1
|
Ren H, Ou Q, Pu Q, Lou Y, Yang X, Han Y, Liu S. Comprehensive Review on Bimolecular Fluorescence Complementation and Its Application in Deciphering Protein-Protein Interactions in Cell Signaling Pathways. Biomolecules 2024; 14:859. [PMID: 39062573 PMCID: PMC11274695 DOI: 10.3390/biom14070859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Signaling pathways are responsible for transmitting information between cells and regulating cell growth, differentiation, and death. Proteins in cells form complexes by interacting with each other through specific structural domains, playing a crucial role in various biological functions and cell signaling pathways. Protein-protein interactions (PPIs) within cell signaling pathways are essential for signal transmission and regulation. The spatiotemporal features of PPIs in signaling pathways are crucial for comprehending the regulatory mechanisms of signal transduction. Bimolecular fluorescence complementation (BiFC) is one kind of imaging tool for the direct visualization of PPIs in living cells and has been widely utilized to uncover novel PPIs in various organisms. BiFC demonstrates significant potential for application in various areas of biological research, drug development, disease diagnosis and treatment, and other related fields. This review systematically summarizes and analyzes the technical advancement of BiFC and its utilization in elucidating PPIs within established cell signaling pathways, including TOR, PI3K/Akt, Wnt/β-catenin, NF-κB, and MAPK. Additionally, it explores the application of this technology in revealing PPIs within the plant hormone signaling pathways of ethylene, auxin, Gibberellin, and abscisic acid. Using BiFC in conjunction with CRISPR-Cas9, live-cell imaging, and ultra-high-resolution microscopy will enhance our comprehension of PPIs in cell signaling pathways.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Shiping Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China; (H.R.); (Q.O.); (Q.P.); (Y.L.); (X.Y.); (Y.H.)
| |
Collapse
|
2
|
Berr A, Chabouté ME. The art of painting chromosome loops. QUANTITATIVE PLANT BIOLOGY 2023; 4:e11. [PMID: 37901685 PMCID: PMC10600566 DOI: 10.1017/qpb.2023.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023]
Abstract
How to get a metre of DNA into a tiny space while preserving its functional characteristics? This question seems easy to pose, but the answer is far from being trivial. Facing this riddle, salvation came from technical improvements in microscopy and in situ hybridisation techniques applied to cytogenetics. Here, we would like to look into the past at one of these pure cytogenetics articles that makes a breakthrough in addressing this question in plant science. Our choice fell on the work published two decades ago by Fransz et al. (2002). Besides the elegant manner in which DNA probes were organised to bring into light the out-looping arrangement of interphase chromosomes in Arabidopsis thaliana nuclei, this article perfectly illustrates that painting is not reserved to the fine art. As for whether emotional expression prioritised by artists can sometimes hide behind scientific empirical evidence, there is only a small step to make to the general case.
Collapse
Affiliation(s)
- Alexandre Berr
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
| |
Collapse
|
3
|
Okamoto K, Fujita H, Okada Y, Shinkai S, Onami S, Abe K, Fujimoto K, Sasaki K, Shioi G, Watanabe TM. Single-molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance. EMBO J 2023; 42:e112305. [PMID: 37609947 PMCID: PMC10505915 DOI: 10.15252/embj.2022112305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 08/24/2023] Open
Abstract
Nanog and Oct4 are core transcription factors that form part of a gene regulatory network to regulate hundreds of target genes for pluripotency maintenance in mouse embryonic stem cells (ESCs). To understand their function in the pluripotency maintenance, we visualised and quantified the dynamics of single molecules of Nanog and Oct4 in a mouse ESCs during pluripotency loss. Interestingly, Nanog interacted longer with its target loci upon reduced expression or at the onset of differentiation, suggesting a feedback mechanism to maintain the pluripotent state. The expression level and interaction time of Nanog and Oct4 correlate with their fluctuation and interaction frequency, respectively, which in turn depend on the ESC differentiation status. The DNA viscoelasticity near the Oct4 target locus remained flexible during differentiation, supporting its role either in chromatin opening or a preferred binding to uncondensed chromatin regions. Based on these results, we propose a new negative feedback mechanism for pluripotency maintenance via the DNA condensation state-dependent interplay of Nanog and Oct4.
Collapse
Affiliation(s)
- Kazuko Okamoto
- Laboratory for Comprehensive BioimagingRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
- Amphibian Research CenterHiroshima UniversityHiroshimaJapan
| | - Hideaki Fujita
- Department of Stem Cell Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHigashi‐HiroshimaJapan
| | - Yasushi Okada
- Laboratory for Cell Polarity RegulationRIKEN Center for Biosystems Dynamics Research (BDR)OsakaJapan
- Department of Cell BiologyGraduate School of Medicine, The University of TokyoTokyoJapan
- Department of PhysicsUniversal Biology Institute (UBI)Graduate School of Science, The University of TokyoTokyoJapan
- International Research Center for Neurointelligence (WPI‐IRCN)Institutes for Advanced Study, The University of TokyoTokyoJapan
| | - Soya Shinkai
- Laboratory for Developmental DynamicsRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD)Hiroshima UniversityHiroshimaJapan
| | - Shuichi Onami
- Laboratory for Developmental DynamicsRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome DynamicsRIKEN BioResource Research Center (BRC)TsukubaJapan
| | - Kenta Fujimoto
- Department of Stem Cell Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHigashi‐HiroshimaJapan
| | - Kensuke Sasaki
- Laboratory for Comprehensive BioimagingRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Go Shioi
- Laboratory for Comprehensive BioimagingRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive BioimagingRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
- Department of Stem Cell Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHigashi‐HiroshimaJapan
| |
Collapse
|
4
|
Lu S, Hou Y, Zhang XE, Gao Y. Live cell imaging of DNA and RNA with fluorescent signal amplification and background reduction techniques. Front Cell Dev Biol 2023; 11:1216232. [PMID: 37342234 PMCID: PMC10277805 DOI: 10.3389/fcell.2023.1216232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Illuminating DNA and RNA dynamics in live cell can elucidate their life cycle and related biochemical activities. Various protocols have been developed for labeling the regions of interest in DNA and RNA molecules with different types of fluorescent probes. For example, CRISPR-based techniques have been extensively used for imaging genomic loci. However, some DNA and RNA molecules can still be difficult to tag and observe dynamically, such as genomic loci in non-repetitive regions. In this review, we will discuss the toolbox of techniques and methodologies that have been developed for imaging DNA and RNA. We will also introduce optimized systems that provide enhanced signal intensity or low background fluorescence for those difficult-to-tag molecules. These strategies can provide new insights for researchers when designing and using techniques to visualize DNA or RNA molecules.
Collapse
Affiliation(s)
- Song Lu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yu Hou
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| |
Collapse
|
5
|
Balasooriya GI, Spector DL. Allele pairing at Sun1-enriched domains at the nuclear periphery via T1A3 tandem DNA repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536031. [PMID: 37066204 PMCID: PMC10104147 DOI: 10.1101/2023.04.07.536031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Spatiotemporal gene regulation is fundamental to the biology of diploid cells. Therefore, effective communication between two alleles and their geometry in the nucleus is important. However, the mechanism that fine-tunes the expression from each of the two alleles of an autosome is enigmatic. Establishing an allele-specific gene expression visualization system in living cells, we show that alleles of biallelically expressed Cth and Ttc4 genes are paired prior to acquiring monoallelic expression. We found that active alleles of monoallelic genes are preferentially localized at Sun1-enriched domains at the nuclear periphery. These peripherally localized active DNA loci are enriched with adenine-thymidine-rich tandem repeats that interact with Hnrnpd and reside in a Hi-C-defined A compartment within the B compartment. Our results demonstrate the biological significance of T 1 A 3 tandem repeat sequences in genome organization and how the regulation of gene expression, at the level of individual alleles, relates to their spatial arrangement.
Collapse
|
6
|
Chang L, Li M, Shao S, Li C, Ai S, Xue B, Hou Y, Zhang Y, Li R, Fan X, He A, Li C, Sun Y. Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells. Protein Cell 2022; 13:258-280. [PMID: 33155082 PMCID: PMC8934373 DOI: 10.1007/s13238-020-00794-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood. Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to detachment of lamina-associated domains (LADs) from the nuclear periphery accompanied with global chromatin redistribution and decompaction. Consequently, the inter-chromosomal as well as inter-compartment interactions are increased, but the structure of topologically associating domains (TADs) is not affected. Using live-cell genomic loci tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm. Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, chromatin compaction, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.
Collapse
Affiliation(s)
- Lei Chang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510530 China
| | - Mengfan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Shipeng Shao
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Chen Li
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Shanshan Ai
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yiwen Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Ruifeng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Xiaoying Fan
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510530 China
| | - Aibin He
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
- Center for Statistical Science, Peking University, Beijing, 100871 China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| |
Collapse
|
7
|
A Protocol for Studying Transcription Factor Dynamics Using Fast Single-Particle Tracking and Spot-On Model-Based Analysis. Methods Mol Biol 2022; 2458:151-174. [PMID: 35103967 DOI: 10.1007/978-1-0716-2140-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Single-particle tracking (SPT) makes it possible to directly observe single protein diffusion dynamics in living cells over time. Thus, SPT has emerged as a powerful method to quantify the dynamics of nuclear proteins such as transcription factors (TFs). Here, we provide a protocol for conducting and analyzing SPT experiments with a focus on fast tracking ("fastSPT") of TFs in mammalian cells. First, we explore how to engineer and prepare cells for SPT experiments. Next, we examine how to optimize SPT experiments by imaging at low densities to minimize tracking errors and by using stroboscopic excitation to minimize motion-blur. Next, we discuss how to convert raw SPT data into single-particle trajectories. Finally, we illustrate how to analyze these trajectories using the kinetic modeling package Spot-On. We discuss how to use Spot-On to fit histograms of displacements and extract useful information such as the fraction of TFs that are bound and freely diffusing, and their associated diffusion coefficients.
Collapse
|
8
|
Wang Z, Deng W. Dynamic transcription regulation at the single-molecule level. Dev Biol 2021; 482:67-81. [PMID: 34896367 DOI: 10.1016/j.ydbio.2021.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 02/07/2023]
Abstract
Cell fate changes during development, differentiation, and reprogramming are largely controlled at the transcription level. The DNA-binding transcription factors (TFs) often act in a combinatorial fashion to alter chromatin states and drive cell type-specific gene expression. Recent advances in fluorescent microscopy technologies have enabled direct visualization of biomolecules involved in the process of transcription and its regulatory events at the single-molecule level in living cells. Remarkably, imaging and tracking individual TF molecules at high temporal and spatial resolution revealed that they are highly dynamic in searching and binding cognate targets, rather than static and binding constantly. In combination with investigation using techniques from biochemistry, structure biology, genetics, and genomics, a more well-rounded view of transcription regulation is emerging. In this review, we briefly cover the technical aspects of live-cell single-molecule imaging and focus on the biological relevance and interpretation of the single-molecule dynamic features of transcription regulatory events observed in the native chromatin environment of living eukaryotic cells. We also discuss how these dynamic features might shed light on mechanistic understanding of transcription regulation.
Collapse
Affiliation(s)
- Zuhui Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences (CLS), Peking University, Beijing, 100871, China; School of Life Sciences, Peking University, Beijing, 100871, China.
| |
Collapse
|
9
|
Podh NK, Paliwal S, Dey P, Das A, Morjaria S, Mehta G. In-vivo Single-Molecule Imaging in Yeast: Applications and Challenges. J Mol Biol 2021; 433:167250. [PMID: 34537238 DOI: 10.1016/j.jmb.2021.167250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Single-molecule imaging has gained momentum to quantify the dynamics of biomolecules in live cells, as it provides direct real-time measurements of various cellular activities under their physiological environment. Yeast, a simple and widely used eukaryote, serves as a good model system to quantify single-molecule dynamics of various cellular processes because of its low genomic and cellular complexities, as well as its facile ability to be genetically manipulated. In the past decade, significant developments have been made regarding the intracellular labeling of biomolecules (proteins, mRNA, fatty acids), the microscopy setups to visualize single-molecules and capture their fast dynamics, and the data analysis pipelines to interpret such dynamics. In this review, we summarize the current state of knowledge for the single-molecule imaging in live yeast cells to provide a ready reference for beginners. We provide a comprehensive table to demonstrate how various labs tailored the imaging regimes and data analysis pipelines to estimate various biophysical parameters for a variety of biological processes. Lastly, we present current challenges and future directions for developing better tools and resources for single-molecule imaging in live yeast cells.
Collapse
Affiliation(s)
- Nitesh Kumar Podh
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India. https://twitter.com/@PodhNitesh
| | - Sheetal Paliwal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India. https://twitter.com/@Sheetal62666036
| | - Partha Dey
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India. https://twitter.com/@ParthaD63416958
| | - Ayan Das
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India. https://twitter.com/@AyanDas76471821
| | - Shruti Morjaria
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, The Maharaja Sayajirao University of Baroda, Vadodara, India. https://twitter.com/@shruti_morjaria
| | - Gunjan Mehta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India.
| |
Collapse
|
10
|
Mazzocca M, Colombo E, Callegari A, Mazza D. Transcription factor binding kinetics and transcriptional bursting: What do we really know? Curr Opin Struct Biol 2021; 71:239-248. [PMID: 34481381 DOI: 10.1016/j.sbi.2021.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022]
Abstract
In eukaryotes, transcription is a discontinuous process with mRNA being generated in bursts, after the binding of transcription factors (TFs) to regulatory elements on the genome. Live-cell single-molecule microscopy has highlighted that transcriptional bursting can be controlled by tuning TF/DNA binding kinetics. Yet the timescales of these two processes seem disconnected with TF/DNA interactions typically lasting orders of magnitude shorter than transcriptional bursts. To test models that could reconcile these discrepancies, reliable measurements of TF binding kinetics are needed, also accounting for the current limitations in performing these single-molecule measurements at specific regulatory elements. Here, we review the recent studies linking TF binding kinetics to transcriptional bursting and outline some current and future challenges that need to be addressed to provide a microscopic description of transcriptional regulation kinetics.
Collapse
Affiliation(s)
- Matteo Mazzocca
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Emanuele Colombo
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | | | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.
| |
Collapse
|
11
|
Xue B, Zhou C, Qin Y, Li Y, Sun Y, Chang L, Shao S, Li Y, Zhang M, Sun C, He R, Peter Su Q, Sun Y. PN-ImTLSM facilitates high-throughput low background single-molecule localization microscopy deep in the cell. BIOPHYSICS REPORTS 2021; 7:313-325. [PMID: 37287761 PMCID: PMC10233473 DOI: 10.52601/bpr.2021.210014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/15/2021] [Indexed: 06/09/2023] Open
Abstract
When imaging the nucleus structure of a cell, the out-of-focus fluorescence acts as background and hinders the detection of weak signals. Light-sheet fluorescence microscopy (LSFM) is a wide-field imaging approach which has the best of both background removal and imaging speed. However, the commonly adopted orthogonal excitation/detection scheme is hard to be applied to single-cell imaging due to steric hindrance. For LSFMs capable of high spatiotemporal single-cell imaging, the complex instrument design and operation largely limit their throughput of data collection. Here, we propose an approach for high-throughput background-free fluorescence imaging of single cells facilitated by the Immersion Tilted Light Sheet Microscopy (ImTLSM). ImTLSM is based on a light-sheet projected off the optical axis of a water immersion objective. With the illumination objective and the detection objective placed opposingly, ImTLSM can rapidly patrol and optically section multiple individual cells while maintaining single-molecule detection sensitivity and resolution. Further, the simplicity and robustness of ImTLSM in operation and maintenance enables high-throughput image collection to establish background removal datasets for deep learning. Using a deep learning model to train the mapping from epi-illumination images to ImTLSM illumination images, namely PN-ImTLSM, we demonstrated cross-modality fluorescence imaging, transforming the epi-illumination image to approach the background removal performance obtained with ImTLSM. We demonstrated that PN-ImTLSM can be generalized to large-field homogeneous illumination imaging, thereby further improving the imaging throughput. In addition, compared to commonly used background removal methods, PN-ImTLSM showed much better performance for areas where the background intensity changes sharply in space, facilitating high-density single-molecule localization microscopy. In summary, PN-ImTLSM paves the way for background-free fluorescence imaging on ordinary inverted microscopes.
Collapse
Affiliation(s)
- Boxin Xue
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Caiwei Zhou
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yizhi Qin
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yongzheng Li
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yuao Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Lei Chang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Shipeng Shao
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Yongliang Li
- Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Chaoying Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Renxi He
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Qian Peter Su
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- School of Future Technology, Peking University, Beijing 100871, China
| |
Collapse
|
12
|
Vu XH, Dien ND, Pham TTH, Jaffiol R, Vézy C, Ca NX, Trang TT. Evaluation of diffusion coefficient of P-glycoprotein molecules labeled with green fluorescent protein in living cell membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183721. [PMID: 34352241 DOI: 10.1016/j.bbamem.2021.183721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022]
Abstract
The movement of individual molecules inside living cells has recently been resolved by single particles tracking (SPT) method which is a powerful tool for probing the organization and dynamics of the plasma membrane constituents. Effective treatment of metastatic cancers requires the toxic chemotherapy, however this therapy leads to the multidrug resistance phenomenon of the cancer cells, in which the cancer cells resist simultaneously to different drugs with different targets and chemical structures. P-glycoprotein molecules which are responsible for multidrug resistance of many cancer cells have been studied by cancer biologists during past haft of century. Recently, advances in laser and detector technologies have enabled single fluorophores to be visualized in aqueous solution. The development of the total internal reflection fluorescent microscope (TIRFM) provided means to monitor dynamic molecular localization in living cells. In this paper, P-glycoproteins (PGP) were labeled with green fluorescent protein (GFP) in living cell membrane of Madin-Darby canine kidney (MDCK) and the TIRFM method was used to characterize the dynamics of individual protein molecules on the surface of living cells. An evanescent field was produced by a totally internally reflected and a laser beam was illuminated the glass-water interface. GFP-PGP proteins that entered the evanescent field appeared as individual spots of light which were slighter than background fluorescence. We obtained high-resolution images and diffusion maps of membrane proteins on cell surface and showed the local diffusion properties of specific proteins on single cells. We also determined the diffusion coefficient, the mean square displacement and the average velocity of the tracked particles, as well as the heterogeneity of the cell environment. This study enabled us to understand single-molecule features in living cell and measure the diffusion kinetics of membrane-bound molecules.
Collapse
Affiliation(s)
- Xuan Hoa Vu
- Institute of Science and Technology, TNU- University of Sciences (TNUS), Tan Thinh ward, Thai Nguyen city, Viet Nam
| | - Nguyen Dac Dien
- Faculty of Labour Protection, Vietnam Trade Union University, 169 Tay Son street, Hanoi city, Viet Nam
| | - Thi Thu Ha Pham
- Faculty of Chemistry, TNU- University of Sciences (TNUS), Tan Thinh ward, Thai Nguyen city, Viet Nam.
| | - Rodolphe Jaffiol
- Laboratoire de Nanotechnologie et d'Instrumentation Optique, Institut Charles Delaunay, UMR CNRS 6281, Université de Technologie de Troyes, 12 Rue Marie Curie, CS 42060, 10 004 Troyes Cedex, France.
| | - Cyrille Vézy
- Laboratoire de Nanotechnologie et d'Instrumentation Optique, Institut Charles Delaunay, UMR CNRS 6281, Université de Technologie de Troyes, 12 Rue Marie Curie, CS 42060, 10 004 Troyes Cedex, France
| | - Nguyen Xuan Ca
- Institute of Science and Technology, TNU- University of Sciences (TNUS), Tan Thinh ward, Thai Nguyen city, Viet Nam
| | - Tran Thu Trang
- Institute of Science and Technology, TNU- University of Sciences (TNUS), Tan Thinh ward, Thai Nguyen city, Viet Nam
| |
Collapse
|
13
|
Shao S, Zhang H, Zeng Y, Li Y, Sun C, Sun Y. TagBiFC technique allows long-term single-molecule tracking of protein-protein interactions in living cells. Commun Biol 2021; 4:378. [PMID: 33742089 PMCID: PMC7979928 DOI: 10.1038/s42003-021-01896-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/12/2021] [Indexed: 01/09/2023] Open
Abstract
Protein-protein interactions (PPIs) are critical for cellular activity regulation. Visualization of PPIs using bimolecular fluorescence complementation (BiFC) techniques helps to understand how PPIs implement their functions. However, current BiFC is based on fluorescent proteins and the brightness and photostability are suboptimal for single molecule tracking experiments, resulting in either low spatiotemporal resolution or incapability of tracking for extended time course. Here, we developed the TagBiFC technique based on split HaloTag, a self-labeling tag that could conjugate an organic dye molecule and thus offered better brightness and photostability than fluorescent proteins for PPI visualization inside living cells. Through screening and optimization, we demonstrated that the reconstituted HaloTag exhibited higher localization precision and longer tracking length than previous methods. Using TagBiFC, we reveal that the dynamic interactions of transcription factor dimers with chromatin DNA are distinct and closely related to their dimeric states, indicating a general regulatory mechanism for these kinds of transcription factors. In addition, we also demonstrated the advantageous applications of TagBiFC in single nucleosome imaging, light-burden imaging of single mRNA, low background imaging of cellular structures. We believe these superior properties of our TagBiFC system will have broad applications in the studies of single molecule imaging inside living cells.
Collapse
Affiliation(s)
- Shipeng Shao
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.,Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Hongchen Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Yong Zeng
- Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yongliang Li
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.,The Second Dental Center, Peking University School and Hospital of Stomatology, Beijing, China
| | - Chaoying Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.
| |
Collapse
|
14
|
Cremer T, Cremer M, Hübner B, Silahtaroglu A, Hendzel M, Lanctôt C, Strickfaden H, Cremer C. The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus. Bioessays 2020; 42:e1900132. [PMID: 31994771 DOI: 10.1002/bies.201900132] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/24/2019] [Indexed: 12/11/2022]
Abstract
This article focuses on the role of the interchromatin compartment (IC) in shaping nuclear landscapes. The IC is connected with nuclear pore complexes (NPCs) and harbors splicing speckles and nuclear bodies. It is postulated that the IC provides routes for imported transcription factors to target sites, for export routes of mRNA as ribonucleoproteins toward NPCs, as well as for the intranuclear passage of regulatory RNAs from sites of transcription to remote functional sites (IC hypothesis). IC channels are lined by less-compacted euchromatin, called the perichromatin region (PR). The PR and IC together form the active nuclear compartment (ANC). The ANC is co-aligned with the inactive nuclear compartment (INC), comprising more compacted heterochromatin. It is postulated that the INC is accessible for individual transcription factors, but inaccessible for larger macromolecular aggregates (limited accessibility hypothesis). This functional nuclear organization depends on still unexplored movements of genes and regulatory sequences between the two compartments.
Collapse
Affiliation(s)
- Thomas Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Marion Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Barbara Hübner
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Asli Silahtaroglu
- Department of Cellular and Molecular Medicine Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Byg.18.03, 2200, Copenhagen N, Denmark
| | - Michael Hendzel
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christian Lanctôt
- Integration Santé, 1250 Avenue de la Station local 2-304, Shawinigan, Québec, G9N 8K9, Canada
| | - Hilmar Strickfaden
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christoph Cremer
- Institute of Molecular Biology (IMB) Ackermannweg 4, 55128 Mainz, Germany, and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| |
Collapse
|
15
|
Agbleke AA, Amitai A, Buenrostro JD, Chakrabarti A, Chu L, Hansen AS, Koenig KM, Labade AS, Liu S, Nozaki T, Ovchinnikov S, Seeber A, Shaban HA, Spille JH, Stephens AD, Su JH, Wadduwage D. Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields. Mol Cell 2020; 79:881-901. [PMID: 32768408 PMCID: PMC7888594 DOI: 10.1016/j.molcel.2020.07.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/12/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022]
Abstract
Nucleosomes package genomic DNA into chromatin. By regulating DNA access for transcription, replication, DNA repair, and epigenetic modification, chromatin forms the nexus of most nuclear processes. In addition, dynamic organization of chromatin underlies both regulation of gene expression and evolution of chromosomes into individualized sister objects, which can segregate cleanly to different daughter cells at anaphase. This collaborative review shines a spotlight on technologies that will be crucial to interrogate key questions in chromatin and chromosome biology including state-of-the-art microscopy techniques, tools to physically manipulate chromatin, single-cell methods to measure chromatin accessibility, computational imaging with neural networks and analytical tools to interpret chromatin structure and dynamics. In addition, this review provides perspectives on how these tools can be applied to specific research fields such as genome stability and developmental biology and to test concepts such as phase separation of chromatin.
Collapse
Affiliation(s)
| | - Assaf Amitai
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Aditi Chakrabarti
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Lingluo Chu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kristen M Koenig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; JHDSF Program, Harvard University, Cambridge, MA 02138, USA
| | - Ajay S Labade
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sirui Liu
- FAS Division of Science, Harvard University, Cambridge, MA 02138, USA
| | - Tadasu Nozaki
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sergey Ovchinnikov
- JHDSF Program, Harvard University, Cambridge, MA 02138, USA; FAS Division of Science, Harvard University, Cambridge, MA 02138, USA
| | - Andrew Seeber
- JHDSF Program, Harvard University, Cambridge, MA 02138, USA; Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA.
| | - Haitham A Shaban
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA; Spectroscopy Department, Physics Division, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Jan-Hendrik Spille
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Andrew D Stephens
- Biology Department, University of Massachusetts, Amherst, Amherst, MA 01003, USA
| | - Jun-Han Su
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dushan Wadduwage
- JHDSF Program, Harvard University, Cambridge, MA 02138, USA; Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
16
|
Luo F, Qin G, Xia T, Fang X. Single-Molecule Imaging of Protein Interactions and Dynamics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:337-361. [PMID: 32228033 DOI: 10.1146/annurev-anchem-091619-094308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
Collapse
Affiliation(s)
- Fang Luo
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gege Qin
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tie Xia
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohong Fang
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
17
|
Cattoglio C, Pustova I, Darzacq X, Tjian R, Hansen AS. Assessing Self-interaction of Mammalian Nuclear Proteins by Co-immunoprecipitation. Bio Protoc 2020; 10:e3526. [PMID: 33654750 PMCID: PMC7842838 DOI: 10.21769/bioprotoc.3526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/25/2020] [Accepted: 01/13/2020] [Indexed: 11/02/2022] Open
Abstract
Protein-protein interactions constitute the molecular foundations of virtually all biological processes. Co-immunoprecipitation (CoIP) experiments are probably the most widely used method to probe both heterotypic and homotypic protein-protein interactions. Recent advances in super-resolution microscopy have revealed that several nuclear proteins such as transcription factors are spatially distributed into local high-concentration clusters in mammalian cells, suggesting that many nuclear proteins self-interact. These observations have further underscored the need for orthogonal biochemical approaches for testing if self-association occurs, and if so, what the mechanisms are. Here, we describe a CoIP protocol specifically optimized to test self-association of endogenously tagged nuclear proteins (self-CoIP), and to evaluate the role of nucleic acids in such self-interaction. This protocol has proven reliable and robust in our hands, and it can be used to test both homotypic and heterotypic (CoIP) protein-protein interactions.
Collapse
Affiliation(s)
- Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Iryna Pustova
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Anders S. Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| |
Collapse
|
18
|
Cattoglio C, Pustova I, Walther N, Ho JJ, Hantsche-Grininger M, Inouye CJ, Hossain MJ, Dailey GM, Ellenberg J, Darzacq X, Tjian R, Hansen AS. Determining cellular CTCF and cohesin abundances to constrain 3D genome models. eLife 2019; 8:e40164. [PMID: 31205001 PMCID: PMC6579579 DOI: 10.7554/elife.40164] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 03/28/2019] [Indexed: 01/02/2023] Open
Abstract
Achieving a quantitative and predictive understanding of 3D genome architecture remains a major challenge, as it requires quantitative measurements of the key proteins involved. Here, we report the quantification of CTCF and cohesin, two causal regulators of topologically associating domains (TADs) in mammalian cells. Extending our previous imaging studies (Hansen et al., 2017), we estimate bounds on the density of putatively DNA loop-extruding cohesin complexes and CTCF binding site occupancy. Furthermore, co-immunoprecipitation studies of an endogenously tagged subunit (Rad21) suggest the presence of cohesin dimers and/or oligomers. Finally, based on our cell lines with accurately measured protein abundances, we report a method to conveniently determine the number of molecules of any Halo-tagged protein in the cell. We anticipate that our results and the established tool for measuring cellular protein abundances will advance a more quantitative understanding of 3D genome organization, and facilitate protein quantification, key to comprehend diverse biological processes.
Collapse
Affiliation(s)
- Claudia Cattoglio
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - Iryna Pustova
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - Nike Walther
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Jaclyn J Ho
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | | | - Carla J Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - M Julius Hossain
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Gina M Dailey
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Jan Ellenberg
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - Anders S Hansen
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| |
Collapse
|
19
|
Single-molecule imaging of the transcription factor SRF reveals prolonged chromatin-binding kinetics upon cell stimulation. Proc Natl Acad Sci U S A 2018; 116:880-889. [PMID: 30598445 PMCID: PMC6338867 DOI: 10.1073/pnas.1812734116] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
How transcription factors (TFs) activate transcription is a long-standing but still unsolved question. We analyzed serum response factor (SRF), a stimulus-responsive TF mediating immediate early gene (IEG) and cytoskeletal gene expression at single-molecule resolution. Cell stimulation enhanced SRF activity by increasing the number of long chromatin-associated SRF molecules in an oscillating pattern. Further, stimulation enhanced the SRF chromatin residence time, and SRF binding events segregated into three distinct residence time regimes (short, intermediate, and long bound). In summary, our single-molecule imaging study reveals highly dynamic and diverse SRF interactions with DNA. Thus, cell stimulation regulates TF activity by several interconnected mechanisms including nucleus−cytoplasm shuttling, TF phosphorylation, cofactor recruitment, and extension of chromatin residence time and enhancing chromatin-bound TF numbers. Serum response factor (SRF) mediates immediate early gene (IEG) and cytoskeletal gene expression programs in almost any cell type. So far, SRF transcriptional dynamics have not been investigated at single-molecule resolution. We provide a study of single Halo-tagged SRF molecules in fibroblasts and primary neurons. In both cell types, individual binding events of SRF molecules segregated into three chromatin residence time regimes, short, intermediate, and long binding, indicating a cell type-independent SRF property. The chromatin residence time of the long bound fraction was up to 1 min in quiescent cells and significantly increased upon stimulation. Stimulation also enhanced the long bound SRF fraction at specific timepoints (20 and 60 min) in both cell types. These peaks correlated with activation of the SRF cofactors MRTF-A and MRTF-B (myocardin-related transcription factors). Interference with signaling pathways and cofactors demonstrated modulation of SRF chromatin occupancy by actin signaling, MAP kinases, and MRTFs.
Collapse
|