1
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Larkin A, Kunze C, Seman M, Levashkevich A, Curran J, Morris-Evans D, Lemieux S, Khalil AS, Ragunathan K. Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation. Dev Cell 2024; 59:2222-2238.e4. [PMID: 39094565 PMCID: PMC11338711 DOI: 10.1016/j.devcel.2024.07.006] [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: 07/21/2023] [Revised: 04/04/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Epigenetic mechanisms enable cells to develop novel adaptive phenotypes without altering their genetic blueprint. Recent studies show histone modifications, such as heterochromatin-defining H3K9 methylation (H3K9me), can be redistributed to establish adaptive phenotypes. We developed a precision-engineered genetic approach to trigger heterochromatin misregulation on-demand in fission yeast. This enabled us to trace genome-scale RNA and H3K9me changes over time in long-term, continuous cultures. Adaptive H3K9me establishes over remarkably slow timescales relative to the initiating stress. We captured dynamic H3K9me redistribution events which depend on an RNA binding complex MTREC, ultimately leading to cells converging on an optimal adaptive solution. Upon stress removal, cells relax to new transcriptional and chromatin states, establishing memory that is tunable and primed for future adaptive epigenetic responses. Collectively, we identify the slow kinetics of epigenetic adaptation that allow cells to discover and heritably encode novel adaptive solutions, with implications for drug resistance and response to infection.
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Affiliation(s)
- Ajay Larkin
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Colin Kunze
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Melissa Seman
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | - Justin Curran
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | - Sophia Lemieux
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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2
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Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. The molecular architecture of the nuclear basket. Cell 2024:S0092-8674(24)00780-3. [PMID: 39127037 DOI: 10.1016/j.cell.2024.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/24/2024] [Accepted: 07/12/2024] [Indexed: 08/12/2024]
Abstract
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of nucleoporins (Nups) in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.
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Affiliation(s)
- Digvijay Singh
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neelesh Soni
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Farhaz Shaikh
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Madeleine Duquette
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sergey Suslov
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kelly Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Elizabeth Villa
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.
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3
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VanBelzen J, Sakelaris B, Brickner DG, Marcou N, Riecke H, Mangan N, Brickner JH. Chromatin endogenous cleavage provides a global view of RNA polymerase II transcription kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602535. [PMID: 39026809 PMCID: PMC11257477 DOI: 10.1101/2024.07.08.602535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Chromatin immunoprecipitation (ChIP-seq) is the most common approach to observe global binding of proteins to DNA in vivo. The occupancy of transcription factors (TFs) from ChIP-seq agrees well with an alternative method, chromatin endogenous cleavage (ChEC-seq2). However, ChIP-seq and ChEC-seq2 reveal strikingly different patterns of enrichment of yeast RNA polymerase II. We hypothesized that this reflects distinct populations of RNAPII, some of which are captured by ChIP-seq and some of which are captured by ChEC-seq2. RNAPII association with enhancers and promoters - predicted from biochemical studies - is detected well by ChEC-seq2 but not by ChIP-seq. Enhancer/promoter bound RNAPII correlates with transcription levels and matches predicted occupancy based on published rates of enhancer recruitment, preinitiation assembly, initiation, elongation and termination. The occupancy from ChEC-seq2 allowed us to develop a stochastic model for global kinetics of RNAPII transcription which captured both the ChEC-seq2 data and changes upon chemical-genetic perturbations to transcription. Finally, RNAPII ChEC-seq2 and kinetic modeling suggests that a mutation in the Gcn4 transcription factor that blocks interaction with the NPC destabilizes promoter-associated RNAPII without altering its recruitment to the enhancer.
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Affiliation(s)
- Jake VanBelzen
- Department of Molecular Biosciences, Northwestern University
| | - Bennet Sakelaris
- Department of Engineering Sciences and Applied Mathematics, Northwestern University
| | | | - Nikita Marcou
- Department of Molecular Biosciences, Northwestern University
- Current address: Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
| | - Hermann Riecke
- Department of Engineering Sciences and Applied Mathematics, Northwestern University
| | - Niall Mangan
- Department of Engineering Sciences and Applied Mathematics, Northwestern University
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4
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Ge T, Brickner DG, Zehr K, VanBelzen DJ, Zhang W, Caffalette C, Ungerleider S, Marcou N, Chait B, Rout MP, Brickner JH. Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593355. [PMID: 38798450 PMCID: PMC11118273 DOI: 10.1101/2024.05.09.593355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Nuclear pore proteins (Nups) in yeast, flies and mammals physically interact with hundreds or thousands of chromosomal sites, which impacts transcriptional regulation. In budding yeast, transcription factors mediate interaction of Nups with enhancers of highly active genes. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC) without altering its DNA binding or activation domains. SILAC mass spectrometry revealed that this mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 both interacts with the same sites as Nups genome-wide and is required for Nup2 to interact with the yeast genome. In vivo, Crm1 undergoes extensive and stable interactions with the NPC. In vitro, Crm1 binds to Gcn4 and these proteins form a complex with the nuclear pore protein Nup2. Importantly, the interaction between Crm1 and Gcn4 does not require Ran-GTP, suggesting that it is not through the nuclear export sequence binding site. Finally, Crm1 stimulates DNA binding by Gcn4, supporting a model in which allosteric coupling between Crm1 binding and DNA binding permits docking of transcription factor-bound enhancers at the NPC.
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Affiliation(s)
- Tiffany Ge
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | | | - Kara Zehr
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - D Jake VanBelzen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | | | - Sara Ungerleider
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Nikita Marcou
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
- Current address: Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
| | - Brian Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
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5
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Larkin A, Kunze C, Seman M, Levashkevich A, Curran J, Morris-Evans D, Lemieux S, Khalil AS, Ragunathan K. Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.10.548368. [PMID: 37503217 PMCID: PMC10369875 DOI: 10.1101/2023.07.10.548368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
A classical and well-established mechanism that enables cells to adapt to new and adverse conditions is the acquisition of beneficial genetic mutations. Much less is known about epigenetic mechanisms that allow cells to develop novel and adaptive phenotypes without altering their genetic blueprint. It has been recently proposed that histone modifications, such as heterochromatin-defining H3K9 methylation (H3K9me), normally reserved to maintain genome integrity, can be redistributed across the genome to establish new and potentially adaptive phenotypes. To uncover the dynamics of this process, we developed a precision engineered genetic approach to trigger H3K9me redistribution on-demand in fission yeast. This enabled us to trace genome-scale RNA and chromatin changes over time prior to and during adaptation in long-term continuous cultures. Establishing adaptive H3K9me occurs over remarkably slow time-scales relative to the initiating stress. During this time, we captured dynamic H3K9me redistribution events ultimately leading to cells converging on an optimal adaptive solution. Upon removal of stress, cells relax to new transcriptional and chromatin states rather than revert to their initial (ground) state, establishing a tunable memory for a future adaptive epigenetic response. Collectively, our tools uncover the slow kinetics of epigenetic adaptation that allow cells to search for and heritably encode adaptive solutions, with implications for drug resistance and response to infection.
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6
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Ge T, Brickner JH. Inheritance of epigenetic transcriptional memory. Curr Opin Genet Dev 2024; 85:102174. [PMID: 38430840 PMCID: PMC10947848 DOI: 10.1016/j.gde.2024.102174] [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: 11/09/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Epigenetic memory allows organisms to stably alter their transcriptional program in response to developmental or environmental stimuli. Such transcriptional programs are mediated by heritable regulation of the function of enhancers and promoters. Memory involves read-write systems that enable self-propagation and mitotic inheritance of cis-acting epigenetic marks to induce stable changes in transcription. Also, in response to environmental cues, cells can induce epigenetic transcriptional memory to poise inducible genes for faster induction in the future. Here, we discuss modes of epigenetic inheritance and the molecular basis of epigenetic transcriptional memory.
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Affiliation(s)
- Tiffany Ge
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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7
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Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. The Molecular Architecture of the Nuclear Basket. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587068. [PMID: 38586009 PMCID: PMC10996695 DOI: 10.1101/2024.03.27.587068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of Nups in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.
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Affiliation(s)
- Digvijay Singh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Neelesh Soni
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Farhaz Shaikh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeleine Duquette
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergey Suslov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kelly Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
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8
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Zhang X, Bradford B, Baweja S, Tan T, Lee HW, Jose CC, Kim N, Katari M, Cuddapah S. Nickel-induced transcriptional memory in lung epithelial cells promotes interferon signaling upon nicotine exposure. Toxicol Appl Pharmacol 2023; 481:116753. [PMID: 37951547 PMCID: PMC11065478 DOI: 10.1016/j.taap.2023.116753] [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: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Exposure to nickel, an environmental respiratory toxicant, is associated with lung diseases including asthma, pulmonary fibrosis, bronchitis and cancers. Our previous studies have shown that a majority of the nickel-induced transcriptional changes are persistent and do not reverse even after the termination of exposure. This suggested transcriptional memory, wherein the cell 'remembers' past nickel exposure. Transcriptional memory, due to which the cells respond more robustly to a previously encountered stimulus has been identified in a number of organisms. Therefore, transcriptional memory has been described as an adaptive mechanism. However, transcriptional memory caused by environmental toxicant exposures has not been well investigated. Moreover, how the transcriptional memory caused by an environmental toxicant might influence the outcome of exposure to a second toxicant has not been explored. In this study, we investigated whether nickel-induced transcriptional memory influences the outcome of the cell's response to a second respiratory toxicant, nicotine. Nicotine, an addictive compound in tobacco, is associated with the development of chronic lung diseases including chronic obstructive pulmonary disease (COPD) and pulmonary fibrosis. Our results show that nicotine exposure upregulated a subset of genes only in the cells previously exposed to nickel. Furthermore, our analyses indicate robust activation of interferon (IFN) signaling in these cells. IFN signaling is a driver of inflammation, which is associated with many chronic lung diseases. Therefore, our results suggest that nicotine exposure of lung cells that retain the transcriptional memory of previous nickel exposure could result in increased susceptibility to developing chronic inflammatory lung diseases.
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Affiliation(s)
- Xiaoru Zhang
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Beatrix Bradford
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Sahdev Baweja
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Taotao Tan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Hyun-Wook Lee
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Cynthia C Jose
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Nicholas Kim
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Manpreet Katari
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
| | - Suresh Cuddapah
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA.
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9
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Choudhry SK, Neal ML, Li S, Navare AT, Van Eeuwen T, Wozniak RW, Mast FD, Rout MP, Aitchison JD. Nuclear pore complexes mediate subtelomeric gene silencing by regulating PCNA levels on chromatin. J Cell Biol 2023; 222:e202207060. [PMID: 37358474 PMCID: PMC10292210 DOI: 10.1083/jcb.202207060] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 04/02/2023] [Accepted: 06/07/2023] [Indexed: 06/27/2023] Open
Abstract
The nuclear pore complex (NPC) physically interacts with chromatin and regulates gene expression. The Saccharomyces cerevisiae inner ring nucleoporin Nup170 has been implicated in chromatin organization and the maintenance of gene silencing in subtelomeric regions. To gain insight into how Nup170 regulates this process, we used protein-protein interactions, genetic interactions, and transcriptome correlation analyses to identify the Ctf18-RFC complex, an alternative proliferating cell nuclear antigen (PCNA) loader, as a facilitator of the gene regulatory functions of Nup170. The Ctf18-RFC complex is recruited to a subpopulation of NPCs that lack the nuclear basket proteins Mlp1 and Mlp2. In the absence of Nup170, PCNA levels on DNA are reduced, resulting in the loss of silencing of subtelomeric genes. Increasing PCNA levels on DNA by removing Elg1, which is required for PCNA unloading, rescues subtelomeric silencing defects in nup170Δ. The NPC, therefore, mediates subtelomeric gene silencing by regulating PCNA levels on DNA.
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Affiliation(s)
- Sanjeev Kumar Choudhry
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Maxwell L. Neal
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Song Li
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Arti T. Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Trevor Van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | | | - Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Departments of Pediatrics and Biochemistry, University of Washington, Seattle, WA, USA
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10
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Tehrani SSH, Kogan A, Mikulski P, Jansen LET. Remembering foods and foes: emerging principles of transcriptional memory. Cell Death Differ 2023:10.1038/s41418-023-01200-6. [PMID: 37563261 DOI: 10.1038/s41418-023-01200-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Transcriptional memory is characterized by a primed cellular state, induced by an external stimulus that results in an altered expression of primed genes upon re-exposure to the inducing signal. Intriguingly, the primed state is heritably maintained across somatic cell divisions even after the initial stimulus and target gene transcription cease. This phenomenon is widely observed across various organisms and appears to enable cells to retain a memory of external signals, thereby adapting to environmental changes. Signals range from nutrient supplies (food) to a variety of stress signals, including exposure to pathogens (foes), leading to long-term memory such as in the case of trained immunity in plants and mammals. Here, we review these priming phenomena and our current understanding of transcriptional memory. We consider different mechanistic models for how memory can work and discuss existing evidence for potential carriers of memory. Key molecular signatures include: the poising of RNA polymerase II machinery, maintenance of histone marks, as well as alterations in nuclear positioning and long-range chromatin interactions. Finally, we discuss the potential adaptive roles of transcriptional memory in the organismal response to its environment from nutrient sensing to trained immunity.
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Affiliation(s)
- Sahar S H Tehrani
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Anna Kogan
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Pawel Mikulski
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK.
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK.
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11
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Brickner JH. Inheritance of epigenetic transcriptional memory through read-write replication of a histone modification. Ann N Y Acad Sci 2023; 1526:50-58. [PMID: 37391188 PMCID: PMC11216120 DOI: 10.1111/nyas.15033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Epigenetic transcriptional regulation frequently requires histone modifications. Some, but not all, of these modifications are able to template their own inheritance. Here, I discuss the molecular mechanisms by which histone modifications can be inherited and relate these ideas to new results about epigenetic transcriptional memory, a phenomenon that poises recently repressed genes for faster reactivation and has been observed in diverse organisms. Recently, we found that the histone H3 lysine 4 dimethylation that is associated with this phenomenon plays a critical role in sustaining memory and, when factors critical for the establishment of memory are inactivated, can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism may involve a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1- COMPASS. This is the first example of a chromatin-mediated inheritance of a mark that promotes transcription.
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Affiliation(s)
- Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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12
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Deshpande N, Bryk M. Diverse and dynamic forms of gene regulation by the S. cerevisiae histone methyltransferase Set1. Curr Genet 2023; 69:91-114. [PMID: 37000206 DOI: 10.1007/s00294-023-01265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023]
Abstract
Gene transcription is an essential and highly regulated process. In eukaryotic cells, the structural organization of nucleosomes with DNA wrapped around histone proteins impedes transcription. Chromatin remodelers, transcription factors, co-activators, and histone-modifying enzymes work together to make DNA accessible to RNA polymerase. Histone lysine methylation can positively or negatively regulate gene transcription. Methylation of histone 3 lysine 4 by SET-domain-containing proteins is evolutionarily conserved from yeast to humans. In higher eukaryotes, mutations in SET-domain proteins are associated with defects in the development and segmentation of embryos, skeletal and muscle development, and diseases, including several leukemias. Since histone methyltransferases are evolutionarily conserved, the mechanisms of gene regulation mediated by these enzymes are also conserved. Budding yeast Saccharomyces cerevisiae is an excellent model system to study the impact of histone 3 lysine 4 (H3K4) methylation on eukaryotic gene regulation. Unlike larger eukaryotes, yeast cells have only one enzyme that catalyzes H3K4 methylation, Set1. In this review, we summarize current knowledge about the impact of Set1-catalyzed H3K4 methylation on gene transcription in S. cerevisiae. We describe the COMPASS complex, factors that influence H3K4 methylation, and the roles of Set1 in gene silencing at telomeres and heterochromatin, as well as repression and activation at euchromatic loci. We also discuss proteins that "read" H3K4 methyl marks to regulate transcription and summarize alternate functions for Set1 beyond H3K4 methylation.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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13
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Rubio LS, Gross DS. Dynamic coalescence of yeast Heat Shock Protein genes bypasses the requirement for actin. Genetics 2023; 223:iyad006. [PMID: 36659814 PMCID: PMC10319981 DOI: 10.1093/genetics/iyad006] [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: 07/22/2022] [Revised: 07/22/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Nuclear actin has been implicated in dynamic chromatin rearrangements in diverse eukaryotes. In mammalian cells, it is required to reposition double-strand DNA breaks to enable homologous recombination repair and to enhance transcription by facilitating RNA Pol II recruitment to gene promoters. In the yeast Saccharomyces cerevisiae, nuclear actin modulates interphase chromosome dynamics and is required to reposition the induced INO1 gene to the nuclear periphery. Here, we have investigated the role of actin in driving intergenic interactions between Heat Shock Factor 1 (Hsf1)-regulated Heat Shock Protein (HSP) genes in budding yeast. These genes, dispersed on multiple chromosomes, dramatically reposition following exposure of cells to acute thermal stress, leading to their clustering within dynamic biomolecular condensates. Using an auxin-induced degradation strategy, we found that conditional depletion of nucleators of either linear or branched F-actin (Bni1/Bnr1 and Arp2, respectively) had little or no effect on heat shock-induced HSP gene coalescence or transcription. In addition, we found that pretreatment of cells with latrunculin A, an inhibitor of both filamentous and monomeric actin, failed to affect intergenic interactions between activated HSP genes and their heat shock-induced intragenic looping and folding. Moreover, latrunculin A pretreatment had little effect on HSP gene expression at either RNA or protein levels. In notable contrast, we confirmed that repositioning of activated INO1 to the nuclear periphery and its proper expression do require actin. Collectively, our work suggests that transcriptional activation and 3D genome restructuring of thermally induced, Hsf1-regulated genes can occur in the absence of actin.
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Affiliation(s)
- Linda S Rubio
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
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14
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Li B, Zeis P, Zhang Y, Alekseenko A, Fürst E, Sanchez YP, Lin G, Tekkedil MM, Piazza I, Steinmetz LM, Pelechano V. Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation. Nat Commun 2023; 14:910. [PMID: 36801853 PMCID: PMC9936472 DOI: 10.1038/s41467-023-36586-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Chromatin organization has been shown to play a role in the faster response of primed cells. However, the contribution of post-transcriptional regulation is not yet explored. Here we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose. We find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. Our work shows that gene-specific differences in intrinsic nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that primed cells present altered levels of RNA degradation machinery and that both nuclear and cytoplasmic mRNA decay modulate transcriptional memory. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.
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Affiliation(s)
- Bingnan Li
- Department of Diagnostics, Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Patrice Zeis
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Alisa Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Eliska Fürst
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Yerma Pareja Sanchez
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Gen Lin
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,AbbVie Pte Ltd, Singapore, Singapore
| | - Manu M Tekkedil
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
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15
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Sump B, Brickner J. Establishment and inheritance of epigenetic transcriptional memory. Front Mol Biosci 2022; 9:977653. [PMID: 36120540 PMCID: PMC9479176 DOI: 10.3389/fmolb.2022.977653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
For certain inducible genes, the rate and molecular mechanism of transcriptional activation depends on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation and requires both changes in chromatin structure and recruitment of poised RNA Polymerase II (RNAPII) to the promoter. Forms of epigenetic transcriptional memory have been identified in S. cerevisiae, D. melanogaster, C. elegans, and mammals. A well-characterized model of memory is found in budding yeast where memory of inositol starvation involves a positive feedback loop between gene-and condition-specific transcription factors, which mediate an interaction with the nuclear pore complex and a characteristic histone modification: histone H3 lysine 4 dimethylation (H3K4me2). This histone modification permits recruitment of a memory-specific pre-initiation complex, poising RNAPII at the promoter. During memory, H3K4me2 is essential for recruitment of RNAPII and faster reactivation, but RNAPII is not required for H3K4me2. Unlike the RNAPII-dependent H3K4me2 associated with active transcription, RNAPII-independent H3K4me2 requires Nup100, SET3C, the Leo1 subunit of the Paf1 complex and can be inherited through multiple cell cycles upon disrupting the interaction with the Nuclear Pore Complex. The H3K4 methyltransferase (COMPASS) physically interacts with the potential reader (SET3C), suggesting a molecular mechanism for the spreading and re-incorporation of H3K4me2 following DNA replication. Thus, epigenetic transcriptional memory is a conserved adaptation that utilizes a heritable chromatin state, allowing cells and organisms to alter their gene expression programs in response to recent experiences over intermediate time scales.
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16
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Gomar‐Alba M, Pozharskaia V, Cichocki B, Schaal C, Kumar A, Jacquel B, Charvin G, Igual JC, Mendoza M. Nuclear pore complex acetylation regulates mRNA export and cell cycle commitment in budding yeast. EMBO J 2022; 41:e110271. [PMID: 35735140 PMCID: PMC9340480 DOI: 10.15252/embj.2021110271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Nuclear pore complexes (NPCs) mediate communication between the nucleus and the cytoplasm, and regulate gene expression by interacting with transcription and mRNA export factors. Lysine acetyltransferases (KATs) promote transcription through acetylation of chromatin-associated proteins. We find that Esa1, the KAT subunit of the yeast NuA4 complex, also acetylates the nuclear pore basket component Nup60 to promote mRNA export. Acetylation of Nup60 recruits the mRNA export factor Sac3, the scaffolding subunit of the Transcription and Export 2 (TREX-2) complex, to the nuclear basket. The Esa1-mediated nuclear export of mRNAs in turn promotes entry into S phase, which is inhibited by the Hos3 deacetylase in G1 daughter cells to restrain their premature commitment to a new cell division cycle. This mechanism is not only limited to G1/S-expressed genes but also inhibits the expression of the nutrient-regulated GAL1 gene specifically in daughter cells. Overall, these results reveal how acetylation can contribute to the functional plasticity of NPCs in mother and daughter yeast cells. In addition, our work demonstrates dual gene expression regulation by the evolutionarily conserved NuA4 complex, at the level of transcription and at the stage of mRNA export by modifying the nucleoplasmic entrance to nuclear pores.
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Affiliation(s)
- Mercè Gomar‐Alba
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia MolecularUniversitat de ValènciaBurjassotSpain
| | | | - Bogdan Cichocki
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
| | - Celia Schaal
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
| | - Arun Kumar
- Department of Cell BiologyUniversitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Basile Jacquel
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- Centre National de la Recherche Scientifique, UMR7104IllkirchFrance
- Institut National de la Santé et de la Recherche Médicale, U964IllkirchFrance
- Université de StrasbourgStrasbourgFrance
| | - J Carlos Igual
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia MolecularUniversitat de ValènciaBurjassotSpain
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- Centre National de la Recherche Scientifique, UMR7104IllkirchFrance
- Institut National de la Santé et de la Recherche Médicale, U964IllkirchFrance
- Université de StrasbourgStrasbourgFrance
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17
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Tan YS, Zhang RK, Liu ZH, Li BZ, Yuan YJ. Microbial Adaptation to Enhance Stress Tolerance. Front Microbiol 2022; 13:888746. [PMID: 35572687 PMCID: PMC9093737 DOI: 10.3389/fmicb.2022.888746] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 01/28/2023] Open
Abstract
Microbial cell factories have been widely used in the production of various chemicals. Although synthetic biology is useful in improving the cell factories, adaptation is still widely applied to enhance its complex properties. Adaptation is an important strategy for enhancing stress tolerance in microbial cell factories. Adaptation involves gradual modifications of microorganisms in a stressful environment to enhance their tolerance. During adaptation, microorganisms use different mechanisms to enhance non-preferred substrate utilization and stress tolerance, thereby improving their ability to adapt for growth and survival. In this paper, the progress on the effects of adaptation on microbial substrate utilization capacity and environmental stress tolerance are reviewed, and the mechanisms involved in enhancing microbial adaptive capacity are discussed.
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Affiliation(s)
- Yong-Shui Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Ren-Kuan Zhang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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18
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Sump B, Brickner DG, D'Urso A, Kim SH, Brickner JH. Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory. eLife 2022; 11:e77646. [PMID: 35579426 PMCID: PMC9129879 DOI: 10.7554/elife.77646] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/15/2022] [Indexed: 11/13/2022] Open
Abstract
For some inducible genes, the rate and molecular mechanism of transcriptional activation depend on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation, and requires both changes in chromatin structure and recruitment of poised RNA polymerase II (RNAPII) to the promoter. Memory of inositol starvation in budding yeast involves a positive feedback loop between transcription factor-dependent interaction with the nuclear pore complex and histone H3 lysine 4 dimethylation (H3K4me2). While H3K4me2 is essential for recruitment of RNAPII and faster reactivation, RNAPII is not required for H3K4me2. Unlike RNAPII-dependent H3K4me2 associated with transcription, RNAPII-independent H3K4me2 requires Nup100, SET3C, the Leo1 subunit of the Paf1 complex and, upon degradation of an essential transcription factor, is inherited through multiple cell cycles. The writer of this mark (COMPASS) physically interacts with the potential reader (SET3C), suggesting a molecular mechanism for the spreading and re-incorporation of H3K4me2 following DNA replication.
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Affiliation(s)
- Bethany Sump
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Donna G Brickner
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Agustina D'Urso
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Seo Hyun Kim
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
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19
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Khan A, Khan V, Pandey K, Sopory SK, Sanan-Mishra N. Thermo-Priming Mediated Cellular Networks for Abiotic Stress Management in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:866409. [PMID: 35646001 PMCID: PMC9136941 DOI: 10.3389/fpls.2022.866409] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/25/2022] [Indexed: 05/05/2023]
Abstract
Plants can adapt to different environmental conditions and can survive even under very harsh conditions. They have developed elaborate networks of receptors and signaling components, which modulate their biochemistry and physiology by regulating the genetic information. Plants also have the abilities to transmit information between their different parts to ensure a holistic response to any adverse environmental challenge. One such phenomenon that has received greater attention in recent years is called stress priming. Any milder exposure to stress is used by plants to prime themselves by modifying various cellular and molecular parameters. These changes seem to stay as memory and prepare the plants to better tolerate subsequent exposure to severe stress. In this review, we have discussed the various ways in which plants can be primed and illustrate the biochemical and molecular changes, including chromatin modification leading to stress memory, with major focus on thermo-priming. Alteration in various hormones and their subsequent role during and after priming under various stress conditions imposed by changing climate conditions are also discussed.
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Affiliation(s)
| | | | | | | | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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20
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Using Single Molecule RNA FISH to Determine Nuclear Export and Transcription Phenotypes in Drosophila Tissues. Methods Mol Biol 2022; 2502:113-125. [PMID: 35412235 DOI: 10.1007/978-1-0716-2337-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single molecule RNA fluorescence in situ hybridization (smRNA FISH) is a widely used method for examining cellular localization of RNA and assessing gene expression outputs. The Nuclear Pore Complex (NPC) is a nuclear macro-complex known to both mediate nucleocytoplasmic transport and influence transcription via interactions with chromatin. Consequently, depletion of NPC proteins can result in defects in either transcription or nuclear export of mRNA. To distinguish between these two different functions of NPC components, it is preferable to analyze transcription and mRNA export simultaneously or in the same cell. Here, we present a smRNA FISH protocol with downstream custom MATLAB image analysis for application in Drosophila larval salivary gland tissues. This method can detect both nuclear export and transcriptional phenotypes in the same cell and as a single assay, and can be adapted to many other cell types and organisms.
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21
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Pascual-Garcia P, Little SC, Capelson M. Nup98-dependent transcriptional memory is established independently of transcription. eLife 2022; 11:e63404. [PMID: 35289742 PMCID: PMC8923668 DOI: 10.7554/elife.63404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/26/2022] [Indexed: 12/31/2022] Open
Abstract
Cellular ability to mount an enhanced transcriptional response upon repeated exposure to external cues is termed transcriptional memory, which can be maintained epigenetically through cell divisions and can depend on a nuclear pore component Nup98. The majority of mechanistic knowledge on transcriptional memory has been derived from bulk molecular assays. To gain additional perspective on the mechanism and contribution of Nup98 to memory, we used single-molecule RNA FISH (smFISH) to examine the dynamics of transcription in Drosophila cells upon repeated exposure to the steroid hormone ecdysone. We combined smFISH with mathematical modeling and found that upon hormone exposure, cells rapidly activate a low-level transcriptional response, but simultaneously begin a slow transition into a specialized memory state characterized by a high rate of expression. Strikingly, our modeling predicted that this transition between non-memory and memory states is independent of the transcription stemming from initial activation. We confirmed this prediction experimentally by showing that inhibiting transcription during initial ecdysone exposure did not interfere with memory establishment. Together, our findings reveal that Nup98's role in transcriptional memory is to stabilize the forward rate of conversion from low to high expressing state, and that induced genes engage in two separate behaviors - transcription itself and the establishment of epigenetically propagated transcriptional memory.
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Affiliation(s)
- Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Shawn C Little
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Maya Capelson
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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22
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Abstract
The nuclear pore complex (NPC) is a highly conserved channel in the nuclear envelope that mediates mRNA export to the cytosol and bidirectional protein transport. Many chromosomal loci physically interact with nuclear pore proteins (Nups), and interactions with Nups can promote transcriptional repression, transcriptional activation, and transcriptional poising. Interaction with the NPC also affects the spatial arrangement of genes, interchromosomal clustering, and folding of topologically associated domains. Thus, the NPC is a spatial organizer of the genome and regulator of genome function.
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Affiliation(s)
- Michael Chas Sumner
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Jason Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
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23
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Tan YS, Wang L, Wang YY, He QE, Liu ZH, Zhu Z, Song K, Li BZ, Yuan YJ. Protein acetylation regulates xylose metabolism during adaptation of Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:241. [PMID: 34920742 PMCID: PMC8684234 DOI: 10.1186/s13068-021-02090-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND As the second most abundant polysaccharide in nature, hemicellulose can be degraded to xylose as the feedstock for bioconversion to fuels and chemicals. To enhance xylose conversion, the engineered Saccharomyces cerevisiae with xylose metabolic pathway is usually adapted with xylose as the carbon source in the laboratory. However, the mechanism under the adaptation phenomena of the engineered strain is still unclear. RESULTS In this study, xylose-utilizing S. cerevisiae was constructed and used for the adaptation study. It was found that xylose consumption rate increased 1.24-fold in the second incubation of the yYST12 strain in synthetic complete-xylose medium compared with the first incubation. The study figured out that it was observed at the single-cell level that the stagnation time for xylose utilization was reduced after adaptation with xylose medium in the microfluidic device. Such transient memory of xylose metabolism after adaptation with xylose medium, named "xylose consumption memory", was observed in the strains with both xylose isomerase pathway and xylose reductase and xylitol dehydrogenase pathways. In further, the proteomic acetylation of the strains before and after adaptation was investigated, and it was revealed that H4K5 was one of the most differential acetylation sites related to xylose consumption memory of engineered S. cerevisiae. We tested 8 genes encoding acetylase or deacetylase, and it was found that the knockout of the GCN5 and HPA2 encoding acetylases enhanced the xylose consumption memory. CONCLUSIONS The behavior of xylose consumption memory in engineered S. cerevisiae can be successfully induced with xylose in the adaptation. H4K5Ac and two genes of GCN5 and HPA2 are related to xylose consumption memory of engineered S. cerevisiae during adaptation. This study provides valuable insights into the xylose adaptation of engineered S. cerevisiae.
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Affiliation(s)
- Yong-Shui Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Li Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Ying-Ying Wang
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Qi-En He
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhen Zhu
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Kai Song
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
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24
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Ptak C, Saik NO, Premashankar A, Lapetina DL, Aitchison JD, Montpetit B, Wozniak RW. Phosphorylation-dependent mitotic SUMOylation drives nuclear envelope-chromatin interactions. J Cell Biol 2021; 220:212843. [PMID: 34787675 PMCID: PMC8641411 DOI: 10.1083/jcb.202103036] [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: 03/05/2021] [Revised: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 12/15/2022] Open
Abstract
In eukaryotes, chromatin binding to the inner nuclear membrane (INM) and nuclear pore complexes (NPCs) contributes to spatial organization of the genome and epigenetic programs important for gene expression. In mitosis, chromatin–nuclear envelope (NE) interactions are lost and then formed again as sister chromosomes segregate to postmitotic nuclei. Investigating these processes in S. cerevisiae, we identified temporally and spatially controlled phosphorylation-dependent SUMOylation events that positively regulate postmetaphase chromatin association with the NE. Our work establishes a phosphorylation-mediated targeting mechanism of the SUMO ligase Siz2 to the INM during mitosis, where Siz2 binds to and SUMOylates the VAP protein Scs2. The recruitment of Siz2 through Scs2 is further responsible for a wave of SUMOylation along the INM that supports the assembly and anchorage of subtelomeric chromatin at the INM and localization of an active gene (INO1) to NPCs during the later stages of mitosis and into G1-phase.
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Affiliation(s)
- Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Natasha O Saik
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Diego L Lapetina
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada.,Department of Viticulture and Enology, University of California Davis, Davis, CA
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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25
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Ito N, Sakamoto T, Matsunaga S. Components of the Nuclear Pore Complex are Rising Stars in the Formation of a Subnuclear Platform of Chromatin Organization beyond Their Structural Role as a Nuclear Gate. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Nanami Ito
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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26
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Hackerott S, Martell HA, Eirin-Lopez JM. Coral environmental memory: causes, mechanisms, and consequences for future reefs. Trends Ecol Evol 2021; 36:1011-1023. [PMID: 34366170 DOI: 10.1016/j.tree.2021.06.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022]
Abstract
The apparent ability of corals to acquire and maintain enhanced stress tolerance through a dose-dependent environmental memory, which may persist for multiple years, has critical implications for coral reef conservation research. Such responses are variable across coral species and environmental stressors, with primed corals exhibiting a modified response to secondary stress exposures. While the mechanisms underlying coral memory responses are poorly understood, they likely involve both the coral host and microbiome. With advances in molecular technologies, it is now possible to investigate potential memory mechanisms in non-model organisms, including transcriptional regulation through epigenetic modifications. We integrate evidence of coral environmental memory and suggest future research directions to evaluate the potential for this process to enhance coral resilience under climate change.
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Affiliation(s)
- Serena Hackerott
- Environmental Epigenetics Laboratory, Institute of Environment, Biological Sciences Department, Florida International University, North Miami, FL, 33181, USA
| | - Harmony A Martell
- Climate and Coastal Ecosystem Laboratory, Department of Geography & Institute of Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Biological Sciences Department, Florida International University, North Miami, FL, 33181, USA.
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27
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Weinhouse C. The roles of inducible chromatin and transcriptional memory in cellular defense system responses to redox-active pollutants. Free Radic Biol Med 2021; 170:85-108. [PMID: 33789123 PMCID: PMC8382302 DOI: 10.1016/j.freeradbiomed.2021.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022]
Abstract
People are exposed to wide range of redox-active environmental pollutants. Air pollution, heavy metals, pesticides, and endocrine disrupting chemicals can disrupt cellular redox status. Redox-active pollutants in our environment all trigger their own sets of specific cellular responses, but they also activate a common set of general stress responses that buffer the cell against homeostatic insults. These cellular defense system (CDS) pathways include the heat shock response, the oxidative stress response, the hypoxia response, the unfolded protein response, the DNA damage response, and the general stress response mediated by the stress-activated p38 mitogen-activated protein kinase. Over the past two decades, the field of environmental epigenetics has investigated epigenetic responses to environmental pollutants, including redox-active pollutants. Studies of these responses highlight the role of chromatin modifications in controlling the transcriptional response to pollutants and the role of transcriptional memory, often referred to as "epigenetic reprogramming", in predisposing previously exposed individuals to more potent transcriptional responses on secondary challenge. My central thesis in this review is that high dose or chronic exposure to redox-active pollutants leads to transcriptional memories at CDS target genes that influence the cell's ability to mount protective responses. To support this thesis, I will: (1) summarize the known chromatin features required for inducible gene activation; (2) review the known forms of transcriptional memory; (3) discuss the roles of inducible chromatin and transcriptional memory in CDS responses that are activated by redox-active environmental pollutants; and (4) propose a conceptual framework for CDS pathway responsiveness as a readout of total cellular exposure to redox-active pollutants.
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Affiliation(s)
- Caren Weinhouse
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97214, USA.
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28
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Sumner MC, Torrisi SB, Brickner DG, Brickner JH. Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates inter-chromosomal movement. eLife 2021; 10:66238. [PMID: 34002694 PMCID: PMC8195609 DOI: 10.7554/elife.66238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Hundreds of genes interact with the yeast nuclear pore complex (NPC), localizing at the nuclear periphery and clustering with co-regulated genes. Dynamic tracking of peripheral genes shows that they cycle on and off the NPC and that interaction with the NPC slows their sub-diffusive movement. Furthermore, NPC-dependent inter-chromosomal clustering leads to coordinated movement of pairs of loci separated by hundreds of nanometers. We developed fractional Brownian motion simulations for chromosomal loci in the nucleoplasm and interacting with NPCs. These simulations predict the rate and nature of random sub-diffusion during repositioning from nucleoplasm to periphery and match measurements from two different experimental models, arguing that recruitment to the nuclear periphery is due to random sub-diffusion and transient capture by NPCs. Finally, the simulations do not lead to inter-chromosomal clustering or coordinated movement, suggesting that interaction with the NPC is necessary, but not sufficient, to cause clustering.
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Affiliation(s)
- Michael Chas Sumner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Steven B Torrisi
- Department of Physics, Harvard University, Cambridge, United States
| | - Donna G Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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29
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One Ring to Rule them All? Structural and Functional Diversity in the Nuclear Pore Complex. Trends Biochem Sci 2021; 46:595-607. [PMID: 33563541 DOI: 10.1016/j.tibs.2021.01.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
The nuclear pore complex (NPC) is the massive protein assembly that regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent breakthroughs have provided major insights into the structure of the NPC in different eukaryotes, revealing a previously unsuspected diversity of NPC architectures. In parallel, the NPC has been shown to be a key player in regulating essential nuclear processes such as chromatin organization, gene expression, and DNA repair. However, our knowledge of the NPC structure has not been able to address the molecular mechanisms underlying its regulatory roles. We discuss potential explanations, including the coexistence of alternative NPC architectures with specific functional roles.
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30
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Karoutas A, Akhtar A. Functional mechanisms and abnormalities of the nuclear lamina. Nat Cell Biol 2021; 23:116-126. [PMID: 33558730 DOI: 10.1038/s41556-020-00630-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Alterations in nuclear shape are present in human diseases and ageing. A compromised nuclear lamina is molecularly interlinked to altered chromatin functions and genomic instability. Whether these alterations are a cause or a consequence of the pathological state are important questions in biology. Here, we summarize the roles of nuclear envelope components in chromatin organization, phase separation and transcriptional and epigenetic regulation. Examining these functions in healthy backgrounds will guide us towards a better understanding of pathological alterations.
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Affiliation(s)
- Adam Karoutas
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Francis Crick Institute, London, UK
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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31
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Shevelyov YY. The Role of Nucleoporin Elys in Nuclear Pore Complex Assembly and Regulation of Genome Architecture. Int J Mol Sci 2020; 21:ijms21249475. [PMID: 33322130 PMCID: PMC7764596 DOI: 10.3390/ijms21249475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/25/2022] Open
Abstract
For a long time, the nuclear lamina was thought to be the sole scaffold for the attachment of chromosomes to the nuclear envelope (NE) in metazoans. However, accumulating evidence indicates that nuclear pore complexes (NPCs) comprised of nucleoporins (Nups) participate in this process as well. One of the Nups, Elys, initiates NPC reassembly at the end of mitosis. Elys directly binds the decondensing chromatin and interacts with the Nup107–160 subcomplex of NPCs, thus serving as a seeding point for the subsequent recruitment of other NPC subcomplexes and connecting chromatin with the re-forming NE. Recent studies also uncovered the important functions of Elys during interphase where it interacts with chromatin and affects its compactness. Therefore, Elys seems to be one of the key Nups regulating chromatin organization. This review summarizes the current state of our knowledge about the participation of Elys in the post-mitotic NPC reassembly as well as the role that Elys and other Nups play in the maintenance of genome architecture.
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Affiliation(s)
- Yuri Y Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", 123182 Moscow, Russia
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32
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Zhao Z, Zhang Z, Li J, Dong Q, Xiong J, Li Y, Lan M, Li G, Zhu B. Sustained TNF-α stimulation leads to transcriptional memory that greatly enhances signal sensitivity and robustness. eLife 2020; 9:61965. [PMID: 33155547 PMCID: PMC7704108 DOI: 10.7554/elife.61965] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/05/2020] [Indexed: 12/11/2022] Open
Abstract
Transcriptional memory allows certain genes to respond to previously experienced signals more robustly. However, whether and how the key proinflammatory cytokine TNF-α mediates transcriptional memory are poorly understood. Using HEK293F cells as a model system, we report that sustained TNF-α stimulation induces transcriptional memory dependent on TET enzymes. The hypomethylated status of transcriptional regulatory regions can be inherited, facilitating NF-κB binding and more robust subsequent activation. A high initial methylation level and CpG density around κB sites are correlated with the functional potential of transcriptional memory modules. Interestingly, the CALCB gene, encoding the proven migraine therapeutic target CGRP, exhibits the best transcriptional memory. A neighboring primate-specific endogenous retrovirus stimulates more rapid, more strong, and at least 100-fold more sensitive CALCB induction in subsequent TNF-α stimulation. Our study reveals that TNF-α-mediated transcriptional memory is governed by active DNA demethylation and greatly sensitizes memory genes to much lower doses of inflammatory cues. Genes are the instruction manuals of life and contain the information needed to build the building blocks that keep cells alive. To read these instructions, cells use specific signals that activate genes. The process, known as gene expression, is tightly controlled and for the most part, fairly stable. But gene expression can be modified in various ways. Epigenetics is a broad term for describing reversible changes made to genes to switch them on and off. Sometimes, certain genes even develop a kind of ‘transcriptional memory’ where over time, their expression is enhanced and speeds up with repeated activation signals. But this may also have harmful effects. For example, the signalling molecule called tumour necrosis factor α (TNF-α) is an essential part of the immune system. But it is also implicated in chronic inflammatory diseases, such as rheumatoid arthritis. In these conditions, cell signalling pathways triggering inflammation are overactive. One possibility is that TNF-α could be inducing the transcriptional memory of certain genes, amplifying their expression. But little is known about which fraction of genes exhibits transcriptional memory, and what differentiates memory genes from genes with stable expression. Here, Zhao et al. treated cells grown in the laboratory with TNF-α to investigate its role in transcriptional memory and find out what epigenetic features might govern the process. The experiments showed that mimicking a sustained inflammation by stimulating TNF-α, triggered a transcriptional memory in some genes, and enabled them to respond to much lower levels of TNF-α on subsequent exposure. Zhao et al. also discovered that genes tagged with methyl groups are more likely to show transcriptional memory when stimulated by TNF-α. However, they also found that these groups must be removed to consolidate any transcriptional memory. This work shows how TNF-α influences can alter the expression of certain genes. It also suggests that transcriptional memory, stimulated by TNF-α, may be a possible mechanism underlying chronic inflammatory conditions. This could help future research in identifying more genes with transcriptional memory.
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Affiliation(s)
- Zuodong Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jingjing Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Dong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Mengying Lan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Li
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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33
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Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
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34
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Cho UH, Hetzer MW. Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging. Neuron 2020; 106:899-911. [PMID: 32553207 DOI: 10.1016/j.neuron.2020.05.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 12/27/2022]
Abstract
In recent years, the nuclear pore complex (NPC) has emerged as a key player in genome regulation and cellular homeostasis. New discoveries have revealed that the NPC has multiple cellular functions besides mediating the molecular exchange between the nucleus and the cytoplasm. In this review, we discuss non-transport aspects of the NPC focusing on the NPC-genome interaction, the extreme longevity of the NPC proteins, and NPC dysfunction in age-related diseases. The examples summarized herein demonstrate that the NPC, which first evolved to enable the biochemical communication between the nucleus and the cytoplasm, now doubles as the gatekeeper of cellular identity and aging.
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Affiliation(s)
- Ukrae H Cho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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35
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Capelson M. How Genes Move: Spatial Repositioning of Activated Genes Is Driven by Nuclear Actin-Based Pathway. Dev Cell 2020; 52:252-254. [PMID: 32049034 DOI: 10.1016/j.devcel.2020.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Spatial repositioning of genes in nuclear space has been extensively linked to regulation of gene expression, but the mechanisms behind this directed movement have remained uncertain. In this issue of Developmental Cell, Wang et al. (2020) describe a nuclear actin-myosin-based pathway driving the movement of activated genes to the nuclear periphery.
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Affiliation(s)
- Maya Capelson
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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36
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Tamura K. Nuclear pore complex-mediated gene expression in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2020; 133:449-455. [PMID: 32170459 DOI: 10.1007/s10265-020-01177-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/08/2020] [Indexed: 05/20/2023]
Abstract
Nuclear pore complexes (NPCs) are large multi-protein complexes that control bidirectional trafficking of macromolecules between the nucleus and cytoplasm. This trafficking is highly regulated and participates in a considerably broader range of cellular activities, including defense responses against pathogens in plants. Recently, NPC is emerging as a platform to physically associate the underlying chromatin with the nuclear periphery, thus regulating chromatin structure and gene expression. For instance, NPC components have been shown to promote the formation of specific genomics loops, which is linked to transcriptional memory for rapid reactivation of genes. With newly developed techniques and tools, our insight in this area has been substantially advanced. This review summarizes recent works on the molecular function of NPC machinery as hubs for transcriptional regulation and compares systems between plant and non-plant organisms.
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Affiliation(s)
- Kentaro Tamura
- Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
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37
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Saik NO, Park N, Ptak C, Adames N, Aitchison JD, Wozniak RW. Recruitment of an Activated Gene to the Yeast Nuclear Pore Complex Requires Sumoylation. Front Genet 2020; 11:174. [PMID: 32211027 PMCID: PMC7067905 DOI: 10.3389/fgene.2020.00174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/13/2020] [Indexed: 01/10/2023] Open
Abstract
In addition to their role in regulating transport across the nuclear envelope, increasing evidence suggests nuclear pore complexes (NPCs) function in regulating gene expression. For example, the induction of certain genes (e.g., yeast INO1) is accompanied by their movement from the nuclear interior to NPCs. As sumoylation has been linked to the regulation of chromatin spatial organization and transcriptional activity, we investigated the role of sumoylation in the expression and NPC recruitment of the INO1 gene. We observed that induction of INO1 is accompanied by both increased and decreased sumoylation of proteins associated with specific regions along the INO1 locus. Furthermore, we show that the E3 ligase Siz2/Nfi1 is required for targeting the INO1 locus to the NPC where it interacts with the SUMO isopeptidase Ulp1. Our data suggest that this interaction is required for both the association of INO1 with the NPC and for its normal expression. These results imply that sumoylation is a key regulator of INO1 targeting to the NPC, and a cycle of sumoylation and NPC-associated desumoylation events contribute to the regulation of INO1 expression.
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Affiliation(s)
- Natasha O Saik
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Nogi Park
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada.,Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Neil Adames
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada.,New Culture, San Francisco, CA, United States
| | - John D Aitchison
- Seattle Children's Research Institute, Seattle, WA, United States
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
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38
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Abstract
Background Organisms can be primed by metabolic exposures to continue expressing response genes even once the metabolite is no longer available, and can affect the speed and magnitude of responsive gene expression during subsequent exposures. This “metabolic transcriptional memory” can have a profound impact on the survivability of organisms in fluctuating environments. Scope of review Here I present several examples of metabolic transcriptional memory in the microbial world and discuss what is known so far regarding the underlying mechanisms, which mainly focus on chromatin modifications, protein inheritance, and broad changes in metabolic network. From these lessons learned in microbes, some insights into the yet understudied human metabolic memory can be gained. I thus discuss the implications of metabolic memory in disease progression in humans – i.e., the memory of high blood sugar exposure and the resulting effects on diabetic complications. Major conclusions Carbon source shifts from glucose to other less preferred sugars such as lactose, galactose, and maltose for energy metabolism as well as starvation of a signal transduction precursor sugar inositol are well-studied examples of metabolic transcriptional memory in Escherichia coli and Saccharomyces cerevisiae. Although the specific factors guiding metabolic transcriptional memory are not necessarily conserved from microbes to humans, the same basic mechanisms are in play, as is observed in hyperglycemic memory. Exploration of new metabolic transcriptional memory systems as well as further detailed mechanistic analyses of known memory contexts in microbes is therefore central to understanding metabolic memory in humans, and may be of relevance for the successful treatment of the ever-growing epidemic of diabetes. Metabolic exposures can prime genes to have memory. Memory of carbon source shifts occurs in all kingdoms of life. Memory is maintained through multiple mechanisms including chromatin modifications, proteins, and metabolic network. Metabolic transcriptional memory in unicellular organisms is a part of “bet-hedging” strategies to ensure survival. Hyperglycemic memory in humans contributes to diabetes and aging.
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Affiliation(s)
- Poonam Bheda
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
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39
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Wang A, Kolhe JA, Gioacchini N, Baade I, Brieher WM, Peterson CL, Freeman BC. Mechanism of Long-Range Chromosome Motion Triggered by Gene Activation. Dev Cell 2020; 52:309-320.e5. [PMID: 31902656 PMCID: PMC7108666 DOI: 10.1016/j.devcel.2019.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 11/18/2019] [Accepted: 12/12/2019] [Indexed: 12/18/2022]
Abstract
Movement of chromosome sites within interphase cells is critical for numerous pathways including RNA transcription and genome organization. Yet, a mechanism for reorganizing chromatin in response to these events had not been reported. Here, we delineate a molecular chaperone-dependent pathway for relocating activated gene loci in yeast. Our presented data support a model in which a two-authentication system mobilizes a gene promoter through a dynamic network of polymeric nuclear actin. Transcription factor-dependent nucleation of a myosin motor propels the gene locus through the actin matrix, and fidelity of the actin association was ensured by ARP-containing chromatin remodelers. Motor activity of nuclear myosin was dependent on the Hsp90 chaperone. Hsp90 further contributed by biasing the remodeler-actin interaction toward nucleosomes with the non-canonical histone H2A.Z, thereby focusing the pathway on select sites such as transcriptionally active genes. Together, the system provides a rapid and effective means to broadly yet selectively mobilize chromatin sites.
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Affiliation(s)
- Anqi Wang
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Janhavi A Kolhe
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nate Gioacchini
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Imke Baade
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - William M Brieher
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brian C Freeman
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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40
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Brickner DG, Randise-Hinchliff C, Lebrun Corbin M, Liang JM, Kim S, Sump B, D'Urso A, Kim SH, Satomura A, Schmit H, Coukos R, Hwang S, Watson R, Brickner JH. The Role of Transcription Factors and Nuclear Pore Proteins in Controlling the Spatial Organization of the Yeast Genome. Dev Cell 2020; 49:936-947.e4. [PMID: 31211995 DOI: 10.1016/j.devcel.2019.05.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/18/2019] [Accepted: 05/10/2019] [Indexed: 12/15/2022]
Abstract
Loss of nuclear pore complex (NPC) proteins, transcription factors (TFs), histone modification enzymes, Mediator, and factors involved in mRNA export disrupts the physical interaction of chromosomal sites with NPCs. Conditional inactivation and ectopic tethering experiments support a direct role for the TFs Gcn4 and Nup2 in mediating interaction with the NPC but suggest an indirect role for factors involved in mRNA export or transcription. A conserved "positioning domain" within Gcn4 controls interaction with the NPC and inter-chromosomal clustering and promotes transcription of target genes. Such a function may be quite common; a comprehensive screen reveals that tethering of most yeast TFs is sufficient to promote targeting to the NPC. While some TFs require Nup100, others do not, suggesting two distinct targeting mechanisms. These results highlight an important and underappreciated function of TFs in controlling the spatial organization of the yeast genome through interaction with the NPC.
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Affiliation(s)
- Donna Garvey Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | | | - Marine Lebrun Corbin
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Julie Ming Liang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Stephanie Kim
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Bethany Sump
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Agustina D'Urso
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Seo Hyun Kim
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Atsushi Satomura
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Heidi Schmit
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Subin Hwang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Raven Watson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA.
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41
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Gomar-Alba M, Mendoza M. Modulation of Cell Identity by Modification of Nuclear Pore Complexes. Front Genet 2020; 10:1301. [PMID: 31969901 PMCID: PMC6960265 DOI: 10.3389/fgene.2019.01301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/26/2019] [Indexed: 11/17/2022] Open
Abstract
Nuclear pore complexes (NPCs) are protein assemblies that form channels across the nuclear envelope to mediate communication between the nucleus and the cytoplasm. Additionally, NPCs interact with chromatin and influence the position and expression of multiple genes. Interestingly, the composition of NPCs can vary in different cell-types, tissues, and developmental states. Here, we review recent findings suggesting that modifications of NPC composition, including post-translational modifications, play an instructive role in cell fate establishment. In particular, we focus on the role of cell-specific NPC deacetylation in asymmetrically dividing budding yeast, which modulates transport-dependent and transport-independent NPC functions to determine the time of commitment to a new division cycle in daughter cells. By modulating protein localization and gene expression, NPCs are therefore emerging as central regulators of cell identity.
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Affiliation(s)
- Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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42
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Choi S, Pfleger J, Jeon YH, Yang Z, He M, Shin H, Sayed D, Astrof S, Abdellatif M. Oxoglutarate dehydrogenase and acetyl-CoA acyltransferase 2 selectively associate with H2A.Z-occupied promoters and are required for histone modifications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:194436. [PMID: 31682939 PMCID: PMC7187930 DOI: 10.1016/j.bbagrm.2019.194436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 12/26/2022]
Abstract
Histone H2A.Z plays an essential role in regulating transcriptional rates and memory. Interestingly, H2A.Z-bound nucleosomes are located in both transcriptionally active and inactive promotors, with no clear understanding of the mechanisms via which it differentially regulates transcription. We hypothesized that its functions are mediated through recruitment of regulatory proteins to promoters. Using rapid chromatin immunoprecipitation-mass spectrometry, we uncovered the association of H2A.Z-bound chromatin with the metabolic enzymes, oxoglutarate dehydrogenase (OGDH) and acetyl-CoA acyltransferase 2 (ACAA2). Recombinant green florescence fusion proteins, combined with mutations of predicted nuclear localization signals, confirmed their nuclear localization and chromatin binding. Conclusively, chromatin immunoprecipitation-deep sequencing, confirmed the predominant association of OGDH and ACAA2 with H2A.Z-occupied transcription start sites and enhancers, the former of which we confirmed is conserved in both mouse and human tissue. Furthermore, H2A.Z-deficient human HAP1 cells exhibited reduced chromatin-bound metabolic enzymes, accompanied with reduced posttranslational histone modifications, including acetylation and succinylation. Specifically, knockdown of OGDH diminished H4 succinylation. Thus, the data reveal that select metabolic enzymes are assembled at active, H2A.Z-occupied, promoters, for potential site-directed production of metabolic intermediates that are required for histone modifications.
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Affiliation(s)
- Sujung Choi
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Jessica Pfleger
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Yong Heui Jeon
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Zhi Yang
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Minzhen He
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Hyewon Shin
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Danish Sayed
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Sophie Astrof
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Maha Abdellatif
- Department of Cellular Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States of America.
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43
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Mechanisms of Interplay between Transcription Factors and the 3D Genome. Mol Cell 2019; 76:306-319. [PMID: 31521504 DOI: 10.1016/j.molcel.2019.08.010] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/20/2019] [Accepted: 08/09/2019] [Indexed: 12/31/2022]
Abstract
Transcription factors (TFs) bind DNA in a sequence-specific manner and thereby serve as the protein anchors and determinants of 3D genome organization. Conversely, chromatin conformation shapes TF activity, for example, by looping TF-bound enhancers to distally located target genes. Despite considerable effort, our understanding of the mechanistic relation between TFs and 3D genome organization remains limited, in large part due to this interdependency. In this review, we summarize the evidence for the diverse mechanisms by which TFs and their activity shape the 3D genome and vice versa. We further highlight outstanding questions and potential approaches for untangling the complex relation between TF activity and the 3D genome.
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44
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Kuhn TM, Pascual-Garcia P, Gozalo A, Little SC, Capelson M. Chromatin targeting of nuclear pore proteins induces chromatin decondensation. J Cell Biol 2019; 218:2945-2961. [PMID: 31366666 PMCID: PMC6719443 DOI: 10.1083/jcb.201807139] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 04/05/2019] [Accepted: 07/08/2019] [Indexed: 12/03/2022] Open
Abstract
Nuclear pore complexes have emerged in recent years as chromatin-binding nuclear scaffolds, able to influence target gene expression. However, how nucleoporins (Nups) exert this control remains poorly understood. Here we show that ectopically tethering Drosophila Nups, especially Sec13, to chromatin is sufficient to induce chromatin decondensation. This decondensation is mediated through chromatin-remodeling complex PBAP, as PBAP is both robustly recruited by Sec13 and required for Sec13-induced decondensation. This phenomenon is not correlated with localization of the target locus to the nuclear periphery, but is correlated with robust recruitment of Nup Elys. Furthermore, we identified a biochemical interaction between endogenous Sec13 and Elys with PBAP, and a role for endogenous Elys in global as well as gene-specific chromatin decompaction. Together, these findings reveal a functional role and mechanism for specific nuclear pore components in promoting an open chromatin state.
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Affiliation(s)
- Terra M Kuhn
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
| | - Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
| | - Alejandro Gozalo
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
| | - Shawn C Little
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
| | - Maya Capelson
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, University of Pennsylvania, Philadelphia, PA
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45
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Buchwalter A, Kaneshiro JM, Hetzer MW. Coaching from the sidelines: the nuclear periphery in genome regulation. Nat Rev Genet 2019; 20:39-50. [PMID: 30356165 DOI: 10.1038/s41576-018-0063-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing.
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Affiliation(s)
- Abigail Buchwalter
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.,Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Jeanae M Kaneshiro
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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46
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Torres ES, Deal RB. The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:144-162. [PMID: 30742338 PMCID: PMC7259472 DOI: 10.1111/tpj.14281] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/28/2018] [Accepted: 12/18/2018] [Indexed: 05/17/2023]
Abstract
Plants adapt to environmental changes by regulating transcription and chromatin organization. The histone H2A variant H2A.Z and the SWI2/SNF2 ATPase BRAHMA (BRM) have overlapping roles in positively and negatively regulating environmentally responsive genes in Arabidopsis, but the extent of this overlap was uncharacterized. Both factors have been associated with various changes in nucleosome positioning and stability in different contexts, but their specific roles in transcriptional regulation and chromatin organization need further characterization. We show that H2A.Z and BRM co-localize at thousands of sites, where they interact both cooperatively and antagonistically in transcriptional repression and activation of genes involved in development and responses to environmental stimuli. We identified eight classes of genes that show distinct relationships between H2A.Z and BRM with respect to their roles in transcription. These include activating and silencing transcription both redundantly and antagonistically. We found that H2A.Z contributes to a range of different nucleosome properties, while BRM stabilizes nucleosomes where it binds and destabilizes or repositions flanking nucleosomes. We also found that, at many genes regulated by both BRM and H2A.Z, both factors overlap with binding sites of the light-regulated transcription factor FAR1-Related Sequence 9 (FRS9) and that a subset of these FRS9 binding sites are dependent on H2A.Z and BRM for accessibility. Collectively, we comprehensively characterized the antagonistic and cooperative contributions of H2A.Z and BRM to transcriptional regulation, and illuminated several interrelated roles in chromatin organization. The variability observed in their individual functions implies that both BRM and H2A.Z have more context-dependent roles than previously assumed.
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Affiliation(s)
- E. Shannon Torres
- Department of Biology, Emory University, Atlanta, GA 30322
- Graduate Program in Genetics and Molecular Biology of the Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Roger B. Deal
- Department of Biology, Emory University, Atlanta, GA 30322
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47
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Hyperosmotic Stress Response Memory is Modulated by Gene Positioning in Yeast. Cells 2019; 8:cells8060582. [PMID: 31200564 PMCID: PMC6627694 DOI: 10.3390/cells8060582] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022] Open
Abstract
Cellular memory is a critical ability that allows microorganisms to adapt to potentially detrimental environmental fluctuations. In the unicellular eukaryote Saccharomyces cerevisiae, cellular memory can take the form of faster or slower responses within the cell population to repeated stresses. Using microfluidics and fluorescence time-lapse microscopy, we studied how yeast responds to short, pulsed hyperosmotic stresses at the single-cell level by analyzing the dynamic behavior of the stress-responsive STL1 promoter (pSTL1) fused to a fluorescent reporter. We established that pSTL1 exhibits variable successive activation patterns following two repeated short stresses. Despite this variability, most cells exhibited a memory of the first stress as decreased pSTL1 activity in response to the second stress. Notably, we showed that genomic location is important for the memory effect, since displacement of the promoter to a pericentromeric chromatin domain decreased the transcriptional strength of pSTL1 and led to a loss of memory. This study provides a quantitative description of a cellular memory that includes single-cell variability and highlights the contribution of chromatin structure to stress memory.
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48
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Histone Methylation and Memory of Environmental Stress. Cells 2019; 8:cells8040339. [PMID: 30974922 PMCID: PMC6523599 DOI: 10.3390/cells8040339] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/05/2019] [Accepted: 04/07/2019] [Indexed: 02/07/2023] Open
Abstract
Cellular adaptation to environmental stress relies on a wide range of tightly controlled regulatory mechanisms, including transcription. Changes in chromatin structure and organization accompany the transcriptional response to stress, and in some cases, can impart memory of stress exposure to subsequent generations through mechanisms of epigenetic inheritance. In the budding yeast Saccharomyces cerevisiae, histone post-translational modifications, and in particular histone methylation, have been shown to confer transcriptional memory of exposure to environmental stress conditions through mitotic divisions. Recent evidence from Caenorhabditis elegans also implicates histone methylation in transgenerational inheritance of stress responses, suggesting a more widely conserved role in epigenetic memory.
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49
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Cerulus B, Jariani A, Perez-Samper G, Vermeersch L, Pietsch JMJ, Crane MM, New AM, Gallone B, Roncoroni M, Dzialo MC, Govers SK, Hendrickx JO, Galle E, Coomans M, Berden P, Verbandt S, Swain PS, Verstrepen KJ. Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources. eLife 2018; 7:e39234. [PMID: 30299256 PMCID: PMC6211830 DOI: 10.7554/elife.39234] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/05/2018] [Indexed: 01/24/2023] Open
Abstract
Cells constantly adapt to environmental fluctuations. These physiological changes require time and therefore cause a lag phase during which the cells do not function optimally. Interestingly, past exposure to an environmental condition can shorten the time needed to adapt when the condition re-occurs, even in daughter cells that never directly encountered the initial condition. Here, we use the molecular toolbox of Saccharomyces cerevisiae to systematically unravel the molecular mechanism underlying such history-dependent behavior in transitions between glucose and maltose. In contrast to previous hypotheses, the behavior does not depend on persistence of proteins involved in metabolism of a specific sugar. Instead, presence of glucose induces a gradual decline in the cells' ability to activate respiration, which is needed to metabolize alternative carbon sources. These results reveal how trans-generational transitions in central carbon metabolism generate history-dependent behavior in yeast, and provide a mechanistic framework for similar phenomena in other cell types.
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Affiliation(s)
- Bram Cerulus
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Abbas Jariani
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Gemma Perez-Samper
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Lieselotte Vermeersch
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Julian MJ Pietsch
- Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Matthew M Crane
- Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
- Department of PathologyUniversity of WashingtonWashingtonUnited States
| | - Aaron M New
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Brigida Gallone
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Miguel Roncoroni
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Maria C Dzialo
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Sander K Govers
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Jhana O Hendrickx
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Eva Galle
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Maarten Coomans
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Pieter Berden
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Sara Verbandt
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
| | - Peter S Swain
- Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Kevin J Verstrepen
- VIB Laboratory for Systems BiologyVIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Departement Microbiële en Moleculaire Systemen (M2S)CMPG Laboratory of Genetics and GenomicsLeuvenBelgium
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50
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Rodriguez-Bravo V, Pippa R, Song WM, Carceles-Cordon M, Dominguez-Andres A, Fujiwara N, Woo J, Koh AP, Ertel A, Lokareddy RK, Cuesta-Dominguez A, Kim RS, Rodriguez-Fernandez I, Li P, Gordon R, Hirschfield H, Prats JM, Reddy EP, Fatatis A, Petrylak DP, Gomella L, Kelly WK, Lowe SW, Knudsen KE, Galsky MD, Cingolani G, Lujambio A, Hoshida Y, Domingo-Domenech J. Nuclear Pores Promote Lethal Prostate Cancer by Increasing POM121-Driven E2F1, MYC, and AR Nuclear Import. Cell 2018; 174:1200-1215.e20. [PMID: 30100187 DOI: 10.1016/j.cell.2018.07.015] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/16/2018] [Accepted: 07/10/2018] [Indexed: 12/19/2022]
Abstract
Nuclear pore complexes (NPCs) regulate nuclear-cytoplasmic transport, transcription, and genome integrity in eukaryotic cells. However, their functional roles in cancer remain poorly understood. We interrogated the evolutionary transcriptomic landscape of NPC components, nucleoporins (Nups), from primary to advanced metastatic human prostate cancer (PC). Focused loss-of-function genetic screen of top-upregulated Nups in aggressive PC models identified POM121 as a key contributor to PC aggressiveness. Mechanistically, POM121 promoted PC progression by enhancing importin-dependent nuclear transport of key oncogenic (E2F1, MYC) and PC-specific (AR-GATA2) transcription factors, uncovering a pharmacologically targetable axis that, when inhibited, decreased tumor growth, restored standard therapy efficacy, and improved survival in patient-derived pre-clinical models. Our studies molecularly establish a role of NPCs in PC progression and give a rationale for NPC-regulated nuclear import targeting as a therapeutic strategy for lethal PC. These findings may have implications for understanding how NPC deregulation contributes to the pathogenesis of other tumor types.
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Affiliation(s)
- Veronica Rodriguez-Bravo
- Cancer Biology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Medical Oncology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Pathology Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Raffaella Pippa
- Cancer Biology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Medical Oncology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Pathology Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Won-Min Song
- Genetic and Genomic Sciences Department. Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marc Carceles-Cordon
- Pathology Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana Dominguez-Andres
- Cancer Biology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Medical Oncology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Pathology Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Naoto Fujiwara
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jungreem Woo
- Cancer Biology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Medical Oncology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Pathology Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna P Koh
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam Ertel
- Cancer Biology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Alvaro Cuesta-Dominguez
- Oncological Sciences Department. Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Liver Diseases, Medicine Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rosa S Kim
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Peiyao Li
- Cancer Biology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Medical Oncology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ronald Gordon
- Pathology Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hadassa Hirschfield
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Josep M Prats
- Urology Department, Hospital de Calella, Barcelona 08370, Spain
| | - E Premkumar Reddy
- Oncological Sciences Department. Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alessandro Fatatis
- Pharmacology and Physiology Department, Drexler University, Philadelphia, PA 19104, USA
| | - Daniel P Petrylak
- Medical Oncology Department, Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Leonard Gomella
- Urology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - W Kevin Kelly
- Cancer Biology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Medical Oncology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Urology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Karen E Knudsen
- Cancer Biology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Medical Oncology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Urology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Matthew D Galsky
- Medical Oncology Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Amaia Lujambio
- Oncological Sciences Department. Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Liver Diseases, Medicine Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Josep Domingo-Domenech
- Cancer Biology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Medical Oncology Department, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Pathology Department, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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