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Sekulovski N, Wettstein JC, Carleton AE, Juga LN, Taniguchi LE, Ma X, Rao S, Schmidt JK, Golos TG, Lin CW, Taniguchi K. Temporally resolved early bone morphogenetic protein-driven transcriptional cascade during human amnion specification. eLife 2024; 12:RP89367. [PMID: 39051990 PMCID: PMC11272160 DOI: 10.7554/elife.89367] [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] [Indexed: 07/27/2024] Open
Abstract
Amniogenesis, a process critical for continuation of healthy pregnancy, is triggered in a collection of pluripotent epiblast cells as the human embryo implants. Previous studies have established that bone morphogenetic protein (BMP) signaling is a major driver of this lineage specifying process, but the downstream BMP-dependent transcriptional networks that lead to successful amniogenesis remain to be identified. This is, in part, due to the current lack of a robust and reproducible model system that enables mechanistic investigations exclusively into amniogenesis. Here, we developed an improved model of early amnion specification, using a human pluripotent stem cell-based platform in which the activation of BMP signaling is controlled and synchronous. Uniform amniogenesis is seen within 48 hr after BMP activation, and the resulting cells share transcriptomic characteristics with amnion cells of a gastrulating human embryo. Using detailed time-course transcriptomic analyses, we established a previously uncharacterized BMP-dependent amniotic transcriptional cascade, and identified markers that represent five distinct stages of amnion fate specification; the expression of selected markers was validated in early post-implantation macaque embryos. Moreover, a cohort of factors that could potentially control specific stages of amniogenesis was identified, including the transcription factor TFAP2A. Functionally, we determined that, once amniogenesis is triggered by the BMP pathway, TFAP2A controls the progression of amniogenesis. This work presents a temporally resolved transcriptomic resource for several previously uncharacterized amniogenesis states and demonstrates a critical intermediate role for TFAP2A during amnion fate specification.
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Affiliation(s)
- Nikola Sekulovski
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of WisconsinMilwaukeeUnited States
| | - Jenna C Wettstein
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of WisconsinMilwaukeeUnited States
| | - Amber E Carleton
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of WisconsinMilwaukeeUnited States
| | - Lauren N Juga
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of WisconsinMilwaukeeUnited States
| | - Linnea E Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of WisconsinMilwaukeeUnited States
| | - Xiaolong Ma
- Division of Biostatistics, Institute for Health and Equity, Medical College of WisconsinMilwaukeeUnited States
| | - Sridhar Rao
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of WisconsinMilwaukeeUnited States
- Department of Pediatrics, Medical College of WisconsinMilwaukeeUnited States
- Versiti Blood Research InstituteMilwaukeeUnited States
| | - Jenna K Schmidt
- Wisconsin National Primate Research CenterMilwaukeeUnited States
| | - Thaddeus G Golos
- Wisconsin National Primate Research CenterMilwaukeeUnited States
- Department of Obstetrics and Gynecology, University of Wisconsin - Madison School of Medicine and Public HealthMadisonUnited States
- Department of Comparative Biosciences, University of Wisconsin - Madison School of Veterinary MedicineMadisonUnited States
| | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Equity, Medical College of WisconsinMilwaukeeUnited States
| | - Kenichiro Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of WisconsinMilwaukeeUnited States
- Department of Pediatrics, Medical College of WisconsinMilwaukeeUnited States
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2
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Sekulovski N, Wettstein JC, Carleton AE, Juga LN, Taniguchi LE, Ma X, Rao S, Schmidt JK, Golos TG, Lin CW, Taniguchi K. Temporally resolved early BMP-driven transcriptional cascade during human amnion specification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.19.545574. [PMID: 38496419 PMCID: PMC10942271 DOI: 10.1101/2023.06.19.545574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Amniogenesis, a process critical for continuation of healthy pregnancy, is triggered in a collection of pluripotent epiblast cells as the human embryo implants. Previous studies have established that BMP signaling is a major driver of this lineage specifying process, but the downstream BMP-dependent transcriptional networks that lead to successful amniogenesis remain to be identified. This is, in part, due to the current lack of a robust and reproducible model system that enables mechanistic investigations exclusively into amniogenesis. Here, we developed an improved model of early amnion specification, using a human pluripotent stem cell-based platform in which the activation of BMP signaling is controlled and synchronous. Uniform amniogenesis is seen within 48 hours after BMP activation, and the resulting cells share transcriptomic characteristics with amnion cells of a gastrulating human embryo. Using detailed time-course transcriptomic analyses, we established a previously uncharacterized BMP-dependent amniotic transcriptional cascade, and identified markers that represent five distinct stages of amnion fate specification; the expression of selected markers was validated in early post-implantation macaque embryos. Moreover, a cohort of factors that could potentially control specific stages of amniogenesis was identified, including the transcription factor TFAP2A. Functionally, we determined that, once amniogenesis is triggered by the BMP pathway, TFAP2A controls the progression of amniogenesis. This work presents a temporally resolved transcriptomic resource for several previously uncharacterized amniogenesis states and demonstrates a critical intermediate role for TFAP2A during amnion fate specification.
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Affiliation(s)
- Nikola Sekulovski
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jenna C. Wettstein
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Amber E. Carleton
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Lauren N. Juga
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Linnea E. Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Xiaolong Ma
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sridhar Rao
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Versiti Blood Research Institute, Milwaukee, WI 53226 USA
| | - Jenna K. Schmidt
- Wisconsin National Primate Research Center (WNPRC), Madison, WI, USA
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center (WNPRC), Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin - Madison School of Medicine and Public Health, Madison, WI USA
- Department of Comparative Biosciences, University of Wisconsin - Madison School of Veterinary Medicine, Madison, WI, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kenichiro Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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3
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Hamed MM, Taniguchi K, Duncan MC. Monitoring Effects of Membrane Traffic Via Changes in Cell Polarity and Morphogenesis in Three-Dimensional Human Pluripotent Stem Cell Cysts. Methods Mol Biol 2023; 2557:83-98. [PMID: 36512211 PMCID: PMC10276343 DOI: 10.1007/978-1-0716-2639-9_7] [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] [Indexed: 12/15/2022]
Abstract
Membrane traffic at the Golgi and endosomes plays many critical roles in the polarization and the morphogenesis of epithelial tissues. Studies into the roles of traffic in morphogenesis in mammals are often complicated by early embryonic lethality of mutations in membrane traffic as well as the inherent difficulty in imaging developing embryos posed by their size and location. Increasingly, human pluripotent stem cell (hPSC)-derived embryo- and organ-like systems (e.g., embryoids, organoids) provide a useful platform to illuminate the requirements of traffic in human embryonic tissue morphogenesis because these in vitro models are highly amenable to fluorescence microscopy and provide the ability to examine the role of essential genes not possible with animal studies. Here, we present a method to generate hPSC-cysts, a 3-D hPSC-based model of human epiblast lumen formation. This system provides unique opportunities to examine the role of membrane traffic during epithelial morphogenesis. We also present methods to process hPSC-cysts for immunofluorescence and staining with commonly used fluorescence labels useful for detecting defects in polarization and morphogenesis caused by defects in membrane traffic.
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Affiliation(s)
- Maha M Hamed
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Kenichiro Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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4
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Carleton AE, Duncan MC, Taniguchi K. Human epiblast lumenogenesis: From a cell aggregate to a lumenal cyst. Semin Cell Dev Biol 2022; 131:117-123. [PMID: 35637065 PMCID: PMC9529837 DOI: 10.1016/j.semcdb.2022.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 12/14/2022]
Abstract
The formation of a central lumen in the human epiblast is a critical step for development. However, because the lumen forms in the epiblast coincident with implantation, the molecular and cellular events of this early lumenogenesis process cannot be studied in vivo. Recent developments using new model systems have revealed insight into the underpinnings of epiblast formation. To provide an up-to-date comprehensive review of human epiblast lumenogenesis, we highlight recent findings from human and mouse models with an emphasis on new molecular understanding of a newly described apicosome compartment, a novel 'formative' state of pluripotency that coordinates with epiblast polarization, and new evidence about the physical and polarized trafficking mechanisms contributing to lumenogenesis.
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Affiliation(s)
- Amber E. Carleton
- Departments of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin USA
| | - Mara C. Duncan
- Departments of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan USA,Co-corresponding authors
| | - Kenichiro Taniguchi
- Departments of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin USA,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin USA,Co-corresponding authors
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5
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Nakashima Y, Yoshida S, Tsukahara M. Semi-3D cultures using Laminin 221 as a coating material for human induced pluripotent stem cells. Regen Biomater 2022; 9:rbac060. [PMID: 36176714 PMCID: PMC9514851 DOI: 10.1093/rb/rbac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/09/2022] [Accepted: 08/21/2022] [Indexed: 11/19/2022] Open
Abstract
It was previously believed that human induced pluripotent stem cells (hiPSCs) did not show adhesion to the coating material Laminin 221, which is known to have specific affinity for cardiomyocytes. In this study, we report that human mononuclear cell-derived hiPSCs, established with Sendai virus vector, form peninsular-like colonies rather than embryonic stem cell-like colonies; these peninsular-like colonies can be passaged more than 10 times after establishment. Additionally, initialization-deficient cells with residual Sendai virus vector adhered to the coating material Laminin 511 but not to Laminin 221. Therefore, the expression of undifferentiated markers tended to be higher in hiPSCs established on Laminin 221 than on Laminin 511. On Laminin 221, hiPSCs15M66 showed a semi-floating colony morphology. The expression of various markers of cell polarity was significantly lower in hiPSCs cultured on Laminin 221 than in hiPSCs cultured on Laminin 511. Furthermore, 201B7 and 15M66 hiPSCs showed 3D cardiomyocyte differentiation on Laminin 221. Thus, the coating material Laminin 221 provides semi-floating culture conditions for the establishment, culture and induced differentiation of hiPSCs.
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Affiliation(s)
- Yoshiki Nakashima
- Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation), Facility for iPS Cell Therapy (FiT), Kyoto 606-8397, Japan
| | - Shinsuke Yoshida
- Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation), Facility for iPS Cell Therapy (FiT), Kyoto 606-8397, Japan
| | - Masayoshi Tsukahara
- Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation), Facility for iPS Cell Therapy (FiT), Kyoto 606-8397, Japan
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6
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Critcher M, Huang ML. Excavating proteoglycan structure-function relationships: Modern approaches to capture the interactions of ancient biomolecules. Am J Physiol Cell Physiol 2022; 323:C415-C422. [PMID: 35759439 PMCID: PMC9359657 DOI: 10.1152/ajpcell.00222.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteoglycans are now well regarded as key facilitators of cell biology. While a majority of their interactions and functions are attributed to the decorating glycosaminoglycan chains, there is a growing appreciation for the roles of the proteoglycan core protein and for considering proteoglycans as replete protein-glycan conjugates. This appreciation, seeded by early work in proteoglycan biology, is now being advanced and exalted by modern approaches in chemical glycobiology. In this review, we discuss up-and-coming methods to unearth the fine-scale architecture of proteoglycans that modulate their functions and interactions. Crucial to these efforts is the production of chemically defined materials, including semi-synthetic proteoglycans and the in situ capture of interacting proteins. Together, the integration of chemical biology approaches promises to expedite the dissection of the structural heterogeneity of proteoglycans and deliver refined insight into their functions.
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Affiliation(s)
- Meg Critcher
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, CA.,Department of Molecular Medicine, Scripps Research, La Jolla, CA
| | - Mia L Huang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, CA.,Department of Molecular Medicine, Scripps Research, La Jolla, CA.,Department of Chemistry, Scripps Research, La Jolla, CA
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7
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Lin A, Piehowski PD, Tsai CF, Makushok T, Yi L, Diaz U, Yan C, Summers D, Sood P, Smith RD, Liu T, Marshall WF. Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells. Curr Biol 2022; 32:2300-2308.e4. [PMID: 35447087 PMCID: PMC9133221 DOI: 10.1016/j.cub.2022.03.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/08/2022] [Accepted: 03/30/2022] [Indexed: 12/18/2022]
Abstract
Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell.1-4 Patterning within cells can extend down to the level of individual proteins and mRNA.5,6 But how much of the proteome is actually localized with respect to cell polarity axes? Proteomics combined with cellular fractionation7-11 has shown that most proteins localize to one or more organelles but does not tell us how many proteins have a polarized localization with respect to the large-scale polarity axes of the intact cell. Genome-wide localization studies in yeast12-15 found that only a few percent of proteins have a localized position relative to the cell polarity axis defined by sites of polarized cell growth. Here, we describe an approach for analyzing protein distribution within a cell with a visibly obvious global patterning-the giant ciliate Stentor coeruleus.16,17 Ciliates, including Stentor, have highly polarized cell shapes with visible surface patterning.1,18 A Stentor cell is roughly 2 mm long, allowing a "proteomic dissection" in which microsurgery is used to separate cellular fragments along the anterior-posterior axis, followed by comparative proteomic analysis. In our analysis, 25% of the proteome, including signaling proteins, centrin/SFI proteins, and GAS2 orthologs, shows a polarized location along the cell's anterior-posterior axis. We conclude that a large proportion of all proteins are polarized with respect to global cell polarity axes and that proteomic dissection provides a simple and effective approach for spatial proteomics.
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Affiliation(s)
- Athena Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Paul D Piehowski
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Chia-Feng Tsai
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lian Yi
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ulises Diaz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Connie Yan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diana Summers
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pranidhi Sood
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Richard D Smith
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tao Liu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, United States of America.
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8
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Dionne U, Gingras AC. Proximity-Dependent Biotinylation Approaches to Explore the Dynamic Compartmentalized Proteome. Front Mol Biosci 2022; 9:852911. [PMID: 35309513 PMCID: PMC8930824 DOI: 10.3389/fmolb.2022.852911] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
In recent years, proximity-dependent biotinylation approaches, including BioID, APEX, and their derivatives, have been widely used to define the compositions of organelles and other structures in cultured cells and model organisms. The associations between specific proteins and given compartments are regulated by several post-translational modifications (PTMs); however, these effects have not been systematically investigated using proximity proteomics. Here, we discuss the progress made in this field and how proximity-dependent biotinylation strategies could elucidate the contributions of PTMs, such as phosphorylation, to the compartmentalization of proteins.
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Affiliation(s)
- Ugo Dionne
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Anne-Claude Gingras,
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Sari B, Isik M, Eylem CC, Kilic C, Okesola BO, Karakaya E, Emregul E, Nemutlu E, Derkus B. Omics Technologies for High-Throughput-Screening of Cell-Biomaterial Interactions. Mol Omics 2022; 18:591-615. [DOI: 10.1039/d2mo00060a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent research effort in biomaterial development has largely focused on engineering bio-instructive materials to stimulate specific cell signaling. Assessing the biological performance of these materials using time-consuming and trial-and-error traditional...
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10
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Shkel O, Kharkivska Y, Kim YK, Lee JS. Proximity Labeling Techniques: A Multi-Omics Toolbox. Chem Asian J 2021; 17:e202101240. [PMID: 34850572 DOI: 10.1002/asia.202101240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/29/2021] [Indexed: 01/17/2023]
Abstract
Proximity labeling techniques are emerging high-throughput methods for studying protein-protein, protein-RNA, and protein-DNA interactions with temporal and spatial precision. Proximity labeling methods take advantage of enzymes that can covalently label biomolecules with reactive substrates. These labeled biomolecules can be identified using mass spectrometry or next-generation sequencing. The main advantage of these methods is their ability to capture weak or transient interactions between biomolecules. Proximity labeling is indispensable for studying organelle interactomes. Additionally, it can be used to resolve spatial composition of macromolecular complexes. Many of these methods have only recently been introduced; nonetheless, they have already provided new and deep insights into the biological processes at the cellular, organ, and organism levels. In this paper, we review a broad range of proximity labeling techniques, their development, drawbacks and advantages, and implementations in recent studies.
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Affiliation(s)
- Olha Shkel
- Convergence Research Center for Diagnosis Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Yevheniia Kharkivska
- Convergence Research Center for Diagnosis Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Yun Kyung Kim
- Convergence Research Center for Diagnosis Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Jun-Seok Lee
- Department of Pharmacology, Korea University College of Medicine, Seoul, Republic of Korea
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