1
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Trzaskoma P, Jung S, Pękowska A, Bohrer CH, Wang X, Naz F, Dell’Orso S, Dubois WD, Olivera A, Vartak SV, Zhao Y, Nayak S, Overmiller A, Morasso MI, Sartorelli V, Larson DR, Chow CC, Casellas R, O’Shea JJ. 3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network. SCIENCE ADVANCES 2024; 10:eadl4893. [PMID: 39121214 PMCID: PMC11313860 DOI: 10.1126/sciadv.adl4893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 07/08/2024] [Indexed: 08/11/2024]
Abstract
Discontinuous transcription is evolutionarily conserved and a fundamental feature of gene regulation; yet, the exact mechanisms underlying transcriptional bursting are unresolved. Analyses of bursting transcriptome-wide have focused on the role of cis-regulatory elements, but other factors that regulate this process remain elusive. We applied mathematical modeling to single-cell RNA sequencing data to infer bursting dynamics transcriptome-wide under multiple conditions to identify possible molecular mechanisms. We found that Mediator complex subunit 26 (MED26) primarily regulates frequency, MYC regulates burst size, while cohesin and Bromodomain-containing protein 4 (BRD4) can modulate both. Despite comparable effects on RNA levels among these perturbations, acute depletion of MED26 had the most profound impact on the entire gene regulatory network, acting downstream of chromatin spatial architecture and without affecting TATA box-binding protein (TBP) recruitment. These results indicate that later steps in the initiation of transcriptional bursts are primary nodes for integrating gene networks in single cells.
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Affiliation(s)
- Pawel Trzaskoma
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - SeolKyoung Jung
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aleksandra Pękowska
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | | | - Xiang Wang
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Faiza Naz
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Stefania Dell’Orso
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wendy D. Dubois
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ana Olivera
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Supriya V. Vartak
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yongbing Zhao
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Subhashree Nayak
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Overmiller
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Maria I. Morasso
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vittorio Sartorelli
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel R. Larson
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carson C. Chow
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rafael Casellas
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John J. O’Shea
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
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2
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Dong P, Zhang S, Gandin V, Xie L, Wang L, Lemire AL, Li W, Otsuna H, Kawase T, Lander AD, Chang HY, Liu ZJ. Cohesin prevents cross-domain gene coactivation. Nat Genet 2024; 56:1654-1664. [PMID: 39048795 PMCID: PMC11319207 DOI: 10.1038/s41588-024-01852-1] [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: 02/08/2023] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The contrast between the disruption of genome topology after cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome and chromatin accessibility at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic coexpression tendencies of cis-linked genes in single cells. Notably, cohesin loss induces widespread gene coactivation and chromatin co-opening tens of million bases apart in cis. Spatial genome and protein imaging reveals that cohesin prevents gene co-bursting along the chromosome and blocks spatial mixing of transcriptional hubs. Single-molecule imaging shows that cohesin confines the exploration of diverse enhancer and core promoter binding transcriptional regulators. Together, these results support that cohesin arranges nuclear topology to control gene coexpression in single cells.
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Affiliation(s)
- Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Shu Zhang
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Valentina Gandin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Cancer Biology and Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Wenhong Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Hideo Otsuna
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Takashi Kawase
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Arthur D Lander
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Zhe J Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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3
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Hsiao YT, Liao IH, Wu BK, Chu HPC, Hsieh CL. Probing chromatin condensation dynamics in live cells using interferometric scattering correlation spectroscopy. Commun Biol 2024; 7:763. [PMID: 38914653 PMCID: PMC11196589 DOI: 10.1038/s42003-024-06457-2] [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: 11/24/2023] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
Chromatin organization and dynamics play important roles in governing the regulation of nuclear processes of biological cells. However, due to the constant diffusive motion of chromatin, examining chromatin nanostructures in living cells has been challenging. In this study, we introduce interferometric scattering correlation spectroscopy (iSCORS) to spatially map nanoscopic chromatin configurations within unlabeled live cell nuclei. This label-free technique captures time-varying linear scattering signals generated by the motion of native chromatin on a millisecond timescale, allowing us to deduce chromatin condensation states. Using iSCORS imaging, we quantitatively examine chromatin dynamics over extended periods, revealing spontaneous fluctuations in chromatin condensation and heterogeneous compaction levels in interphase cells, independent of cell phases. Moreover, we observe changes in iSCORS signals of chromatin upon transcription inhibition, indicating that iSCORS can probe nanoscopic chromatin structures and dynamics associated with transcriptional activities. Our scattering-based optical microscopy, which does not require labeling, serves as a powerful tool for visualizing dynamic chromatin nano-arrangements in live cells. This advancement holds promise for studying chromatin remodeling in various crucial cellular processes, such as stem cell differentiation, mechanotransduction, and DNA repair.
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Affiliation(s)
- Yi-Teng Hsiao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - I-Hsin Liao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Bo-Kuan Wu
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | | | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan.
- Department of Physics, National Taiwan University, Taipei, Taiwan.
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4
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Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. Nat Commun 2024; 15:4178. [PMID: 38755200 PMCID: PMC11099156 DOI: 10.1038/s41467-024-48562-0] [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: 11/21/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we present an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrate that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacts nucleosome diffusive properties in a manner that is dependent both on local chromatin density and on relative location within the nucleus. Our results support a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Additionally, they reveal that nuclear heterogeneity arises from both active and passive processes and highlight the need to account for different organizational principles when modeling different chromatin environments.
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Affiliation(s)
- Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yu Shi
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA
| | - Katie L Holland
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Hosein Rostamian
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Joseph Rodriguez
- National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wesley R Legant
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA.
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5
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Hwang DW, Maekiniemi A, Singer RH, Sato H. Real-time single-molecule imaging of transcriptional regulatory networks in living cells. Nat Rev Genet 2024; 25:272-285. [PMID: 38195868 DOI: 10.1038/s41576-023-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
Gene regulatory networks drive the specific transcriptional programmes responsible for the diversification of cell types during the development of multicellular organisms. Although our knowledge of the genes involved in these dynamic networks has expanded rapidly, our understanding of how transcription is spatiotemporally regulated at the molecular level over a wide range of timescales in the small volume of the nucleus remains limited. Over the past few decades, advances in the field of single-molecule fluorescence imaging have enabled real-time behaviours of individual transcriptional components to be measured in living cells and organisms. These efforts are now shedding light on the dynamic mechanisms of transcription, revealing not only the temporal rules but also the spatial coordination of underlying molecular interactions during various biological events.
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Affiliation(s)
- Dong-Woo Hwang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anna Maekiniemi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Robert H Singer
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Hanae Sato
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
- Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan.
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6
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Singhal A, Roth C, Micheva-Viteva SN, Venu V, Lappala A, Lee JT, Starkenburg SR, Steadman CR, Sanbonmatsu KY. Human Coronavirus Infection Reorganizes Spatial Genomic Architecture in Permissive Lung Cells. RESEARCH SQUARE 2024:rs.3.rs-3979539. [PMID: 38559036 PMCID: PMC10980144 DOI: 10.21203/rs.3.rs-3979539/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Chromatin conformation capture followed by next-generation sequencing in combination with large-scale polymer simulations (4DHiC) produces detailed information on genomic loci interactions, allowing for the interrogation of 3D spatial genomic structures. Here, Hi-C data was acquired from the infection of fetal lung fibroblast (MRC5) cells with α-coronavirus 229E (CoV229E). Experimental Hi-C contact maps were used to determine viral-induced changes in genomic architecture over a 48-hour time period following viral infection, revealing substantial alterations in contacts within chromosomes and in contacts between different chromosomes. To gain further structural insight and quantify the underlying changes, we applied the 4DHiC polymer simulation method to reconstruct the 3D genomic structures and dynamics corresponding to the Hi-C maps. The models successfully reproduced experimental Hi-C data, including the changes in contacts induced by viral infection. Our 3D spatial simulations uncovered widespread chromatin restructuring, including increased chromosome compactness and A-B compartment mixing arising from infection. Our model also suggests increased spatial accessibility to regions containing interferon-stimulated genes upon infection with CoV229E, followed by chromatin restructuring at later time points, potentially inducing the migration of chromatin into more compact regions. This is consistent with previously observed suppression of gene expression. Our spatial genomics study provides a mechanistic structural basis for changes in chromosome architecture induced by coronavirus infection in lung cells.
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Affiliation(s)
- Ankush Singhal
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos,NM, USA
| | - Cullen Roth
- Genomics and Bioanalytics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | - Vrinda Venu
- Climate, Ecology & Environment, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Anna Lappala
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Jeannie T. Lee
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, USA
- Departement of Molecular Biology, Massachusetts General Hospital, Boston, USA
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7
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Holland KL, Plutkis SE, Daugird TA, Sau A, Grimm JB, English BP, Zheng Q, Dave S, Rahman F, Xie L, Dong P, Tkachuk AN, Brown TA, Singer RH, Liu Z, Galbraith CG, Musser SM, Legant WR, Lavis LD. A series of spontaneously blinking dyes for super-resolution microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581625. [PMID: 38766149 PMCID: PMC11101128 DOI: 10.1101/2024.02.23.581625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Spontaneously blinking fluorophores permit the detection and localization of individual molecules without reducing buffers or caging groups, thus simplifying single-molecule localization microscopy (SMLM). The intrinsic blinking properties of such dyes are dictated by molecular structure and modulated by environment, which can limit utility. We report a series of tuned spontaneously blinking dyes with duty cycles that span two orders of magnitude, allowing facile SMLM in cells and dense biomolecular structures.
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Affiliation(s)
- Katie L. Holland
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sarah E. Plutkis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothy A. Daugird
- Department of Pharmacology, University of North Carolina-Chapel Hill Medical School, Chapel Hill, NC, USA
| | - Abhishek Sau
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, College Station, TX, USA
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Brian P. English
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sandeep Dave
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, College Station, TX, USA
| | - Fariha Rahman
- Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill and North Carolina State University, Chapel Hill, NC, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ariana N. Tkachuk
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Robert H. Singer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Catherine G. Galbraith
- Department of Biomedical Engineering and Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Siegfried M. Musser
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, College Station, TX, USA
| | - Wesley R. Legant
- Department of Pharmacology, University of North Carolina-Chapel Hill Medical School, Chapel Hill, NC, USA
- Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill and North Carolina State University, Chapel Hill, NC, USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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8
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Han M, Perkins MH, Novaes LS, Xu T, Chang H. Advances in transposable elements: from mechanisms to applications in mammalian genomics. Front Genet 2023; 14:1290146. [PMID: 38098473 PMCID: PMC10719622 DOI: 10.3389/fgene.2023.1290146] [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: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
It has been 70 years since Barbara McClintock discovered transposable elements (TE), and the mechanistic studies and functional applications of transposable elements have been at the forefront of life science research. As an essential part of the genome, TEs have been discovered in most species of prokaryotes and eukaryotes, and the relative proportion of the total genetic sequence they comprise gradually increases with the expansion of the genome. In humans, TEs account for about 40% of the genome and are deeply involved in gene regulation, chromosome structure maintenance, inflammatory response, and the etiology of genetic and non-genetic diseases. In-depth functional studies of TEs in mammalian cells and the human body have led to a greater understanding of these fundamental biological processes. At the same time, as a potent mutagen and efficient genome editing tool, TEs have been transformed into biological tools critical for developing new techniques. By controlling the random insertion of TEs into the genome to change the phenotype in cells and model organisms, critical proteins of many diseases have been systematically identified. Exploiting the TE's highly efficient in vitro insertion activity has driven the development of cutting-edge sequencing technologies. Recently, a new technology combining CRISPR with TEs was reported, which provides a novel targeted insertion system to both academia and industry. We suggest that interrogating biological processes that generally depend on the actions of TEs with TEs-derived genetic tools is a very efficient strategy. For example, excessive activation of TEs is an essential factor in the occurrence of cancer in humans. As potent mutagens, TEs have also been used to unravel the key regulatory elements and mechanisms of carcinogenesis. Through this review, we aim to effectively combine the traditional views of TEs with recent research progress, systematically link the mechanistic discoveries of TEs with the technological developments of TE-based tools, and provide a comprehensive approach and understanding for researchers in different fields.
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Affiliation(s)
- Mei Han
- Guangzhou National Laboratory, Guangzhou, China
| | - Matthew H. Perkins
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Leonardo Santana Novaes
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tao Xu
- Guangzhou National Laboratory, Guangzhou, China
| | - Hao Chang
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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9
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Pierzynska-Mach A, Diaspro A, Cella Zanacchi F. Super-resolution microscopy reveals the nanoscale cluster architecture of the DEK protein cancer biomarker. iScience 2023; 26:108277. [PMID: 38026229 PMCID: PMC10660485 DOI: 10.1016/j.isci.2023.108277] [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: 03/13/2023] [Revised: 09/02/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
DEK protein, a key chromatin regulator, is strongly overexpressed in various forms of cancer. While conventional microscopy revealed DEK as uniformly distributed within the cell nucleus, advanced super-resolution techniques uncovered cluster-like structures. However, a comprehensive understanding of DEK's cellular distribution and its implications in cancer and cell growth remained elusive. To bridge this gap, we employed single-molecule localization microscopy (SMLM) to dissect DEK's nanoscale organization in both normal-like and aggressive breast cancer cell lines. Our investigation included characteristics such as localizations per cluster, cluster areas, and intra-cluster localization densities (ICLDs). We elucidated how cluster features align with different breast cell types and how chromatin decompaction influences DEK clusters in these contexts. Our results indicate that DEK's intra-cluster localization density and nano-organization remain preserved and not significantly influenced by protein overexpression or chromatin compaction changes. This study advances the understanding of DEK's role in cancer and underscores its stable nanoscale behavior.
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Affiliation(s)
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, 16152 Genoa, Italy
- Department of Physics (DIFILAB), Department of Physics, University of Genoa, 16146 Genoa, Italy
| | - Francesca Cella Zanacchi
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, 16152 Genoa, Italy
- Physics Department E. Fermi, University of Pisa, 56127 Pisa, Italy
- Centro per l’Integrazione della Strumentazione dell’Università di Pisa (CISUP), University of Pisa, 56127 Pisa, Italy
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10
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Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566470. [PMID: 38014222 PMCID: PMC10680651 DOI: 10.1101/2023.11.09.566470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we developed an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrated that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacted nucleosome diffusive properties in a manner that was dependent on local chromatin density and supportive of a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Our results reveal that nuclear heterogeneity arises from both active and passive process and highlights the need to account for different organizational principals when modeling different chromatin environments.
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11
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Liang J, Cai D. Membrane-less compartments in the nucleus: Separated or connected phases? Curr Opin Cell Biol 2023; 84:102215. [PMID: 37574634 PMCID: PMC10528681 DOI: 10.1016/j.ceb.2023.102215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Abstract
In recent years, it has become increasingly clear that many nuclear membrane-less compartments have liquid-like properties and may form through the physicochemical process of phase separation. In this review, we will first discuss how various nuclear compartments, such as the genome, transcription compartments, and nuclear bodies are formed through phase separation. Then, we propose that inter-compartmental communications can also be prevalent and may be mediated by inter-compartmental diffusion of macromolecules, fusion among different compartments, and transient or stable contacts among nuclear compartments. Understanding how nuclear compartments communicate with each other represents an exciting new area of research and may reveal important insights about cellular functions and uncover previously under-appreciated disease mechanisms.
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Affiliation(s)
- Jindayi Liang
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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12
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Zhu M, Zhang L, Jin L, Chen Y, Yang H, Ji B, Xu Y. Deep learning-enabled fast DNA-PAINT imaging in cells. BIOPHYSICS REPORTS 2023; 9:177-187. [PMID: 38516619 PMCID: PMC10951475 DOI: 10.52601/bpr.2023.230014] [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: 09/13/2023] [Accepted: 10/07/2023] [Indexed: 03/23/2024] Open
Abstract
DNA-based point accumulation in nanoscale topography (DNA-PAINT) is a well-established technique for single-molecule localization microscopy (SMLM), enabling resolution of up to a few nanometers. Traditionally, DNA-PAINT involves the utilization of tens of thousands of single-molecule fluorescent images to generate a single super-resolution image. This process can be time-consuming, which makes it unfeasible for many researchers. Here, we propose a simplified DNA-PAINT labeling method and a deep learning-enabled fast DNA-PAINT imaging strategy for subcellular structures, such as microtubules. By employing our method, super-resolution reconstruction can be achieved with only one-tenth of the raw data previously needed, along with the option of acquiring the widefield image. As a result, DNA-PAINT imaging is significantly accelerated, making it more accessible to a wider range of biological researchers.
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Affiliation(s)
- Min Zhu
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
| | - Luhao Zhang
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
- Binjiang Institute of Zhejiang University, Hangzhou 310053, China
| | - Luhong Jin
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
| | - Yunyue Chen
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
| | - Haixu Yang
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
| | - Baohua Ji
- Department of Engineering Mechanics, Biomechanics and Biomaterials Laboratory, Zhejiang University, Hangzhou 310027, China
| | - Yingke Xu
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
- Binjiang Institute of Zhejiang University, Hangzhou 310053, China
- Department of Endocrinology, Children’s Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Children’s Health, Hangzhou 310051, China
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13
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Liu Y, Huang Z, Liu H, Ji Z, Arora A, Cai D, Wang H, Liu M, Simko EAJ, Zhang Y, Periz G, Liu Z, Wang J. DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat. Neuron 2023; 111:1205-1221.e9. [PMID: 36822200 PMCID: PMC10121948 DOI: 10.1016/j.neuron.2023.01.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 12/08/2022] [Accepted: 01/27/2023] [Indexed: 02/24/2023]
Abstract
The C9orf72 hexanucleotide repeat expansion (HRE) is the most frequent genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, we describe the pathogenic cascades that are initiated by the C9orf72 HRE DNA. The HRE DNA binds to its protein partner DAXX and promotes its liquid-liquid phase separation, which is capable of reorganizing genomic structures. An HRE-dependent nuclear accumulation of DAXX drives chromatin remodeling and epigenetic changes such as histone hypermethylation and hypoacetylation in patient cells. While regulating global gene expression, DAXX plays a key role in the suppression of basal and stress-inducible expression of C9orf72 via chromatin remodeling and epigenetic modifications of the promoter of the major C9orf72 transcript. Downregulation of DAXX or rebalancing the epigenetic modifications mitigates the stress-induced sensitivity of C9orf72-patient-derived motor neurons. These studies reveal a C9orf72 HRE DNA-dependent regulatory mechanism for both local and genomic architectural changes in the relevant diseases.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Zhiyuan Huang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Honghe Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Duke University, Durham, NC 27710, USA
| | - Amit Arora
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Hongjin Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mingming Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eric A J Simko
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yanjun Zhang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Goran Periz
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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14
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Burgers TCQ, Vlijm R. Fluorescence-based super-resolution-microscopy strategies for chromatin studies. Chromosoma 2023:10.1007/s00412-023-00792-9. [PMID: 37000292 PMCID: PMC10356683 DOI: 10.1007/s00412-023-00792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023]
Abstract
Super-resolution microscopy (SRM) is a prime tool to study chromatin organisation at near biomolecular resolution in the native cellular environment. With fluorescent labels DNA, chromatin-associated proteins and specific epigenetic states can be identified with high molecular specificity. The aim of this review is to introduce the field of diffraction-unlimited SRM to enable an informed selection of the most suitable SRM method for a specific chromatin-related research question. We will explain both diffraction-unlimited approaches (coordinate-targeted and stochastic-localisation-based) and list their characteristic spatio-temporal resolutions, live-cell compatibility, image-processing, and ability for multi-colour imaging. As the increase in resolution, compared to, e.g. confocal microscopy, leads to a central role of the sample quality, important considerations for sample preparation and concrete examples of labelling strategies applicable to chromatin research are discussed. To illustrate how SRM-based methods can significantly improve our understanding of chromatin functioning, and to serve as an inspiring starting point for future work, we conclude with examples of recent applications of SRM in chromatin research.
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Affiliation(s)
- Thomas C Q Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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15
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Yang L, Chen Q, Wang Z, Zhang H, Sun H. Small-molecule fluorescent probes for plasma membrane staining: Design, mechanisms and biological applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Abstract
In animals, the sequences for controlling gene expression do not concentrate just at the transcription start site of genes, but are frequently thousands to millions of base pairs distal to it. The interaction of these sequences with one another and their transcription start sites is regulated by factors that shape the three-dimensional (3D) organization of the genome within the nucleus. Over the past decade, indirect tools exploiting high-throughput DNA sequencing have helped to map this 3D organization, have identified multiple key regulators of its structure and, in the process, have substantially reshaped our view of how 3D genome architecture regulates transcription. Now, new tools for high-throughput super-resolution imaging of chromatin have directly visualized the 3D chromatin organization, settling some debates left unresolved by earlier indirect methods, challenging some earlier models of regulatory specificity and creating hypotheses about the role of chromatin structure in transcriptional regulation.
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17
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Super-resolution microscopy reveals the number and distribution of topoisomerase IIα and CENH3 molecules within barley metaphase chromosomes. Chromosoma 2023; 132:19-29. [PMID: 36719450 PMCID: PMC9981516 DOI: 10.1007/s00412-023-00785-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/25/2022] [Accepted: 12/13/2022] [Indexed: 02/01/2023]
Abstract
Topoisomerase IIα (Topo IIα) and the centromere-specific histone H3 variant CENH3 are key proteins involved in chromatin condensation and centromere determination, respectively. Consequently, they are required for proper chromosome segregation during cell divisions. We combined two super-resolution techniques, structured illumination microscopy (SIM) to co-localize Topo IIα and CENH3, and photoactivated localization microscopy (PALM) to determine their molecule numbers in barley metaphase chromosomes. We detected a dispersed Topo IIα distribution along chromosome arms but an accumulation at centromeres, telomeres, and nucleolus-organizing regions. With a precision of 10-50 nm, we counted ~ 20,000-40,000 Topo IIα molecules per chromosome, 28% of them within the (peri)centromere. With similar precision, we identified ~13,500 CENH3 molecules per centromere where Topo IIα proteins and CENH3-containing chromatin intermingle. In short, we demonstrate PALM as a useful method to count and localize single molecules with high precision within chromosomes. The ultrastructural distribution and the detected amount of Topo IIα and CENH3 are instrumental for a better understanding of their functions during chromatin condensation and centromere determination.
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18
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Ranjan R, Chen X. Quantitative imaging of chromatin inheritance using a dual-color histone in Drosophila germinal stem cells. STAR Protoc 2022; 3:101811. [PMID: 36386868 PMCID: PMC9640340 DOI: 10.1016/j.xpro.2022.101811] [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: 11/11/2022] Open
Abstract
We detail a stepwise protocol for the investigation and quantification of chromatin features during asymmetric cell division (ACD) of Drosophila germline stem cells (GSCs). We describe the use of a dual-color histone to study the inheritance of new and old histones. We detail steps for imaging and analysis of sister chromatid condensation dynamics and nucleosome density changes. In addition, this protocol could be applied to identify stem cells, which can be challenging to identify in intact tissues. For complete details on the use and execution of this protocol, please refer to Tran et al. (2012), Ranjan et al. (2019), and Ranjan et al. (2022).
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Affiliation(s)
- Rajesh Ranjan
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218-2685, USA; Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218-2685, USA.
| | - Xin Chen
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218-2685, USA; Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218-2685, USA.
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19
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
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Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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20
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Urban JA, Ranjan R, Chen X. Asymmetric Histone Inheritance: Establishment, Recognition, and Execution. Annu Rev Genet 2022; 56:113-143. [PMID: 35905975 PMCID: PMC10054593 DOI: 10.1146/annurev-genet-072920-125226] [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: 11/09/2022]
Abstract
The discovery of biased histone inheritance in asymmetrically dividing Drosophila melanogaster male germline stem cells demonstrates one means to produce two distinct daughter cells with identical genetic material. This inspired further studies in different systems, which revealed that this phenomenon may be a widespread mechanism to introduce cellular diversity. While the extent of asymmetric histone inheritance could vary among systems, this phenomenon is proposed to occur in three steps: first, establishment of histone asymmetry between sister chromatids during DNA replication; second, recognition of sister chromatids carrying asymmetric histone information during mitosis; and third, execution of this asymmetry in the resulting daughter cells. By compiling the current knowledge from diverse eukaryotic systems, this review comprehensively details and compares known chromatin factors, mitotic machinery components, and cell cycle regulators that may contribute to each of these three steps. Also discussed are potential mechanisms that introduce and regulate variable histone inheritance modes and how these different modes may contribute to cell fate decisions in multicellular organisms.
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Affiliation(s)
- Jennifer A Urban
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA;
| | - Rajesh Ranjan
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
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21
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Damon LJ, Aaron J, Palmer AE. Single molecule microscopy to profile the effect of zinc status on transcription factor dynamics. Sci Rep 2022; 12:17789. [PMID: 36273101 PMCID: PMC9588069 DOI: 10.1038/s41598-022-22634-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/18/2022] [Indexed: 01/19/2023] Open
Abstract
The regulation of transcription is a complex process that involves binding of transcription factors (TFs) to specific sequences, recruitment of cofactors and chromatin remodelers, assembly of the pre-initiation complex and recruitment of RNA polymerase II. Increasing evidence suggests that TFs are highly dynamic and interact only transiently with DNA. Single molecule microscopy techniques are powerful approaches for tracking individual TF molecules as they diffuse in the nucleus and interact with DNA. Here we employ multifocus microscopy and highly inclined laminated optical sheet microscopy to track TF dynamics in response to perturbations in labile zinc inside cells. We sought to define whether zinc-dependent TFs sense changes in the labile zinc pool by determining whether their dynamics and DNA binding can be modulated by zinc. We used fluorescently tagged versions of the glucocorticoid receptor (GR), with two C4 zinc finger domains, and CCCTC-binding factor (CTCF), with eleven C2H2 zinc finger domains. We found that GR was largely insensitive to perturbations of zinc, whereas CTCF was significantly affected by zinc depletion and its dwell time was affected by zinc elevation. These results indicate that at least some transcription factors are sensitive to zinc dynamics, revealing a potential new layer of transcriptional regulation.
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Affiliation(s)
- Leah J. Damon
- grid.266190.a0000000096214564Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303 USA
| | - Jesse Aaron
- grid.443970.dAdvanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 USA
| | - Amy E. Palmer
- grid.266190.a0000000096214564Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303 USA
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22
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Alemasova EE, Lavrik OI. A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates. Nucleic Acids Res 2022; 50:10817-10838. [PMID: 36243979 DOI: 10.1093/nar/gkac866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/14/2022] [Accepted: 10/09/2022] [Indexed: 11/13/2022] Open
Abstract
Condensates are biomolecular assemblies that concentrate biomolecules without the help of membranes. They are morphologically highly versatile and may emerge via distinct mechanisms. Nucleic acids-DNA, RNA and poly(ADP-ribose) (PAR) play special roles in the process of condensate organization. These polymeric scaffolds provide multiple specific and nonspecific interactions during nucleation and 'development' of macromolecular assemblages. In this review, we focus on condensates formed with PAR. We discuss to what extent the literature supports the phase separation origin of these structures. Special attention is paid to similarities and differences between PAR and RNA in the process of dynamic restructuring of condensates during their functioning.
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Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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23
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Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, Hung KL, Yost KE, Shi Q, Erb ML, Rajkumar U, Wu S, Taschner-Mandl S, Bernkopf M, Swanton C, Liu Z, Huang W, Chang HY, Bafna V, Henssen AG, Werner B, Mischel PS. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nat Genet 2022; 54:1527-1533. [PMID: 36123406 PMCID: PMC9534767 DOI: 10.1038/s41588-022-01177-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/01/2022] [Indexed: 12/21/2022]
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance-random identity by descent-is poorly understood. Also unclear is the impact of ecDNA on somatic variation and selection. Here integrating theoretical models of random segregation, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, we demonstrate that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment. Observed ecDNAs benefit host cell survival or growth and can change within a single cell cycle. ecDNA inheritance can predict, a priori, some of the aggressive features of ecDNA-containing cancers. These properties are facilitated by the ability of ecDNA to rapidly adapt genomes in a way that is not possible through chromosomal oncogene amplification. These results show how the nonchromosomal random inheritance pattern of ecDNA contributes to poor outcomes for patients with cancer.
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Affiliation(s)
- Joshua T Lange
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - John C Rose
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Celine Y Chen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yuriy Pichugin
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA, USA
| | - Jun Tang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcella L Erb
- University of California San Diego Light Microscopy Core Facility, Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Weini Huang
- Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China.
- Department of Mathematics, Queen Mary University of London, London, UK.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Benjamin Werner
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- ChEM-H, Stanford University, Stanford, CA, USA.
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24
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Dehingia B, Milewska M, Janowski M, Pękowska A. CTCF
shapes chromatin structure and gene expression in health and disease. EMBO Rep 2022; 23:e55146. [PMID: 35993175 PMCID: PMC9442299 DOI: 10.15252/embr.202255146] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/31/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bondita Dehingia
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Małgorzata Milewska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Marcin Janowski
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
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25
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Lamberti WF, Zang C. Extracting physical characteristics of higher-order chromatin structures from 3D image data. Comput Struct Biotechnol J 2022; 20:3387-3398. [PMID: 35832633 PMCID: PMC9260447 DOI: 10.1016/j.csbj.2022.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
Higher-order chromatin structures have functional impacts on gene regulation and cell identity determination. Using high-throughput sequencing (HTS)-based methods like Hi-C, active or inactive compartments and open or closed topologically associating domain (TAD) structures can be identified on a cell population level. Recently developed high-resolution three-dimensional (3D) molecular imaging techniques such as 3D electron microscopy with in situ hybridization (3D-EMSIH) and 3D structured illumination microscopy (3D-SIM) enable direct detection of physical representations of chromatin structures in a single cell. However, computational analysis of 3D image data with explainability and interpretability on functional characteristics of chromatin structures is still challenging. We developed Extracting Physical-Characteristics from Images of Chromatin Structures (EPICS), a machine-learning based computational method for processing high-resolution chromatin 3D image data. Using EPICS on images produced by 3D-EMISH or 3D-SIM techniques, we generated more direct 3D representations of higher-order chromatin structures, identified major chromatin domains, and determined the open or closed status of each domain. We identified several high-contributing features from the model as the major physical characteristics that define the open or closed chromatin domains, demonstrating the explainability and interpretability of EPICS. EPICS can be applied to the analysis of other high-resolution 3D molecular imaging data for spatial genomics studies. The R and Python codes of EPICS are available at https://github.com/zang-lab/epics.
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26
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Gabriele M, Brandão HB, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh THS, Mirny L, Zechner C, Hansen AS. Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science 2022; 376:496-501. [PMID: 35420890 PMCID: PMC9069445 DOI: 10.1126/science.abn6583] [Citation(s) in RCA: 180] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF and loop-extruding cohesins, but the live dynamics of loop formation and stability remain unknown. Here, we directly visualized chromatin looping at the Fbn2 TAD in mouse embryonic stem cells using super-resolution live-cell imaging and quantified looping dynamics by Bayesian inference. Unexpectedly, the Fbn2 loop was both rare and dynamic, with a looped fraction of approximately 3 to 6.5% and a median loop lifetime of approximately 10 to 30 minutes. Our results establish that the Fbn2 TAD is highly dynamic, and about 92% of the time, cohesin-extruded loops exist within the TAD without bridging both CTCF boundaries. This suggests that single CTCF boundaries, rather than the fully CTCF-CTCF looped state, may be the primary regulators of functional interactions.
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Affiliation(s)
- Michele Gabriele
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Hugo B. Brandão
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Simon Grosse-Holz
- Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Institut Curie; Paris 75005, France
| | - Asmita Jha
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Gina M. Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Tsung-Han S. Hsieh
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Leonid Mirny
- Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Institut Curie; Paris 75005, France
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Christoph Zechner
- Max Planck Institute of Molecular Cell Biology & Genetics; Dresden, Germany
- Center for Systems Biology Dresden; Dresden, Germany
- Cluster of Excellence Physics of Life and Faculty of Computer Science, TU Dresden; Dresden, Germany
| | - Anders S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
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27
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BET proteins loop and compartmentalize the 3D genome. Nat Genet 2022; 54:370-371. [DOI: 10.1038/s41588-022-01031-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Xie L, Dong P, Qi Y, Hsieh THS, English BP, Jung S, Chen X, De Marzio M, Casellas R, Chang HY, Zhang B, Tjian R, Liu Z. BRD2 compartmentalizes the accessible genome. Nat Genet 2022; 54:481-491. [PMID: 35410381 PMCID: PMC9099420 DOI: 10.1038/s41588-022-01044-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/01/2022] [Indexed: 12/15/2022]
Abstract
Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associated domains (TADs). While the formation of TADs is dependent on Cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after Cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on one hand by Cohesin and on the other by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-Cohesin interplay model of nuclear topology, where genome compartmentalization results from a competition between loop extrusion and chromatin state-specific affinity interactions.
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Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei. BMC Genomics 2022; 23:214. [PMID: 35296236 PMCID: PMC8928671 DOI: 10.1186/s12864-021-08266-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 12/20/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The "Assay for Transposase Accessible Chromatin sequencing" (ATAC-seq) is an efficient and easy to implement protocol to measure chromatin accessibility that has been widely used in multiple applications studying gene regulation. While several modifications or variants of the protocol have been published since it was first described, there has not yet been an extensive evaluation of the effects of specific protocol choices head-to-head in a consistent experimental setting. In this study, we tested multiple protocol options for major ATAC-seq components (including three reaction buffers, two reaction temperatures, two enzyme sources, and the use of either native or fixed nuclei) in a well-characterized cell line. With all possible combinations of components, we created 24 experimental conditions with four replicates for each (a total of 96 samples). In addition, we tested the 12 native conditions in a primary sample type (mouse lung tissue) with two different input amounts. Through these extensive comparisons, we were able to observe the effect of different ATAC-seq conditions on data quality and to examine the utility and potential redundancy of various quality metrics. RESULTS In general, native samples yielded more peaks (particularly at loci not overlapping transcription start sites) than fixed samples, and the temperature at which the enzymatic reaction was carried out had a major impact on data quality metrics for both fixed and native nuclei. However, the effect of various conditions tested was not always consistent between the native and fixed samples. For example, the Nextera and Omni buffers were largely interchangeable across all other conditions, while the THS buffer resulted in markedly different profiles in native samples. In-house and commercial enzymes performed similarly. CONCLUSIONS We found that the relationship between commonly used measures of library quality differed across temperature and fixation, and so evaluating multiple metrics in assessing the quality of a sample is recommended. Notably, we also found that these choices can bias the functional class of elements profiled and so we recommend evaluating several formulations in any new experiments. Finally, we hope the ATAC-seq workflow formulated in this study on crosslinked samples will help to profile archival clinical specimens.
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Hsiao YT, Tsai CN, Chen TH, Hsieh CL. Label-Free Dynamic Imaging of Chromatin in Live Cell Nuclei by High-Speed Scattering-Based Interference Microscopy. ACS NANO 2022; 16:2774-2788. [PMID: 34967599 DOI: 10.1021/acsnano.1c09748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chromatin is a DNA-protein complex that is densely packed in the cell nucleus. The nanoscale chromatin compaction plays critical roles in the modulation of cell nuclear processes. However, little is known about the spatiotemporal dynamics of chromatin compaction states because it remains difficult to quantitatively measure the chromatin compaction level in live cells. Here, we demonstrate a strategy, referenced as DYNAMICS imaging, for mapping chromatin organization in live cell nuclei by analyzing the dynamic scattering signal of molecular fluctuations. Highly sensitive optical interference microscopy, coherent brightfield (COBRI) microscopy, is implemented to detect the linear scattering of unlabeled chromatin at a high speed. A theoretical model is established to determine the local chromatin density from the statistical fluctuation of the measured scattering signal. DYNAMICS imaging allows us to reconstruct a speckle-free nucleus map that is highly correlated to the fluorescence chromatin image. Moreover, together with calibration based on nanoparticle colloids, we show that the DYNAMICS signal is sensitive to the chromatin compaction level at the nanoscale. We confirm the effectiveness of DYNAMICS imaging in detecting the condensation and decondensation of chromatin induced by chemical drug treatments. Importantly, the stable scattering signal supports a continuous observation of the chromatin condensation and decondensation processes for more than 1 h. Using this technique, we detect transient and nanoscopic chromatin condensation events occurring on a time scale of a few seconds. Label-free DYNAMICS imaging offers the opportunity to investigate chromatin conformational dynamics and to explore their significance in various gene activities.
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Affiliation(s)
- Yi-Teng Hsiao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, 1 Roosevelt Road Section 4, Taipei 10617, Taiwan
| | - Chia-Ni Tsai
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, 1 Roosevelt Road Section 4, Taipei 10617, Taiwan
| | - Te-Hsin Chen
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, 1 Roosevelt Road Section 4, Taipei 10617, Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, 1 Roosevelt Road Section 4, Taipei 10617, Taiwan
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31
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Teranikar T, Lim J, Ijaseun T, Lee J. Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm. Int J Mol Sci 2022; 23:1643. [PMID: 35163562 PMCID: PMC8835835 DOI: 10.3390/ijms23031643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.
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Affiliation(s)
| | | | | | - Juhyun Lee
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 75022, USA; (T.T.); (J.L.); (T.I.)
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32
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Bond C, Santiago-Ruiz AN, Tang Q, Lakadamyali M. Technological advances in super-resolution microscopy to study cellular processes. Mol Cell 2022; 82:315-332. [PMID: 35063099 PMCID: PMC8852216 DOI: 10.1016/j.molcel.2021.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/22/2023]
Abstract
Since its initial demonstration in 2000, far-field super-resolution light microscopy has undergone tremendous technological developments. In parallel, these developments have opened a new window into visualizing the inner life of cells at unprecedented levels of detail. Here, we review the technical details behind the most common implementations of super-resolution microscopy and highlight some of the recent, promising advances in this field.
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Affiliation(s)
- Charles Bond
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adriana N Santiago-Ruiz
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qing Tang
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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33
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Abstract
3D genome mapping aims at connecting the physics of chromatin folding to the underlying biological events, and applications of various chromosomal conformation capture (3C) assays continue to discover critical roles of genome folding in regulating nuclear functions. To interrogate the full spectrum of chromatin folding ranging from the level of nucleosomes to full chromosomes in mammals, we developed an enhanced 3C-based method called Micro-C. The protocol employs Micrococcal nuclease (MNase) to fragment the genome, which overcomes the resolution limit of restriction enzyme-based methods, enabling the estimation of contact frequencies between proximal nucleosomes. Such improvements successfully resolve the fine-scale level of chromatin folding, including enhancer-promoter or promoter-promoter interactions, genic and nucleosomal folding, and boost the signal-to-noise ratio in detecting loops and substructures underlying TADs. In this chapter, we will thoroughly discuss the details of the Micro-C protocol and critical parameters to consider for generating high-quality Micro-C maps.
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Affiliation(s)
- Elena Slobodyanyuk
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, 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
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, 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
| | - Tsung-Han S Hsieh
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, 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.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
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Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong ITL, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 2021; 600:731-736. [PMID: 34819668 PMCID: PMC9126690 DOI: 10.1038/s41586-021-04116-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/08/2021] [Indexed: 02/07/2023]
Abstract
Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation1. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression. ecDNAs that encode multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumours. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the bromodomain and extraterminal domain (BET) protein BRD4 in a MYC-amplified colorectal cancer cell line. The BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-derived-oncogene transcription. The BRD4-bound PVT1 promoter is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent expression of MYC. Furthermore, the PVT1 promoter on an exogenous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic silencing of ecDNA enhancers by CRISPR interference reveals intermolecular enhancer-gene activation among multiple oncogene loci that are amplified on distinct ecDNAs. Thus, protein-tethered ecDNA hubs enable intermolecular transcriptional regulation and may serve as units of oncogene function and cooperative evolution and as potential targets for cancer therapy.
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Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Robert Schöpflin
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joshua T Lange
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natasha E Weiser
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Celine Chen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maria E Valieva
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ivy Tsz-Lo Wong
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Connor V Duffy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jun Tang
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - John C Rose
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jordan Friedlein
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Anindya Bagchi
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Stefan Mundlos
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Paul S Mischel
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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35
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Mancebo A, Mehra D, Banerjee C, Kim DH, Puchner EM. Efficient Cross-Correlation Filtering of One- and Two-Color Single Molecule Localization Microscopy Data. FRONTIERS IN BIOINFORMATICS 2021; 1:739769. [PMID: 36303727 PMCID: PMC9581065 DOI: 10.3389/fbinf.2021.739769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/14/2021] [Indexed: 11/25/2022] Open
Abstract
Single molecule localization microscopy has become a prominent technique to quantitatively study biological processes below the optical diffraction limit. By fitting the intensity profile of single sparsely activated fluorophores, which are often attached to a specific biomolecule within a cell, the locations of all imaged fluorophores are obtained with ∼20 nm resolution in the form of a coordinate table. While rendered super-resolution images reveal structural features of intracellular structures below the optical diffraction limit, the ability to further analyze the molecular coordinates presents opportunities to gain additional quantitative insights into the spatial distribution of a biomolecule of interest. For instance, pair-correlation or radial distribution functions are employed as a measure of clustering, and cross-correlation analysis reveals the colocalization of two biomolecules in two-color SMLM data. Here, we present an efficient filtering method for SMLM data sets based on pair- or cross-correlation to isolate localizations that are clustered or appear in proximity to a second set of localizations in two-color SMLM data. In this way, clustered or colocalized localizations can be separately rendered and analyzed to compare other molecular properties to the remaining localizations, such as their oligomeric state or mobility in live cell experiments. Current matrix-based cross-correlation analyses of large data sets quickly reach the limitations of computer memory due to the space complexity of constructing the distance matrices. Our approach leverages k-dimensional trees to efficiently perform range searches, which dramatically reduces memory needs and the time for the analysis. We demonstrate the versatile applications of this method with simulated data sets as well as examples of two-color SMLM data. The provided MATLAB code and its description can be integrated into existing localization analysis packages and provides a useful resource to analyze SMLM data with new detail.
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Affiliation(s)
- Angel Mancebo
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
| | - Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
| | - Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
| | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Elias M. Puchner,
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36
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Goel VY, Hansen AS. The macro and micro of chromosome conformation capture. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2021; 10:e395. [PMID: 32987449 PMCID: PMC8236208 DOI: 10.1002/wdev.395] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022]
Abstract
The 3D organization of the genome facilitates gene regulation, replication, and repair, making it a key feature of genomic function and one that remains to be properly understood. Over the past two decades, a variety of chromosome conformation capture (3C) methods have delineated genome folding from megabase-scale compartments and topologically associating domains (TADs) down to kilobase-scale enhancer-promoter interactions. Understanding the functional role of each layer of genome organization is a gateway to understanding cell state, development, and disease. Here, we discuss the evolution of 3C-based technologies for mapping 3D genome organization. We focus on genomics methods and provide a historical account of the development from 3C to Hi-C. We also discuss ChIP-based techniques that focus on 3D genome organization mediated by specific proteins, capture-based methods that focus on particular regions or regulatory elements, 3C-orthogonal methods that do not rely on restriction digestion and proximity ligation, and methods for mapping the DNA-RNA and RNA-RNA interactomes. We consider the biological discoveries that have come from these methods, examine the mechanistic contributions of CTCF, cohesin, and loop extrusion to genomic folding, and detail the 3D genome field's current understanding of nuclear architecture. Finally, we give special consideration to Micro-C as an emerging frontier in chromosome conformation capture and discuss recent Micro-C findings uncovering fine-scale chromatin organization in unprecedented detail. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics.
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Affiliation(s)
- Viraat Y. Goel
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Anders S. Hansen
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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37
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The spatial position effect: synthetic biology enters the era of 3D genomics. Trends Biotechnol 2021; 40:539-548. [PMID: 34607694 DOI: 10.1016/j.tibtech.2021.09.001] [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: 07/23/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022]
Abstract
Microbial cell factories are critical to achieving green biomanufacturing. A position effect occurs when a synthetic gene circuit is expressed from different positions in the chassis strain genome. Here, we propose the concept of the 'spatial position effect,' which uses technologies in 3D genomics to reveal the spatial structure characteristics of the 3D genome of the chassis. On this basis, we propose to rationally design the integration sites of synthetic gene circuits, use reporter genes for preliminary screening, and integrate synthetic gene circuits into promising sites for further experiments. This approach can produce stable and efficient chassis strains for green biomanufacturing. The proposed spatial position effect brings synthetic biology into the era of 3D genomics.
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38
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Marenda M, Lazarova E, van de Linde S, Gilbert N, Michieletto D. Parameter-free molecular super-structures quantification in single-molecule localization microscopy. J Cell Biol 2021; 220:211893. [PMID: 33734291 PMCID: PMC7980255 DOI: 10.1083/jcb.202010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/06/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Understanding biological function requires the identification and characterization of complex patterns of molecules. Single-molecule localization microscopy (SMLM) can quantitatively measure molecular components and interactions at resolutions far beyond the diffraction limit, but this information is only useful if these patterns can be quantified and interpreted. We provide a new approach for the analysis of SMLM data that develops the concept of structures and super-structures formed by interconnected elements, such as smaller protein clusters. Using a formal framework and a parameter-free algorithm, (super-)structures formed from smaller components are found to be abundant in classes of nuclear proteins, such as heterogeneous nuclear ribonucleoprotein particles (hnRNPs), but are absent from ceramides located in the plasma membrane. We suggest that mesoscopic structures formed by interconnected protein clusters are common within the nucleus and have an important role in the organization and function of the genome. Our algorithm, SuperStructure, can be used to analyze and explore complex SMLM data and extract functionally relevant information.
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Affiliation(s)
- Mattia Marenda
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Elena Lazarova
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Sebastian van de Linde
- Scottish Universities Physics Alliance, Department of Physics, University of Strathclyde, Glasgow, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Davide Michieletto
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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39
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Yang Y, Ye X, Dai R, Li Z, Zhang Y, Xue W, Zhu Y, Feng D, Qin L, Wang X, Lei B, Liao S, Hao B. Phase separation of Epstein-Barr virus EBNA2 protein reorganizes chromatin topology for epigenetic regulation. Commun Biol 2021; 4:967. [PMID: 34400762 PMCID: PMC8368186 DOI: 10.1038/s42003-021-02501-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus nuclear antigen 2 (EBNA2) is a transactivator of viral and cellular gene expression, which plays a critical role in the Epstein-Barr virus-associated diseases. It was reported that EBNA2 regulates gene expression by reorganizing chromatin and manipulating epigenetics. Recent studies showed that liquid-liquid phase separation plays an essential role in epigenetic and transcriptional regulation. Here we show that EBNA2 reorganized chromatin topology to form accessible chromatin domains (ACDs) of the host genome by phase separation. The N-terminal region of EBNA2, which is necessary for phase separation, is sufficient to induce ACDs. The C-terminal domain of EBNA2 promotes the acetylation of accessible chromatin regions by recruiting histone acetylase p300 to ACDs. According to these observations, we proposed a model of EBNA2 reorganizing chromatin topology for its acetylation through phase separation to explain the mechanism of EBNA2 hijacking the host genome by controlling its epigenetics. Yang et al find that phase separation of the Epstein-Barr virus nuclear antigen 2 (EBNA2) is involved in the formation of accessible chromatin domains of the host genome. They also find that EBNA2 recruits histone acetyltransferase to promote histone acetylation on accessible chromatin regions and regulate gene expression and that these two functions are performed by the N- and Cterminus respectively.
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Affiliation(s)
- Yiting Yang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xidong Ye
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ranran Dai
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhaoqiang Li
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yan Zhang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Xue
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yongchang Zhu
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Delong Feng
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Litao Qin
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China
| | - Xin Wang
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China
| | - Bo Lei
- Henan Eye Institute, Henan Eye Hospital, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.
| | - Shixiu Liao
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China. .,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China.
| | - Bingtao Hao
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. .,Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China. .,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China.
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40
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Polavarapu VK, Xing P, Zhang H, Zhao M, Mathot L, Zhao L, Rosen G, Swartling FJ, Sjöblom T, Chen X. Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples. Genome Res 2021; 32:150-161. [PMID: 34261731 PMCID: PMC8744681 DOI: 10.1101/gr.275269.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/08/2021] [Indexed: 11/25/2022]
Abstract
Archived formalin-fixed paraffin-embedded (FFPE) samples are the global standard format for preservation of the majority of biopsies in both basic research and translational cancer studies, and profiling chromatin accessibility in the archived FFPE tissues is fundamental to understanding gene regulation. Accurate mapping of chromatin accessibility from FFPE specimens is challenging because of the high degree of DNA damage. Here, we first showed that standard ATAC-seq can be applied to purified FFPE nuclei but yields lower library complexity and a smaller proportion of long DNA fragments. We then present FFPE-ATAC, the first highly sensitive method for decoding chromatin accessibility in FFPE tissues that combines Tn5-mediated transposition and T7 in vitro transcription. The FFPE-ATAC generates high-quality chromatin accessibility profiles with 500 nuclei from a single FFPE tissue section, enables the dissection of chromatin profiles from the regions of interest with the aid of hematoxylin and eosin (H&E) staining, and reveals disease-associated chromatin regulation from the human colorectal cancer FFPE tissue archived for more than 10 years. In summary, the approach allows decoding of the chromatin states that regulate gene expression in archival FFPE tissues, thereby permitting investigators, to better understand epigenetic regulation in cancer and precision medicine.
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41
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Lin X, Qi Y, Latham AP, Zhang B. Multiscale modeling of genome organization with maximum entropy optimization. J Chem Phys 2021; 155:010901. [PMID: 34241389 PMCID: PMC8253599 DOI: 10.1063/5.0044150] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Three-dimensional (3D) organization of the human genome plays an essential role in all DNA-templated processes, including gene transcription, gene regulation, and DNA replication. Computational modeling can be an effective way of building high-resolution genome structures and improving our understanding of these molecular processes. However, it faces significant challenges as the human genome consists of over 6 × 109 base pairs, a system size that exceeds the capacity of traditional modeling approaches. In this perspective, we review the progress that has been made in modeling the human genome. Coarse-grained models parameterized to reproduce experimental data via the maximum entropy optimization algorithm serve as effective means to study genome organization at various length scales. They have provided insight into the principles of whole-genome organization and enabled de novo predictions of chromosome structures from epigenetic modifications. Applications of these models at a near-atomistic resolution further revealed physicochemical interactions that drive the phase separation of disordered proteins and dictate chromatin stability in situ. We conclude with an outlook on the opportunities and challenges in studying chromosome dynamics.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Andrew P. Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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42
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Xie L, Liu Z. Single-cell imaging of genome organization and dynamics. Mol Syst Biol 2021; 17:e9653. [PMID: 34232558 PMCID: PMC8262488 DOI: 10.15252/msb.20209653] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/13/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Probing the architecture, mechanism, and dynamics of genome folding is fundamental to our understanding of genome function in homeostasis and disease. Most chromosome conformation capture studies dissect the genome architecture with population- and time-averaged snapshots and thus have limited capabilities to reveal 3D nuclear organization and dynamics at the single-cell level. Here, we discuss emerging imaging techniques ranging from light microscopy to electron microscopy that enable investigation of genome folding and dynamics at high spatial and temporal resolution. Results from these studies complement genomic data, unveiling principles underlying the spatial arrangement of the genome and its potential functional links to diverse biological activities in the nucleus.
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Affiliation(s)
- Liangqi Xie
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
| | - Zhe Liu
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
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43
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Xu J, Liu Y. Probing Chromatin Compaction and Its Epigenetic States in situ With Single-Molecule Localization-Based Super-Resolution Microscopy. Front Cell Dev Biol 2021; 9:653077. [PMID: 34178982 PMCID: PMC8222792 DOI: 10.3389/fcell.2021.653077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Chromatin organization play a vital role in gene regulation and genome maintenance in normal biological processes and in response to environmental insults. Disruption of chromatin organization imposes a significant effect on many cellular processes and is often associated with a range of pathological processes such as aging and cancer. Extensive attention has been attracted to understand the structural and functional studies of chromatin architecture. Biochemical assays coupled with the state-of-the-art genomic technologies have been traditionally used to probe chromatin architecture. Recent advances in single molecule localization microscopy (SMLM) open up new opportunities to directly visualize higher-order chromatin architecture, its compaction status and its functional states at nanometer resolution in the intact cells or tissue. In this review, we will first discuss the recent technical advantages and challenges of using SMLM to image chromatin architecture. Next, we will focus on the recent applications of SMLM for structural and functional studies to probe chromatin architecture in key cellular processes. Finally, we will provide our perspectives on the recent development and potential applications of super-resolution imaging of chromatin architecture in improving our understanding in diseases.
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Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Department of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Department of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
- University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, United States
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44
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Wagh K, Ishikawa M, Garcia DA, Stavreva DA, Upadhyaya A, Hager GL. Mechanical Regulation of Transcription: Recent Advances. Trends Cell Biol 2021; 31:457-472. [PMID: 33712293 PMCID: PMC8221528 DOI: 10.1016/j.tcb.2021.02.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/01/2023]
Abstract
Mechanotransduction is the ability of a cell to sense mechanical cues from its microenvironment and convert them into biochemical signals to elicit adaptive transcriptional and other cellular responses. Here, we describe recent advances in the field of mechanical regulation of transcription, highlight mechanical regulation of the epigenome as a key novel aspect of mechanotransduction, and describe recent technological advances that could further elucidate the link between mechanical stimuli and gene expression. In this review, we emphasize the importance of mechanotransduction as one of the governing principles of cancer progression, underscoring the need to conduct further studies of the molecular mechanisms involved in sensing mechanical cues and coordinating transcriptional responses.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Momoko Ishikawa
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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45
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Miriklis EL, Rozario AM, Rothenberg E, Bell TDM, Whelan DR. Understanding DNA organization, damage, and repair with super-resolution fluorescence microscopy. Methods Appl Fluoresc 2021; 9. [PMID: 33765677 DOI: 10.1088/2050-6120/abf239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/25/2021] [Indexed: 11/12/2022]
Abstract
Super-resolution microscopy (SRM) comprises a suite of techniques well-suited to probing the nanoscale landscape of genomic function and dysfunction. Offering the specificity and sensitivity that has made conventional fluorescence microscopy a cornerstone technique of biological research, SRM allows for spatial resolutions as good as 10 nanometers. Moreover, single molecule localization microscopies (SMLMs) enable examination of individual molecular targets and nanofoci allowing for the characterization of subpopulations within a single cell. This review describes how key advances in both SRM techniques and sample preparation have enabled unprecedented insights into DNA structure and function, and highlights many of these new discoveries. Ongoing development and application of these novel, highly interdisciplinary SRM assays will continue to expand the toolbox available for research into the nanoscale genomic landscape.
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Affiliation(s)
| | | | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States of America
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC, Australia
| | - Donna R Whelan
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
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46
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Marenda M, Lazarova E, van de Linde S, Gilbert N, Michieletto D. Parameter-free molecular super-structures quantification in single-molecule localization microscopy. J Cell Biol 2021. [PMID: 33734291 DOI: 10.1101/2020.08.19.254540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Understanding biological function requires the identification and characterization of complex patterns of molecules. Single-molecule localization microscopy (SMLM) can quantitatively measure molecular components and interactions at resolutions far beyond the diffraction limit, but this information is only useful if these patterns can be quantified and interpreted. We provide a new approach for the analysis of SMLM data that develops the concept of structures and super-structures formed by interconnected elements, such as smaller protein clusters. Using a formal framework and a parameter-free algorithm, (super-)structures formed from smaller components are found to be abundant in classes of nuclear proteins, such as heterogeneous nuclear ribonucleoprotein particles (hnRNPs), but are absent from ceramides located in the plasma membrane. We suggest that mesoscopic structures formed by interconnected protein clusters are common within the nucleus and have an important role in the organization and function of the genome. Our algorithm, SuperStructure, can be used to analyze and explore complex SMLM data and extract functionally relevant information.
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Affiliation(s)
- Mattia Marenda
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Elena Lazarova
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Sebastian van de Linde
- Scottish Universities Physics Alliance, Department of Physics, University of Strathclyde, Glasgow, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Davide Michieletto
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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47
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Huang Q, Garrett A, Bose S, Blocker S, Rios AC, Clevers H, Shen X. The frontier of live tissue imaging across space and time. Cell Stem Cell 2021; 28:603-622. [PMID: 33798422 PMCID: PMC8034393 DOI: 10.1016/j.stem.2021.02.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
What you see is what you get-imaging techniques have long been essential for visualization and understanding of tissue development, homeostasis, and regeneration, which are driven by stem cell self-renewal and differentiation. Advances in molecular and tissue modeling techniques in the last decade are providing new imaging modalities to explore tissue heterogeneity and plasticity. Here we describe current state-of-the-art imaging modalities for tissue research at multiple scales, with a focus on explaining key tradeoffs such as spatial resolution, penetration depth, capture time/frequency, and moieties. We explore emerging tissue modeling and molecular tools that improve resolution, specificity, and throughput.
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Affiliation(s)
- Qiang Huang
- Department of Pediatric Surgery, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004 Shaanxi, China; Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Aliesha Garrett
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Shree Bose
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Stephanie Blocker
- Center for In Vitro Microscopy, Duke University, Durham, NC 27708, USA
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht 3584, the Netherlands; Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht 3584, the Netherlands
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Utrecht 3584, the Netherlands; Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht 3584, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht 3584, the Netherlands
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA.
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48
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Affiliation(s)
- Keke Hu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Tho D. K. Nguyen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Pieter E. Oomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
- ParaMedir B.V., 1e Energieweg 13, 9301 LK Roden, The Netherlands
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
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49
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Chu LA, Chang SW, Tang WC, Tseng YT, Chen P, Chen BC. 5D superresolution imaging for a live cell nucleus. Curr Opin Genet Dev 2020; 67:77-83. [PMID: 33383256 DOI: 10.1016/j.gde.2020.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022]
Abstract
With a spatial resolution breaking the diffraction limit of light, superresolution imaging allows the visualization of detailed structures of organelles such as mitochondria, cytoskeleton, nucleus, and so on. With multi-dimensional imaging (x, y, z, t, λ), namely, multi-color 3D live imaging enables us fully understand the function of the cell. It is necessary to analyze structural changes or molecular interactions across a large volume in 3D with different labelled targets. To achieve this goal, scientists recently have expanded the original 2D superresolution microscopic tools into 3D imaging techniques. In this review, we will discuss recent development in superresolution microscopy for live imaging with minimal phototoxicity. We will focus our discussion on the cell nucleus where the genetic materials are stored and processed. Machine learning algorism will be introduced to improve the axial resolution of superresolution imaging.
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Affiliation(s)
- Li-An Chu
- Department of Biomedical Engineering and Environmental Science, National Tsing Hua University, Hsinchu, 30013, Taiwan; Brain Research Center, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Shu-Wei Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Ting Tseng
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Bi-Chang Chen
- Brain Research Center, National Tsing Hua University, Hsinchu, 30013, Taiwan; Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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50
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Qi Y, Reyes A, Johnstone SE, Aryee MJ, Bernstein BE, Zhang B. Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization. Biophys J 2020; 119:1905-1916. [PMID: 33086041 DOI: 10.1016/j.bpj.2020.09.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/24/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Chromosomes are positioned nonrandomly inside the nucleus to coordinate with their transcriptional activity. The molecular mechanisms that dictate the global genome organization and the nuclear localization of individual chromosomes are not fully understood. We introduce a polymer model to study the organization of the diploid human genome. It is data-driven because all parameters can be derived from Hi-C data; it is also a mechanistic model because the energy function is explicitly written out based on a few biologically motivated hypotheses. These two features distinguish the model from existing approaches and make it useful both for reconstructing genome structures and for exploring the principles of genome organization. We carried out extensive validations to show that simulated genome structures reproduce a wide variety of experimental measurements, including chromosome radial positions and spatial distances between homologous pairs. Detailed mechanistic investigations support the importance of both specific interchromosomal interactions and centromere clustering for chromosome positioning. We anticipate the polymer model, when combined with Hi-C experiments, to be a powerful tool for investigating large-scale rearrangements in genome structure upon cell differentiation and tumor progression.
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Affiliation(s)
- Yifeng Qi
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Alejandro Reyes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Data Sciences, Dana Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Sarah E Johnstone
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Bin Zhang
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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