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Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CK. Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. bioRxiv 2024:2024.02.05.576943. [PMID: 38370628 PMCID: PMC10871237 DOI: 10.1101/2024.02.05.576943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
DNA-PAINT combined with total Internal Reflection Fluorescence (TIRF) microscopy enables the highest localization precisions, down to single nanometers in thin biological samples, due to TIRF's unique method for optical sectioning and attaining high contrast. However, most cellular targets elude the accessible TIRF range close to the cover glass and thus require alternative imaging conditions, affecting resolution and image quality. Here, we address this limitation by applying ultrathin physical cryosectioning in combination with DNA-PAINT. With "tomographic & kinetically-enhanced" DNA-PAINT (tokPAINT), we demonstrate the imaging of nuclear proteins with sub-3 nanometer localization precision, advancing the quantitative study of nuclear organization within fixed cells and mouse tissues at the level of single antibodies. We believe that ultrathin sectioning combined with the versatility and multiplexing capabilities of DNA-PAINT will be a powerful addition to the toolbox of quantitative DNA-based super-resolution microscopy in intracellular structural analyses of proteins, RNA and DNA in situ.
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Affiliation(s)
- Johannes Stein
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maria Ericsson
- Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Michel Nofal
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Lorenzo Magni
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Sarah Aufmkolk
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ryan B. McMillan
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Laura Breimann
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Jens Wohlmann
- Department of Biosciences, University of Oslo, Norway
| | - Laura Arguedas-Jimenez
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Peng Yin
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - George M. Church
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chao-Kng Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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2
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Loedige I, Baranovskii A, Mendonsa S, Dantsuji S, Popitsch N, Breimann L, Zerna N, Cherepanov V, Milek M, Ameres S, Chekulaeva M. mRNA stability and m 6A are major determinants of subcellular mRNA localization in neurons. Mol Cell 2023; 83:2709-2725.e10. [PMID: 37451262 PMCID: PMC10529935 DOI: 10.1016/j.molcel.2023.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
For cells to perform their biological functions, they need to adopt specific shapes and form functionally distinct subcellular compartments. This is achieved in part via an asymmetric distribution of mRNAs within cells. Currently, the main model of mRNA localization involves specific sequences called "zipcodes" that direct mRNAs to their proper locations. However, while thousands of mRNAs localize within cells, only a few zipcodes have been identified, suggesting that additional mechanisms contribute to localization. Here, we assess the role of mRNA stability in localization by combining the isolation of the soma and neurites of mouse primary cortical and mESC-derived neurons, SLAM-seq, m6A-RIP-seq, the perturbation of mRNA destabilization mechanisms, and the analysis of multiple mRNA localization datasets. We show that depletion of mRNA destabilization elements, such as m6A, AU-rich elements, and suboptimal codons, functions as a mechanism that mediates the localization of mRNAs associated with housekeeping functions to neurites in several types of neurons.
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Affiliation(s)
- Inga Loedige
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Artem Baranovskii
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Samantha Mendonsa
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Sayaka Dantsuji
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Niko Popitsch
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Laura Breimann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nadja Zerna
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Vsevolod Cherepanov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Miha Milek
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Stefan Ameres
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany.
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Bahry E, Breimann L, Zouinkhi M, Epstein L, Kolyvanov K, Mamrak N, King B, Long X, Harrington KIS, Lionnet T, Preibisch S. RS-FISH: precise, interactive, fast, and scalable FISH spot detection. Nat Methods 2022; 19:1563-1567. [PMID: 36396787 PMCID: PMC9718671 DOI: 10.1038/s41592-022-01669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 09/28/2022] [Indexed: 11/18/2022]
Abstract
Fluorescent in-situ hybridization (FISH)-based methods extract spatially resolved genetic and epigenetic information from biological samples by detecting fluorescent spots in microscopy images, an often challenging task. We present Radial Symmetry-FISH (RS-FISH), an accurate, fast, and user-friendly software for spot detection in two- and three-dimensional images. RS-FISH offers interactive parameter tuning and readily scales to large datasets and image volumes of cleared or expanded samples using distributed processing on workstations, clusters, or the cloud. RS-FISH maintains high detection accuracy and low localization error across a wide range of signal-to-noise ratios, a key feature for single-molecule FISH, spatial transcriptomics, or spatial genomics applications.
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Affiliation(s)
- Ella Bahry
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Laura Breimann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Marwan Zouinkhi
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Leo Epstein
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Helmholtz Imaging Platform, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Klim Kolyvanov
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Nicholas Mamrak
- Institute for Systems Genetics and Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Benjamin King
- Institute for Systems Genetics and Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Xi Long
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Kyle I S Harrington
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
- Helmholtz Imaging Platform, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
| | - Timothée Lionnet
- Institute for Systems Genetics and Department of Cell Biology, NYU School of Medicine, New York, NY, USA.
- Department of Bioengineering, NYU Tandon School of Engineering, Brooklyn, NY, USA.
| | - Stephan Preibisch
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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Breimann L, Morao AK, Kim J, Jimenez DS, Maryn N, Bikkasani K, Carrozza MJ, Albritton SE, Kramer M, Street LA, Cerimi K, Schumann VF, Bahry E, Preibisch S, Woehler A, Ercan S. The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding. J Cell Sci 2021; 135:273768. [PMID: 34918745 PMCID: PMC8917352 DOI: 10.1242/jcs.258818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022] Open
Abstract
Condensin is a multi-subunit structural maintenance of chromosomes (SMC) complex that binds to and compacts chromosomes. Here, we addressed the regulation of condensin binding dynamics using Caenorhabditis elegans condensin DC, which represses X chromosomes in hermaphrodites for dosage compensation. We established fluorescence recovery after photobleaching (FRAP) using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes DPY-27 binding to X chromosomes. Next, we performed FRAP in the background of several chromatin modifier mutants that cause varying degrees of X chromosome derepression. The greatest effect was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of condensin DC reduced from ∼30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Hi-C sequencing data from the dpy-21 null mutant showed little change compared to wild-type data, uncoupling Hi-C-measured long-range DNA contacts from transcriptional repression of the X chromosomes. Taken together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression. Summary: The histone demethylase DPY-21 has catalytic and non-catalytic roles in condensin DC-mediated X chromosome repression. The non-catalytic activity regulates dynamics of condensin DC binding to X chromosomes.
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Affiliation(s)
- Laura Breimann
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute for Biology, Humboldt University of Berlin, Berlin, Germany
| | - Ana Karina Morao
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - David Sebastian Jimenez
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Nina Maryn
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Krishna Bikkasani
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Michael J Carrozza
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Sarah E Albritton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Maxwell Kramer
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Lena Annika Street
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Kustrim Cerimi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Vic-Fabienne Schumann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ella Bahry
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Andrew Woehler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
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La Fortezza M, Grigolon G, Cosolo A, Pindyurin A, Breimann L, Blum H, van Steensel B, Classen AK. Correction to: DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis. Epigenetics Chromatin 2018; 11:38. [PMID: 29970137 PMCID: PMC6029416 DOI: 10.1186/s13072-018-0206-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marco La Fortezza
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Giovanna Grigolon
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Department of Health Sciences and Technology, ETH Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
| | - Andrea Cosolo
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Alexey Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Laura Breimann
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center Munich, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany
| | - Bas van Steensel
- Division Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Anne-Kathrin Classen
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany. .,Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.
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7
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La Fortezza M, Grigolon G, Cosolo A, Pindyurin A, Breimann L, Blum H, van Steensel B, Classen AK. DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis. Epigenetics Chromatin 2018; 11:27. [PMID: 29871666 PMCID: PMC5987561 DOI: 10.1186/s13072-018-0196-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/21/2018] [Indexed: 02/06/2023] Open
Abstract
Background Tracking dynamic protein–chromatin interactions in vivo is key to unravel transcriptional and epigenetic transitions in development and disease. However, limited availability and heterogeneous tissue composition of in vivo source material impose challenges on many experimental approaches. Results Here we adapt cell-type-specific DamID-seq profiling for use in Drosophila imaginal discs and make FLP/FRT-based induction accessible to GAL driver-mediated targeting of specific cell lineages. In a proof-of-principle approach, we utilize ubiquitous DamID expression to describe dynamic transitions of Polycomb-binding sites during wing imaginal disc development and in a scrib tumorigenesis model. We identify Atf3 and Ets21C as novel Polycomb target genes involved in scrib tumorigenesis and suggest that target gene regulation by Atf3 and AP-1 transcription factors, as well as modulation of insulator function, plays crucial roles in dynamic Polycomb-binding at target sites. We establish these findings by DamID-seq analysis of wing imaginal disc samples derived from 10 larvae. Conclusions Our study opens avenues for robust profiling of small cell population in imaginal discs in vivo and provides insights into epigenetic changes underlying transcriptional responses to tumorigenic transformation. Electronic supplementary material The online version of this article (10.1186/s13072-018-0196-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco La Fortezza
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Giovanna Grigolon
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Department of Health Sciences and Technology, ETH Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
| | - Andrea Cosolo
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Alexey Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Laura Breimann
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center Munich, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany
| | - Bas van Steensel
- Division Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Anne-Kathrin Classen
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany. .,Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.
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