and 2-7 d for the automated steps of image analysis.
Collapse
|
10
|
Berrocal A, Lammers NC, Garcia HG, Eisen MB. Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene. eLife 2020; 9:61635. [PMID: 33300492 PMCID: PMC7864633 DOI: 10.7554/elife.61635] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
We used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high-temporal resolution as its seven stripe expression pattern forms, and developed tools to characterize and visualize how transcriptional bursting varies over time and space. We find that despite being created by the independent activity of five enhancers, even-skipped stripes are sculpted by the same kinetic phenomena: a coupled increase of burst frequency and amplitude. By tracking the position and activity of individual nuclei, we show that stripe movement is driven by the exchange of bursting nuclei from the posterior to anterior stripe flanks. Our work provides a conceptual, theoretical and computational framework for dissecting pattern formation in space and time, and reveals how the coordinated transcriptional activity of individual nuclei shapes complex developmental patterns.
Collapse
Affiliation(s)
- Augusto Berrocal
- Department of Molecular & Cell Biology, University of California at Berkeley, Berkeley, United States
| | - Nicholas C Lammers
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, United States
| | - Hernan G Garcia
- Department of Molecular & Cell Biology, University of California at Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California at Berkeley, Berkeley, United States.,Department of Physics, University of California at Berkeley, Berkeley, United States.,Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, United States
| | - Michael B Eisen
- Department of Molecular & Cell Biology, University of California at Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California at Berkeley, Berkeley, United States.,Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, United States.,Department of Integrative Biology, University of California at Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, United States
| |
Collapse
|
11
|
Cortijo S, Locke JCW. Does Gene Expression Noise Play a Functional Role in Plants? TRENDS IN PLANT SCIENCE 2020; 25:1041-1051. [PMID: 32467064 DOI: 10.1016/j.tplants.2020.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/22/2020] [Accepted: 04/28/2020] [Indexed: 05/20/2023]
Abstract
Gene expression in individual cells can be surprisingly noisy. In unicellular organisms this noise can be functional; for example, by allowing a subfraction of the population to prepare for environmental stress. The role of gene expression noise in multicellular organisms has, however, remained unclear. In this review, we discuss how new techniques are revealing an unexpected level of variability in gene expression between and within genetically identical plants. We describe recent progress as well as speculate on the function of transcriptional noise as a mechanism for generating functional phenotypic diversity in plants.
Collapse
Affiliation(s)
- Sandra Cortijo
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK.
| |
Collapse
|
12
|
Hoppe C, Bowles JR, Minchington TG, Sutcliffe C, Upadhyai P, Rattray M, Ashe HL. Modulation of the Promoter Activation Rate Dictates the Transcriptional Response to Graded BMP Signaling Levels in the Drosophila Embryo. Dev Cell 2020; 54:727-741.e7. [PMID: 32758422 PMCID: PMC7527239 DOI: 10.1016/j.devcel.2020.07.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/13/2020] [Accepted: 07/11/2020] [Indexed: 01/08/2023]
Abstract
Morphogen gradients specify cell fates during development, with a classic example being the bone morphogenetic protein (BMP) gradient's conserved role in embryonic dorsal-ventral axis patterning. Here, we elucidate how the BMP gradient is interpreted in the Drosophila embryo by combining live imaging with computational modeling to infer transcriptional burst parameters at single-cell resolution. By comparing burst kinetics in cells receiving different levels of BMP signaling, we show that BMP signaling controls burst frequency by regulating the promoter activation rate. We provide evidence that the promoter activation rate is influenced by both enhancer and promoter sequences, whereas Pol II loading rate is primarily modulated by the enhancer. Consistent with BMP-dependent regulation of burst frequency, the numbers of BMP target gene transcripts per cell are graded across their expression domains. We suggest that graded mRNA output is a general feature of morphogen gradient interpretation and discuss how this can impact on cell-fate decisions.
Collapse
Affiliation(s)
- Caroline Hoppe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan R Bowles
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Thomas G Minchington
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Catherine Sutcliffe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Priyanka Upadhyai
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
| | - Hilary L Ashe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
| |
Collapse
|
13
|
Irizarry J, McGehee J, Kim G, Stein D, Stathopoulos A. Twist-dependent ratchet functioning downstream from Dorsal revealed using a light-inducible degron. Genes Dev 2020; 34:965-972. [PMID: 32467225 PMCID: PMC7328519 DOI: 10.1101/gad.338194.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/24/2020] [Indexed: 11/24/2022]
Abstract
Graded transcription factors are pivotal regulators of embryonic patterning, but whether their role changes over time is unclear. A light-regulated protein degradation system was used to assay temporal dependence of the transcription factor Dorsal in dorsal-ventral axis patterning of Drosophila embryos. Surprisingly, the high-threshold target gene snail only requires Dorsal input early but not late when Dorsal levels peak. Instead, late snail expression can be supported by action of the Twist transcription factor, specifically, through one enhancer, sna.distal This study demonstrates that continuous input is not required for some Dorsal targets and downstream responses, such as twist, function as molecular ratchets.
Collapse
Affiliation(s)
- Jihyun Irizarry
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - James McGehee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Goheun Kim
- Molecular Cell, and Developmental Biology, University of Texas at Austin, , Austin, Texas 78712, USA
| | - David Stein
- Molecular Cell, and Developmental Biology, University of Texas at Austin, , Austin, Texas 78712, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|
14
|
Young AP, Jackson DJ, Wyeth RC. A technical review and guide to RNA fluorescence in situ hybridization. PeerJ 2020; 8:e8806. [PMID: 32219032 PMCID: PMC7085896 DOI: 10.7717/peerj.8806] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
RNA-fluorescence in situ hybridization (FISH) is a powerful tool to visualize target messenger RNA transcripts in cultured cells, tissue sections or whole-mount preparations. As the technique has been developed over time, an ever-increasing number of divergent protocols have been published. There is now a broad selection of options available to facilitate proper tissue preparation, hybridization, and post-hybridization background removal to achieve optimal results. Here we review the technical aspects of RNA-FISH, examining the most common methods associated with different sample types including cytological preparations and whole-mounts. We discuss the application of commonly used reagents for tissue preparation, hybridization, and post-hybridization washing and provide explanations of the functional roles for each reagent. We also discuss the available probe types and necessary controls to accurately visualize gene expression. Finally, we review the most recent advances in FISH technology that facilitate both highly multiplexed experiments and signal amplification for individual targets. Taken together, this information will guide the methods development process for investigators that seek to perform FISH in organisms that lack documented or optimized protocols.
Collapse
Affiliation(s)
- Alexander P Young
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
| | - Daniel J Jackson
- Department of Geobiology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
| |
Collapse
|
15
|
Giri R, Papadopoulos DK, Posadas DM, Potluri HK, Tomancak P, Mani M, Carthew RW. Ordered patterning of the sensory system is susceptible to stochastic features of gene expression. eLife 2020; 9:e53638. [PMID: 32101167 PMCID: PMC7064346 DOI: 10.7554/elife.53638] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/25/2020] [Indexed: 01/23/2023] Open
Abstract
Sensory neuron numbers and positions are precisely organized to accurately map environmental signals in the brain. This precision emerges from biochemical processes within and between cells that are inherently stochastic. We investigated impact of stochastic gene expression on pattern formation, focusing on senseless (sens), a key determinant of sensory fate in Drosophila. Perturbing microRNA regulation or genomic location of sens produced distinct noise signatures. Noise was greatly enhanced when both sens alleles were present in homologous loci such that each allele was regulated in trans by the other allele. This led to disordered patterning. In contrast, loss of microRNA repression of sens increased protein abundance but not sensory pattern disorder. This suggests that gene expression stochasticity is a critical feature that must be constrained during development to allow rapid yet accurate cell fate resolution.
Collapse
Affiliation(s)
- Ritika Giri
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- NSF-Simons Center for Quantitative Biology, Northwestern UniversityEvanstonUnited States
| | | | - Diana M Posadas
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Hemanth K Potluri
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Pavel Tomancak
- Max Planck Institute of Cell Biology and GeneticsDresdenGermany
| | - Madhav Mani
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- NSF-Simons Center for Quantitative Biology, Northwestern UniversityEvanstonUnited States
- Department of Engineering Sciences and Applied Mathematics, Northwestern UniversityEvanstonUnited States
| | - Richard W Carthew
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- NSF-Simons Center for Quantitative Biology, Northwestern UniversityEvanstonUnited States
| |
Collapse
|
16
|
Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M. Nat Protoc 2020; 15:840-876. [PMID: 31969721 DOI: 10.1038/s41596-019-0269-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
Simultaneous observation of 3D chromatin organization and transcription at the single-cell level and with high spatial resolution may hold the key to unveiling the mechanisms regulating embryonic development, cell differentiation and even disease. We recently developed Hi-M, a technology that enables the sequential labeling, 3D imaging and localization of multiple genomic DNA loci, together with RNA expression, in single cells within whole, intact Drosophila embryos. Importantly, Hi-M enables simultaneous detection of RNA expression and chromosome organization without requiring sample unmounting and primary probe rehybridization. Here, we provide a step-by-step protocol describing the design of probes, the preparation of samples, the stable immobilization of embryos in microfluidic chambers, and the complete procedure for image acquisition. The combined RNA/DNA fluorescence in situ hybridization procedure takes 4-5 d, including embryo collection. In addition, we describe image analysis software to segment nuclei, detect genomic spots, correct for drift and produce Hi-M matrices. A typical Hi-M experiment takes 1-2 d to complete all rounds of labeling and imaging and 4 additional days for image analysis. This technology can be easily expanded to investigate cell differentiation in cultured cells or organization of chromatin within complex tissues.
Collapse
|
17
|
Lammers NC, Galstyan V, Reimer A, Medin SA, Wiggins CH, Garcia HG. Multimodal transcriptional control of pattern formation in embryonic development. Proc Natl Acad Sci U S A 2020; 117:836-847. [PMID: 31882445 PMCID: PMC6969519 DOI: 10.1073/pnas.1912500117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Predicting how interactions between transcription factors and regulatory DNA sequence dictate rates of transcription and, ultimately, drive developmental outcomes remains an open challenge in physical biology. Using stripe 2 of the even-skipped gene in Drosophila embryos as a case study, we dissect the regulatory forces underpinning a key step along the developmental decision-making cascade: the generation of cytoplasmic mRNA patterns via the control of transcription in individual cells. Using live imaging and computational approaches, we found that the transcriptional burst frequency is modulated across the stripe to control the mRNA production rate. However, we discovered that bursting alone cannot quantitatively recapitulate the formation of the stripe and that control of the window of time over which each nucleus transcribes even-skipped plays a critical role in stripe formation. Theoretical modeling revealed that these regulatory strategies (bursting and the time window) respond in different ways to input transcription factor concentrations, suggesting that the stripe is shaped by the interplay of 2 distinct underlying molecular processes.
Collapse
Affiliation(s)
| | - Vahe Galstyan
- Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, CA 91126
- Department of Physics, Columbia University, New York, NY 10027
| | - Armando Reimer
- Biophysics Graduate Group, University of California, Berkeley, CA 94720
| | - Sean A Medin
- Department of Physics, University of California, Berkeley, CA 94720
| | - Chris H Wiggins
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027;
- Data Science Institute, Columbia University, New York, NY 10027
- Department of Systems Biology, Columbia University, New York, NY 10027
- Department of Statistics, Columbia University, New York, NY 10027
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California, Berkeley, CA 94720;
- Department of Physics, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA 94720
| |
Collapse
|
18
|
Bandodkar PU, Al Asafen H, Reeves GT. Spatiotemporal control of gene expression boundaries using a feedforward loop. Dev Dyn 2020; 249:369-382. [PMID: 31925874 DOI: 10.1002/dvdy.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND A feedforward loop (FFL) is commonly observed in several biological networks. The FFL network motif has been mostly studied with respect to variation of the input signal in time, with only a few studies of FFL activity in a spatially distributed system such as morphogen-mediated tissue patterning. However, most morphogen gradients also evolve in time. RESULTS We studied the spatiotemporal behavior of a coherent FFL in two contexts: (a) a generic, oscillating morphogen gradient and (b) the dorsal-ventral patterning of the early Drosophila embryo by a gradient of the NF-κB homolog dorsal with its early target Twist. In both models, we found features in the dynamics of the intermediate node-phase difference and noise filtering-that were largely independent of the parameterization of the models, and thus were functions of the structure of the FFL itself. In the dorsal gradient model, we also found that proper target gene expression was not possible without including the effect of maternal pioneer factor Zelda. CONCLUSIONS An FFL buffers fluctuation to changes in the morphogen signal ensuring stable gene expression boundaries.
Collapse
Affiliation(s)
- Prasad U Bandodkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Hadel Al Asafen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Gregory T Reeves
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| |
Collapse
|
19
|
Noise in the Vertebrate Segmentation Clock Is Boosted by Time Delays but Tamed by Notch Signaling. Cell Rep 2019; 23:2175-2185.e4. [PMID: 29768214 PMCID: PMC5989725 DOI: 10.1016/j.celrep.2018.04.069] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 03/05/2018] [Accepted: 04/16/2018] [Indexed: 02/04/2023] Open
Abstract
Taming cell-to-cell variability in gene expression is critical for precise pattern formation during embryonic development. To investigate the source and buffering mechanism of expression variability, we studied a biological clock, the vertebrate segmentation clock, controlling the precise spatiotemporal patterning of the vertebral column. By counting single transcripts of segmentation clock genes in zebrafish, we show that clock genes have low RNA amplitudes and expression variability is primarily driven by gene extrinsic sources, which is suppressed by Notch signaling. We further show that expression noise surprisingly increases from the posterior progenitor zone to the anterior segmentation and differentiation zone. Our computational model reproduces the spatial noise profile by incorporating spatially increasing time delays in gene expression. Our results, suggesting that expression variability is controlled by the balance of time delays and cell signaling in a vertebrate tissue, will shed light on the accuracy of natural clocks in multi-cellular systems and inspire engineering of robust synthetic oscillators.
Collapse
|
20
|
Garcia HG, Berrocal A, Kim YJ, Martini G, Zhao J. Lighting up the central dogma for predictive developmental biology. Curr Top Dev Biol 2019; 137:1-35. [PMID: 32143740 DOI: 10.1016/bs.ctdb.2019.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although the last 30years have witnessed the mapping of the wiring diagrams of the gene regulatory networks that dictate cell fate and animal body plans, specific understanding building on such network diagrams that shows how DNA regulatory regions control gene expression lags far behind. These networks have yet to yield the predictive power necessary to, for example, calculate how the concentration dynamics of input transcription factors and DNA regulatory sequence prescribes output patterns of gene expression that, in turn, determine body plans themselves. Here, we argue that reaching a predictive understanding of developmental decision-making calls for an interplay between theory and experiment aimed at revealing how the regulation of the processes of the central dogma dictate network connections and how network topology guides cells toward their ultimate developmental fate. To make this possible, it is crucial to break free from the snapshot-based understanding of embryonic development facilitated by fixed-tissue approaches and embrace new technologies that capture the dynamics of developmental decision-making at the single cell level, in living embryos.
Collapse
Affiliation(s)
- Hernan G Garcia
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States; Department of Physics, University of California at Berkeley, Berkeley, CA, United States; Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States; Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, United States.
| | - Augusto Berrocal
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States
| | - Gabriella Martini
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, United States
| |
Collapse
|
21
|
Papadopoulos DK, Skouloudaki K, Engström Y, Terenius L, Rigler R, Zechner C, Vukojević V, Tomancak P. Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch. Development 2019; 146:dev.168179. [PMID: 30642837 PMCID: PMC6602345 DOI: 10.1242/dev.168179] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/20/2018] [Indexed: 01/13/2023]
Abstract
The variability in transcription factor concentration among cells is an important developmental determinant, yet how variability is controlled remains poorly understood. Studies of variability have focused predominantly on monitoring mRNA production noise. Little information exists about transcription factor protein variability, as this requires the use of quantitative methods with single-molecule sensitivity. Using Fluorescence Correlation Spectroscopy (FCS), we have characterized the concentration and variability of 14 endogenously tagged TFs in live Drosophila imaginal discs. For the Hox TF Antennapedia, we investigated whether protein variability results from random stochastic events or is developmentally regulated. We found that Antennapedia transitioned from low concentration/high variability early, to high concentration/low variability later, in development. FCS and temporally resolved genetic studies uncovered that Antennapedia itself is necessary and sufficient to drive a developmental regulatory switch from auto-activation to auto-repression, thereby reducing variability. This switch is controlled by progressive changes in relative concentrations of preferentially activating and repressing Antennapedia isoforms, which bind chromatin with different affinities. Mathematical modeling demonstrated that the experimentally supported auto-regulatory circuit can explain the increase of Antennapedia concentration and suppression of variability over time. Summary: Preferentially repressing and activating isoforms of the Hox transcription factor Antennapedia elicit a developmental regulatory switch from auto-activation to auto-repression that increases concentration and suppresses cell-to-cell variability over time.
Collapse
Affiliation(s)
| | - Kassiani Skouloudaki
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Ylva Engström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Lars Terenius
- Center for Molecular Medicine (CMM), Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Rudolf Rigler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden.,Laboratory of Biomedical Optics, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Christoph Zechner
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Vladana Vukojević
- Center for Molecular Medicine (CMM), Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Pavel Tomancak
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| |
Collapse
|
22
|
Stapel LC, Broaddus C, Vastenhouw NL. Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos. Methods Mol Biol 2018; 1649:143-162. [PMID: 29130195 DOI: 10.1007/978-1-4939-7213-5_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single molecule fluorescence in situ hybridization (smFISH) is a method to visualize single mRNA molecules. When combined with cellular and nuclear segmentation, transcripts can be assigned to different cellular compartments resulting in quantitative information on transcript levels at subcellular resolution. The use of smFISH in zebrafish has been limited by the lack of protocols and an automated image analysis pipeline for samples of multicellular organisms. Here we present a protocol for smFISH on zebrafish cryosections. The protocol includes a method to obtain high-quality sections of zebrafish embryos, an smFISH protocol optimized for zebrafish cryosections, and a user-friendly, automated analysis pipeline for cell segmentation and transcript detection. The software is freely available and can be used to analyze sections of any multicellular organism.
Collapse
Affiliation(s)
- L Carine Stapel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden, 01307, Germany
| | - Coleman Broaddus
- Center for Systems Biology Dresden, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden, 01307, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden, 01307, Germany.
| |
Collapse
|
23
|
Stapel LC, Zechner C, Vastenhouw NL. Uniform gene expression in embryos is achieved by temporal averaging of transcription noise. Genes Dev 2017; 31:1635-1640. [PMID: 28903980 PMCID: PMC5647934 DOI: 10.1101/gad.302935.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/16/2017] [Indexed: 11/25/2022]
Abstract
Here, Stapel et al. investigated how stochastic transcription activation can result in uniform expression during development of cellularized embryos. Using smFISH and mathematical modeling, the authors show that during zebrafish embryogenesis, transcription activation is stochastic due to (1) genes acquiring transcriptional competence at different times in different cells, (2) differences in cell cycle stage between cells, and (3) the stochastic nature of transcription. Transcription is often stochastic. This is seemingly incompatible with the importance of gene expression during development. Here we show that during zebrafish embryogenesis, transcription activation is stochastic due to (1) genes acquiring transcriptional competence at different times in different cells, (2) differences in cell cycle stage between cells, and (3) the stochastic nature of transcription. Initially, stochastic transcription causes large cell-to-cell differences in transcript levels. However, variability is reduced by lengthening cell cycles and the accumulation of transcription events in each cell. Temporal averaging might provide a general context in which to understand how embryos deal with stochastic transcription.
Collapse
Affiliation(s)
- L Carine Stapel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Christoph Zechner
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| |
Collapse
|
24
|
Dong P, Liu Z. Shaping development by stochasticity and dynamics in gene regulation. Open Biol 2017; 7:170030. [PMID: 28469006 PMCID: PMC5451542 DOI: 10.1098/rsob.170030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/05/2017] [Indexed: 12/12/2022] Open
Abstract
Animal development is orchestrated by spatio-temporal gene expression programmes that drive precise lineage commitment, proliferation and migration events at the single-cell level, collectively leading to large-scale morphological change and functional specification in the whole organism. Efforts over decades have uncovered two 'seemingly contradictory' mechanisms in gene regulation governing these intricate processes: (i) stochasticity at individual gene regulatory steps in single cells and (ii) highly coordinated gene expression dynamics in the embryo. Here we discuss how these two layers of regulation arise from the molecular and the systems level, and how they might interplay to determine cell fate and to control the complex body plan. We also review recent technological advancements that enable quantitative analysis of gene regulation dynamics at single-cell, single-molecule resolution. These approaches outline next-generation experiments to decipher general principles bridging gaps between molecular dynamics in single cells and robust gene regulations in the embryo.
Collapse
Affiliation(s)
- Peng Dong
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Dr, Ashburn, VA 20147, USA
| | - Zhe Liu
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Dr, Ashburn, VA 20147, USA
| |
Collapse
|
25
|
Yao J. Imaging Transcriptional Regulation of Eukaryotic mRNA Genes: Advances and Outlook. J Mol Biol 2017; 429:14-31. [DOI: 10.1016/j.jmb.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/03/2016] [Accepted: 11/10/2016] [Indexed: 01/07/2023]
|
26
|
Fukaya T, Lim B, Levine M. Enhancer Control of Transcriptional Bursting. Cell 2016; 166:358-368. [PMID: 27293191 DOI: 10.1016/j.cell.2016.05.025] [Citation(s) in RCA: 430] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/13/2016] [Accepted: 05/04/2016] [Indexed: 11/27/2022]
Abstract
Transcription is episodic, consisting of a series of discontinuous bursts. Using live-imaging methods and quantitative analysis, we examine transcriptional bursting in living Drosophila embryos. Different developmental enhancers positioned downstream of synthetic reporter genes produce transcriptional bursts with similar amplitudes and duration but generate very different bursting frequencies, with strong enhancers producing more bursts than weak enhancers. Insertion of an insulator reduces the number of bursts and the corresponding level of gene expression, suggesting that enhancer regulation of bursting frequency is a key parameter of gene control in development. We also show that linked reporter genes exhibit coordinated bursting profiles when regulated by a shared enhancer, challenging conventional models of enhancer-promoter looping.
Collapse
Affiliation(s)
- Takashi Fukaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Bomyi Lim
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
27
|
Noise propagation with interlinked feed-forward pathways. Sci Rep 2016; 6:23607. [PMID: 27029397 PMCID: PMC4814832 DOI: 10.1038/srep23607] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/10/2016] [Indexed: 12/05/2022] Open
Abstract
Functionally similar pathways are often seen in biological systems, forming feed-forward controls. The robustness in network motifs such as feed-forward loops (FFLs) has been reported previously. In this work, we studied noise propagation in a development network that has multiple interlinked FFLs. A FFL has the potential of asymmetric noise-filtering (i.e., it works at either the “ON” or the “OFF” state in the target gene). With multiple, interlinked FFLs, we show that the propagated noises are largely filtered regardless of the states in the input genes. The noise-filtering property of an interlinked FFL can be largely derived from that of the individual FFLs, and with interlinked FFLs, it is possible to filter noises in both “ON” and “OFF” states in the output. We demonstrated the noise filtering effect in the developmental regulatory network of Caenorhabditis elegans that controls the timing of distal tip cell (DTC) migration. The roles of positive feedback loops involving blmp-1 and the degradation regulation of DRE-1 also studied. Our analyses allow for better inference from network structures to noise-filtering properties, and provide insights into the mechanisms behind the precise DTC migration controls in space and time.
Collapse
|
28
|
Ferraro T, Lucas T, Clémot M, De Las Heras Chanes J, Desponds J, Coppey M, Walczak AM, Dostatni N. New methods to image transcription in living fly embryos: the insights so far, and the prospects. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 5:296-310. [PMID: 26894441 PMCID: PMC5021148 DOI: 10.1002/wdev.221] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/28/2015] [Accepted: 10/30/2015] [Indexed: 11/08/2022]
Abstract
The regulation of transcription is a fundamental process underlying the determination of cell identity and its maintenance during development. In the last decades, most of the transcription factors, which have to be expressed at the right place and at the right time for the proper development of the fly embryo, have been identified. However, mostly because of the lack of methods to visualize transcription as the embryo develops, their coordinated spatiotemporal dynamics remains largely unexplored. Efforts have been made to decipher the transcription process with single molecule resolution at the single cell level. Recently, the fluorescent labeling of nascent RNA in developing fly embryos allowed the direct visualization of ongoing transcription at single loci within each nucleus. Together with powerful imaging and quantitative data analysis, these new methods provide unprecedented insights into the temporal dynamics of the transcription process and its intrinsic noise. Focusing on the Drosophila embryo, we discuss how the detection of single RNA molecules enhanced our comprehension of the transcription process and we outline the potential next steps made possible by these new imaging tools. In combination with genetics and theoretical analysis, these new imaging methods will aid the search for the mechanisms responsible for the robustness of development. For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Teresa Ferraro
- Institut Curie, PSL Research University, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,UMR3664/UMR168/UMR8549, CNRS, Paris, France.,Ecole Normale Superieure, PSL Research University, Paris, France
| | - Tanguy Lucas
- Institut Curie, PSL Research University, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,UMR3664/UMR168/UMR8549, CNRS, Paris, France
| | - Marie Clémot
- Institut Curie, PSL Research University, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,UMR3664/UMR168/UMR8549, CNRS, Paris, France
| | - Jose De Las Heras Chanes
- Institut Curie, PSL Research University, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,UMR3664/UMR168/UMR8549, CNRS, Paris, France
| | - Jonathan Desponds
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,UMR3664/UMR168/UMR8549, CNRS, Paris, France.,Ecole Normale Superieure, PSL Research University, Paris, France
| | - Mathieu Coppey
- Institut Curie, PSL Research University, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,UMR3664/UMR168/UMR8549, CNRS, Paris, France
| | - Aleksandra M Walczak
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,UMR3664/UMR168/UMR8549, CNRS, Paris, France.,Ecole Normale Superieure, PSL Research University, Paris, France
| | - Nathalie Dostatni
- Institut Curie, PSL Research University, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,UMR3664/UMR168/UMR8549, CNRS, Paris, France
| |
Collapse
|
29
|
Quantitative Single-Embryo Profile of Drosophila Genome Activation and the Dorsal-Ventral Patterning Network. Genetics 2016; 202:1575-84. [PMID: 26896327 DOI: 10.1534/genetics.116.186783] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/04/2016] [Indexed: 02/01/2023] Open
Abstract
During embryonic development of Drosophila melanogaster, the maternal-to-zygotic transition (MZT) marks a significant and rapid turning point when zygotic transcription begins and control of development is transferred from maternally deposited transcripts. Characterizing the sequential activation of the genome during the MZT requires precise timing and a sensitive assay to measure changes in expression. We utilized the NanoString nCounter instrument, which directly counts messenger RNA transcripts without reverse transcription or amplification, to study >70 genes expressed along the dorsal-ventral (DV) axis of early Drosophila embryos, dividing the MZT into 10 time points. Transcripts were quantified for every gene studied at all time points, providing the first dataset of absolute numbers of transcripts during Drosophila development. We found that gene expression changes quickly during the MZT, with early nuclear cycle 14 (NC14) the most dynamic time for the embryo. twist is one of the most abundant genes in the entire embryo and we use mutants to quantitatively demonstrate how it cooperates with Dorsal to activate transcription and is responsible for some of the rapid changes in transcription observed during early NC14. We also uncovered elements within the gene regulatory network that maintain precise transcript levels for sets of genes that are spatiotemporally cotranscribed within the presumptive mesoderm or dorsal ectoderm. Using these new data, we show that a fine-scale, quantitative analysis of temporal gene expression can provide new insights into developmental biology by uncovering trends in gene networks, including coregulation of target genes and specific temporal input by transcription factors.
Collapse
|
30
|
Ali-Murthy Z, Kornberg TB. Bicoid gradient formation and function in the Drosophila pre-syncytial blastoderm. eLife 2016; 5. [PMID: 26883601 PMCID: PMC4786422 DOI: 10.7554/elife.13222] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/01/2016] [Indexed: 11/29/2022] Open
Abstract
Bicoid (Bcd) protein distributes in a concentration gradient that organizes the anterior/posterior axis of the Drosophila embryo. It has been understood that bcd RNA is sequestered at the anterior pole during oogenesis, is not translated until fertilization, and produces a protein gradient that functions in the syncytial blastoderm after 9–10 nuclear divisions. However, technical issues limited the sensitivity of analysis of pre-syncytial blastoderm embryos and precluded studies of oocytes after stage 13. We developed methods to analyze stage 14 oocytes and pre-syncytial blastoderm embryos, and found that stage 14 oocytes make Bcd protein, that bcd RNA and Bcd protein distribute in matching concentration gradients in the interior of nuclear cycle 2–6 embryos, and that Bcd regulation of target gene expression is apparent at nuclear cycle 7, two cycles prior to syncytial blastoderm. We discuss the implications for the generation and function of the Bcd gradient. DOI:http://dx.doi.org/10.7554/eLife.13222.001 As an embryo develops, a single cell transforms into a collection of different types of cells. One protein that is crucial for this process in fruit fly embryos is Bicoid. Thirty years ago, scientists discovered that Bicoid protein is concentrated at the head end of the embryo and gradually decreases in amount towards the rear end. This concentration gradient of Bicoid protein organizes the embryo body and regulates the expression of many genes, thus directing the cells to develop different identities. Several assumptions had been made about how this gradient is established. It was thought that in the unfertilized egg, the mRNA molecules that will be translated to produce Bicoid proteins are stored in an inactive state in the region of the egg that later develops into the embryo’s head. In the embryo, the mRNA molecules were believed to remain in the head region while being translated, with the newly formed proteins then gradually spreading from this site to create the Bicoid gradient. It was also thought that no Bicoid proteins are stored in the unfertilized egg. However, no known methods were sensitive enough to investigate these assumptions. Now, using newer and more sensitive methods, Ali-Murthy and Kornberg show that Bicoid protein is present in the unfertilized fruit fly egg in the same region as the mRNA molecules that make Bicoid. Furthermore, the Bicoid gradient forms when the embryo has fewer than 32 nuclei, much earlier in development than previously thought. The Bicoid protein also does not appear to spread passively towards the rear of the embryo, but is transported in a more orchestrated manner. Overall, Ali-Murthy and Kornberg’s results suggest that the early fruit fly embryo is more organized and actively regulated than had been previously understood. This paves the way for further studies that use sensitive techniques to investigate this early stage of development. DOI:http://dx.doi.org/10.7554/eLife.13222.002
Collapse
Affiliation(s)
- Zehra Ali-Murthy
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Thomas B Kornberg
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
31
|
Ferraro T, Esposito E, Mancini L, Ng S, Lucas T, Coppey M, Dostatni N, Walczak AM, Levine M, Lagha M. Transcriptional Memory in the Drosophila Embryo. Curr Biol 2016; 26:212-218. [PMID: 26748851 PMCID: PMC4970865 DOI: 10.1016/j.cub.2015.11.058] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/05/2015] [Accepted: 11/12/2015] [Indexed: 02/04/2023]
Abstract
Transmission of active transcriptional states from mother to daughter cells has the potential to foster precision in the gene expression programs underlying development. Such transcriptional memory has been specifically proposed to promote rapid reactivation of complex gene expression profiles after successive mitoses in Drosophila development [1]. By monitoring transcription in living Drosophila embryos, we provide the first evidence for transcriptional memory in animal development. We specifically monitored the activities of stochastically expressed transgenes in order to distinguish active and inactive mother cells and the behaviors of their daughter nuclei after mitosis. Quantitative analyses reveal that there is a 4-fold higher probability for rapid reactivation after mitosis when the mother experienced transcription. Moreover, memory nuclei activate transcription twice as fast as neighboring inactive mothers, thus leading to augmented levels of gene expression. We propose that transcriptional memory is a mechanism of precision, which helps coordinate gene activity during embryogenesis.
Collapse
Affiliation(s)
- Teresa Ferraro
- Institut Curie, PSL Research University, UMR 3664/UMR 168, Paris 75248, France; CNRS, UMR 3664/UMR 168/UMR 8549/UMR 8550, Paris 75248, France; Sorbonne Universités, UPMC University Paris 06, UMR 3664/UMR 168, Paris 75248, France; PSL, Ecole Normale Supérieure, UMR 8549, Paris 75005, France
| | - Emilia Esposito
- Molecular and Cellular Biology Department, GDD, University of California, Berkeley, Berkeley, CA 94720, USA; Lewis-Sigler Institute, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Laure Mancini
- Molecular and Cellular Biology Department, GDD, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sam Ng
- Molecular and Cellular Biology Department, GDD, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Tanguy Lucas
- Institut Curie, PSL Research University, UMR 3664/UMR 168, Paris 75248, France; CNRS, UMR 3664/UMR 168/UMR 8549/UMR 8550, Paris 75248, France; Sorbonne Universités, UPMC University Paris 06, UMR 3664/UMR 168, Paris 75248, France
| | - Mathieu Coppey
- Institut Curie, PSL Research University, UMR 3664/UMR 168, Paris 75248, France; CNRS, UMR 3664/UMR 168/UMR 8549/UMR 8550, Paris 75248, France; Sorbonne Universités, UPMC University Paris 06, UMR 3664/UMR 168, Paris 75248, France
| | - Nathalie Dostatni
- Institut Curie, PSL Research University, UMR 3664/UMR 168, Paris 75248, France; CNRS, UMR 3664/UMR 168/UMR 8549/UMR 8550, Paris 75248, France; Sorbonne Universités, UPMC University Paris 06, UMR 3664/UMR 168, Paris 75248, France
| | - Aleksandra M Walczak
- CNRS, UMR 3664/UMR 168/UMR 8549/UMR 8550, Paris 75248, France; PSL, Ecole Normale Supérieure, UMR 8549, Paris 75005, France
| | - Michael Levine
- Molecular and Cellular Biology Department, GDD, University of California, Berkeley, Berkeley, CA 94720, USA; Lewis-Sigler Institute, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Mounia Lagha
- Molecular and Cellular Biology Department, GDD, University of California, Berkeley, Berkeley, CA 94720, USA; IGMM, CNRS, UMR 5535, Montpellier 34293, France.
| |
Collapse
|
32
|
Stapel LC, Lombardot B, Broaddus C, Kainmueller D, Jug F, Myers EW, Vastenhouw NL. Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos. Development 2015; 143:540-6. [PMID: 26700682 DOI: 10.1242/dev.128918] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/14/2015] [Indexed: 12/25/2022]
Abstract
Analysis of differential gene expression is crucial for the study of cell fate and behavior during embryonic development. However, automated methods for the sensitive detection and quantification of RNAs at cellular resolution in embryos are lacking. With the advent of single-molecule fluorescence in situ hybridization (smFISH), gene expression can be analyzed at single-molecule resolution. However, the limited availability of protocols for smFISH in embryos and the lack of efficient image analysis pipelines have hampered quantification at the (sub)cellular level in complex samples such as tissues and embryos. Here, we present a protocol for smFISH on zebrafish embryo sections in combination with an image analysis pipeline for automated transcript detection and cell segmentation. We use this strategy to quantify gene expression differences between different cell types and identify differences in subcellular transcript localization between genes. The combination of our smFISH protocol and custom-made, freely available, analysis pipeline will enable researchers to fully exploit the benefits of quantitative transcript analysis at cellular and subcellular resolution in tissues and embryos.
Collapse
Affiliation(s)
- L Carine Stapel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01307, Germany
| | - Benoit Lombardot
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01307, Germany
| | - Coleman Broaddus
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01307, Germany
| | - Dagmar Kainmueller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01307, Germany
| | - Florian Jug
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01307, Germany
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01307, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01307, Germany
| |
Collapse
|
33
|
Svendsen PC, Ryu JR, Brook WJ. The expression of the T-box selector gene midline in the leg imaginal disc is controlled by both transcriptional regulation and cell lineage. Biol Open 2015; 4:1707-14. [PMID: 26581591 PMCID: PMC4736030 DOI: 10.1242/bio.013565] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Drosophila Tbx20 homologs midline and H15 act as selector genes for ventral fate in Drosophila legs. midline and H15 expression defines the ventral domain of the leg and the two genes are necessary and sufficient for the development of ventral fate. Ventral-specific expression of midline and H15 is activated by Wingless (Wg) and repressed by Decapentaplegic (Dpp). Here we identify VLE, a 5 kb enhancer that drives ventral specific expression in the leg disc that is very similar to midline expression. Subdivision of VLE identifies two regions that mediate both activation and repression and third region that only mediates repression. Loss- and gain-of-function genetic mosaic analysis shows that the activating and repressing regions respond to Wg and Dpp signaling respectively. All three repression regions depend on the activity of Mothers-against-decapentaplegic, a Drosophila r-Smad that mediates Dpp signaling, and respond to ectopic expression of the Dpp target genes optomoter-blind and Dorsocross 3. However, only one repression region is responsive to loss of schnurri, a co-repressor required for direct repression by Dpp-signaling. Thus, Dpp signaling restricts midline expression through both direct repression and through the activation of downstream repressors. We also find that midline and H15 expression are both subject to cross-repression and feedback inhibition. Finally, a lineage analysis indicates that ventral midline-expressing cells and dorsal omb-expressing cells do not mix during development. Together this data indicates that the ventral-specific expression of midline results from both transcriptional regulation and from a lack of cell-mixing between dorsal and ventral cells.
Collapse
Affiliation(s)
- Pia C Svendsen
- Genes and Development Research Group, Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary T2N4N1, Alberta, Canada
| | - Jae-Ryeon Ryu
- Genes and Development Research Group, Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary T2N4N1, Alberta, Canada
| | - William J Brook
- Genes and Development Research Group, Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary T2N4N1, Alberta, Canada
| |
Collapse
|
34
|
Choubey S, Kondev J, Sanchez A. Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules. PLoS Comput Biol 2015; 11:e1004345. [PMID: 26544860 PMCID: PMC4636183 DOI: 10.1371/journal.pcbi.1004345] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/19/2015] [Indexed: 12/18/2022] Open
Abstract
Deciphering how the regulatory DNA sequence of a gene dictates its expression in response to intra and extracellular cues is one of the leading challenges in modern genomics. The development of novel single-cell sequencing and imaging techniques, as well as a better exploitation of currently available single-molecule imaging techniques, provides an avenue to interrogate the process of transcription and its dynamics in cells by quantifying the number of RNA polymerases engaged in the transcription of a gene (or equivalently the number of nascent RNAs) at a given moment in time. In this paper, we propose that measurements of the cell-to-cell variability in the number of nascent RNAs provide a mostly unexplored method for deciphering mechanisms of transcription initiation in cells. We propose a simple kinetic model of transcription initiation and elongation from which we calculate nascent RNA copy-number fluctuations. To demonstrate the usefulness of this approach, we test our theory against published nascent RNA data for twelve constitutively expressed yeast genes. Rather than transcription being initiated through a single rate limiting step, as it had been previously proposed, our single-cell analysis reveals the presence of at least two rate limiting steps. Surprisingly, half of the genes analyzed have nearly identical rates of transcription initiation, suggesting a common mechanism. Our analytical framework can be used to extract quantitative information about dynamics of transcription from single-cell sequencing data, as well as from single-molecule imaging and electron micrographs of fixed cells, and provides the mathematical means to exploit the quantitative power of these technologies.
Collapse
Affiliation(s)
- Sandeep Choubey
- Department of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Alvaro Sanchez
- Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
35
|
Combining protein and mRNA quantification to decipher transcriptional regulation. Nat Methods 2015; 12:739-42. [PMID: 26098021 PMCID: PMC4521975 DOI: 10.1038/nmeth.3446] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 05/05/2015] [Indexed: 11/23/2022]
Abstract
We combine immunofluorescence and single-molecule fluorescence in situ hybridization (smFISH), followed by automated image analysis, to quantify the concentration of nuclear transcription factors, number of transcription factors bound, and number of nascent mRNAs synthesized at individual gene loci. A theoretical model is used to decipher how transcription-factor binding modulates the stochastic kinetics of mRNA production. We demonstrate this approach by examining the regulation of hunchback in the early Drosophila embryo.
Collapse
|
36
|
Bahar Halpern K, Tanami S, Landen S, Chapal M, Szlak L, Hutzler A, Nizhberg A, Itzkovitz S. Bursty gene expression in the intact mammalian liver. Mol Cell 2015; 58:147-56. [PMID: 25728770 DOI: 10.1016/j.molcel.2015.01.027] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 01/06/2015] [Accepted: 01/20/2015] [Indexed: 10/23/2022]
Abstract
Bursts of nascent mRNA have been shown to lead to substantial cell-cell variation in unicellular organisms, facilitating diverse responses to environmental challenges. It is unknown whether similar bursts and gene-expression noise occur in mammalian tissues. To address this, we combine single molecule transcript counting with dual-color labeling and quantification of nascent mRNA to characterize promoter states, transcription rates, and transcript lifetimes in the intact mouse liver. We find that liver gene expression is highly bursty, with promoters stochastically switching between transcriptionally active and inactive states. Promoters of genes with short mRNA lifetimes are active longer, facilitating rapid response while reducing burst-associated noise. Moreover, polyploid hepatocytes exhibit less noise than diploid hepatocytes, suggesting a possible benefit to liver polyploidy. Thus, temporal averaging and liver polyploidy dampen the intrinsic variability associated with transcriptional bursts. Our approach can be used to study transcriptional bursting in diverse mammalian tissues.
Collapse
Affiliation(s)
- Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Sivan Tanami
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shanie Landen
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Michal Chapal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Liran Szlak
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Anat Hutzler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Anna Nizhberg
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
| |
Collapse
|
37
|
Rao MK, Matsumoto Y, Richardson ME, Panneerdoss S, Bhardwaj A, Ward JM, Shanker S, Bettegowda A, Wilkinson MF. Hormone-induced and DNA demethylation-induced relief of a tissue-specific and developmentally regulated block in transcriptional elongation. J Biol Chem 2014; 289:35087-101. [PMID: 25331959 DOI: 10.1074/jbc.m114.615435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Genome-wide studies have revealed that genes commonly have a high density of RNA polymerase II just downstream of the transcription start site. This has raised the possibility that genes are commonly regulated by transcriptional elongation, but this remains largely untested in vivo, particularly in vertebrates. Here, we show that the proximal promoter from the Rhox5 homeobox gene recruits polymerase II and begins elongating in all tissues and cell lines that we tested, but it only completes elongation in a tissue-specific and developmentally regulated manner. Relief of the elongation block is associated with recruitment of the elongation factor P-TEFb, the co-activator GRIP1, the chromatin remodeling factor BRG1, and specific histone modifications. We provide evidence that two mechanisms relieve the elongation block at the proximal promoter: demethylation and recruitment of androgen receptor. Together, our findings support a model in which promoter proximal pausing helps confer tissue-specific and developmental gene expression through a mechanism regulated by DNA demethylation-dependent nuclear hormone receptor recruitment.
Collapse
Affiliation(s)
- Manjeet K Rao
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Greehey Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Yuiko Matsumoto
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Marcy E Richardson
- the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Subbarayalu Panneerdoss
- the Greehey Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Anjana Bhardwaj
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Jacqueline M Ward
- the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Sreenath Shanker
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Anilkumar Bettegowda
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Miles F Wilkinson
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| |
Collapse
|
38
|
Analytic approaches to stochastic gene expression in multicellular systems. Biophys J 2014; 105:2629-40. [PMID: 24359735 DOI: 10.1016/j.bpj.2013.10.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 10/16/2013] [Indexed: 11/22/2022] Open
Abstract
Deterministic thermodynamic models of the complex systems, which control gene expression in metazoa, are helping researchers identify fundamental themes in the regulation of transcription. However, quantitative single cell studies are increasingly identifying regulatory mechanisms that control variability in expression. Such behaviors cannot be captured by deterministic models and are poorly suited to contemporary stochastic approaches that rely on continuum approximations, such as Langevin methods. Fortunately, theoretical advances in the modeling of transcription have assembled some general results that can be readily applied to systems being explored only through a deterministic approach. Here, I review some of the recent experimental evidence for the importance of genetically regulating stochastic effects during embryonic development and discuss key results from Markov theory that can be used to model this regulation. I then discuss several pairs of regulatory mechanisms recently investigated through a Markov approach. In each case, a deterministic treatment predicts no difference between the mechanisms, but the statistical treatment reveals the potential for substantially different distributions of transcriptional activity. In this light, features of gene regulation that seemed needlessly complex evolutionary baggage may be appreciated for their key contributions to reliability and precision of gene expression.
Collapse
|
39
|
Gregor T, Garcia HG, Little SC. The embryo as a laboratory: quantifying transcription in Drosophila. Trends Genet 2014; 30:364-75. [PMID: 25005921 DOI: 10.1016/j.tig.2014.06.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/08/2014] [Accepted: 06/16/2014] [Indexed: 11/16/2022]
Abstract
Transcriptional regulation of gene expression is fundamental to most cellular processes, including determination of cellular fates. Quantitative studies of transcription in cultured cells have led to significant advances in identifying mechanisms underlying transcriptional control. Recent progress allowed implementation of these same quantitative methods in multicellular organisms to ask how transcriptional regulation unfolds both in vivo and at the single molecule level in the context of embryonic development. Here we review some of these advances in early Drosophila development, which bring the embryo on par with its single celled counterparts. In particular, we discuss progress in methods to measure mRNA and protein distributions in fixed and living embryos, and we highlight some initial applications that lead to fundamental new insights about molecular transcription processes. We end with an outlook on how to further exploit the unique advantages that come with investigating transcriptional control in the multicellular context of development.
Collapse
Affiliation(s)
- Thomas Gregor
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 085444, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Hernan G Garcia
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 085444, USA
| | - Shawn C Little
- Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
40
|
Ji N, Middelkoop TC, Mentink RA, Betist MC, Tonegawa S, Mooijman D, Korswagen HC, van Oudenaarden A. Feedback control of gene expression variability in the Caenorhabditis elegans Wnt pathway. Cell 2014; 155:869-80. [PMID: 24209624 DOI: 10.1016/j.cell.2013.09.060] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 07/26/2013] [Accepted: 09/27/2013] [Indexed: 12/13/2022]
Abstract
Variability in gene expression contributes to phenotypic heterogeneity even in isogenic populations. Here, we used the stereotyped, Wnt signaling-dependent development of the Caenorhabditis elegans Q neuroblast to probe endogenous mechanisms that control gene expression variability. We found that the key Hox gene that orients Q neuroblast migration exhibits increased gene expression variability in mutants in which Wnt pathway activity has been perturbed. Distinct features of the gene expression distributions prompted us on a systematic search for regulatory interactions, revealing a network of interlocked positive and negative feedback loops. Interestingly, positive feedback appeared to cooperate with negative feedback to reduce variability while keeping the Hox gene expression at elevated levels. A minimal model correctly predicts the increased gene expression variability across mutants. Our results highlight the influence of gene network architecture on expression variability and implicate feedback regulation as an effective mechanism to ensure developmental robustness.
Collapse
Affiliation(s)
- Ni Ji
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Wunderlich Z, Bragdon MD, DePace AH. Comparing mRNA levels using in situ hybridization of a target gene and co-stain. Methods 2014; 68:233-41. [PMID: 24434507 DOI: 10.1016/j.ymeth.2014.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/02/2014] [Indexed: 11/29/2022] Open
Abstract
In situ hybridization is an important technique for measuring the spatial expression patterns of mRNA in cells, tissues, and whole animals. However, mRNA levels cannot be compared across experiments using typical protocols. Here we present a semi-quantitative method to compare mRNA levels of a gene across multiple samples. This method yields an estimate of the error in the measurement to allow statistical comparison. Our method uses a typical in situ hybridization protocol to stain for a target gene and an internal standard, which we refer to as a co-stain. As a proof of concept, we apply this method to multiple lines of transgenic Drosophila embryos, harboring constructs that express reporter genes to different levels. We generated this test set by mutating enhancer sequences to contain different numbers of binding sites for Zelda, a transcriptional activator. We demonstrate that using a co-stain with in situ hybridization is an effective method to compare mRNA levels across samples. This method requires only minor modifications to existing in situ hybridization protocols and uses straightforward analysis techniques. This strategy can be broadly applied to detect quantitative, spatially resolved changes in mRNA levels.
Collapse
Affiliation(s)
- Zeba Wunderlich
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA.
| | - Meghan D Bragdon
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA.
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA.
| |
Collapse
|
42
|
Sanchez A, Golding I. Genetic determinants and cellular constraints in noisy gene expression. Science 2013; 342:1188-93. [PMID: 24311680 DOI: 10.1126/science.1242975] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In individual cells, transcription is a random process obeying single-molecule kinetics. Often, it occurs in a bursty, intermittent manner. The frequency and size of these bursts affect the magnitude of temporal fluctuations in messenger RNA and protein content within a cell, creating variation or "noise" in gene expression. It is still unclear to what degree transcriptional kinetics are specific to each gene and determined by its promoter sequence. Alternative scenarios have been proposed, in which the kinetics of transcription are governed by cellular constraints and follow universal rules across the genome. Evidence from genome-wide noise studies and from systematic perturbations of promoter sequences suggest that both scenarios-namely gene-specific versus genome-wide regulation of transcription kinetics-may be present to different degrees in bacteria, yeast, and animal cells.
Collapse
Affiliation(s)
- Alvaro Sanchez
- The Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA
| | | |
Collapse
|
43
|
Lagha M, Bothma JP, Esposito E, Ng S, Stefanik L, Tsui C, Johnston J, Chen K, Gilmour DS, Zeitlinger J, Levine MS. Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo. Cell 2013; 153:976-87. [PMID: 23706736 DOI: 10.1016/j.cell.2013.04.045] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 02/23/2013] [Accepted: 04/22/2013] [Indexed: 11/18/2022]
Abstract
Paused RNA polymerase (Pol II) is a pervasive feature of Drosophila embryos and mammalian stem cells, but its role in development is uncertain. Here, we demonstrate that a spectrum of paused Pol II determines the "time to synchrony"-the time required to achieve coordinated gene expression across the cells of a tissue. To determine whether synchronous patterns of gene activation are significant in development, we manipulated the timing of snail expression, which controls the coordinated invagination of ∼1,000 mesoderm cells during gastrulation. Replacement of the strongly paused snail promoter with moderately paused or nonpaused promoters causes stochastic activation of snail expression and increased variability of mesoderm invagination. Computational modeling of the dorsal-ventral patterning network recapitulates these variable and bistable gastrulation profiles and emphasizes the importance of timing of gene activation in development. We conclude that paused Pol II and transcriptional synchrony are essential for coordinating cell behavior during morphogenesis.
Collapse
Affiliation(s)
- Mounia Lagha
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|