1
|
Lee J, Simpson L, Li Y, Becker S, Zou F, Zhang X, Bai L. Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579062. [PMID: 38370634 PMCID: PMC10871269 DOI: 10.1101/2024.02.06.579062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3D genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro . In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes are clustered in 3D in a Met4-dependent manner. A MET3pr -GFP reporter inserted near several native Met4 binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4 binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion.
Collapse
Affiliation(s)
- James Lee
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Leman Simpson
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yi Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Samuel Becker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Fan Zou
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
2
|
Lopes M, Louzada S, Gama-Carvalho M, Chaves R. Pericentromeric satellite RNAs as flexible protein partners in the regulation of nuclear structure. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1868. [PMID: 38973000 DOI: 10.1002/wrna.1868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 07/09/2024]
Abstract
Pericentromeric heterochromatin is mainly composed of satellite DNA sequences. Although being historically associated with transcriptional repression, some pericentromeric satellite DNA sequences are transcribed. The transcription events of pericentromeric satellite sequences occur in highly flexible biological contexts. Hence, the apparent randomness of pericentromeric satellite transcription incites the discussion about the attribution of biological functions. However, pericentromeric satellite RNAs have clear roles in the organization of nuclear structure. Silencing pericentromeric heterochromatin depends on pericentromeric satellite RNAs, that, in a feedback mechanism, contribute to the repression of pericentromeric heterochromatin. Moreover, pericentromeric satellite RNAs can also act as scaffolding molecules in condensate subnuclear structures (e.g., nuclear stress bodies). Since the formation/dissociation of nuclear condensates provides cell adaptability, pericentromeric satellite RNAs can be an epigenetic platform for regulating (sub)nuclear structure. We review current knowledge about pericentromeric satellite RNAs that, irrespective of the meaning of biological function, should be functionally addressed in regular and disease settings. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Mariana Lopes
- CytoGenomics Lab-Department of Genetics and Biotechnology (DGB), University of Trás os Montes and Alto Douro (UTAD), Vila Real, Portugal
- BioISI: Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Sandra Louzada
- CytoGenomics Lab-Department of Genetics and Biotechnology (DGB), University of Trás os Montes and Alto Douro (UTAD), Vila Real, Portugal
- BioISI: Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Margarida Gama-Carvalho
- BioISI: Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Raquel Chaves
- CytoGenomics Lab-Department of Genetics and Biotechnology (DGB), University of Trás os Montes and Alto Douro (UTAD), Vila Real, Portugal
- BioISI: Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
- RISE-Health: Health Research Network, Faculty of Medicine, University of Porto, Porto, Portugal
- CACTMAD: Trás-os-Montes and Alto Douro Academic Clinic Center,University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| |
Collapse
|
3
|
Furugori K, Suzuki H, Abe R, Horiuchi K, Akiyama T, Hirose T, Toyoda A, Takahashi H. Chimera RNA transcribed from integrated HPV18 genome with adjacent host genomic region promotes oncogenic gene expression through condensate formation. Genes Cells 2024; 29:532-548. [PMID: 38715205 DOI: 10.1111/gtc.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 07/06/2024]
Abstract
Most cervical cancers are caused by human papillomavirus (HPV) infection. In HeLa cells, the HPV18 viral genome is integrated at chromosome 8q24.21 and activates transcription of the proto-oncogene c-Myc. However, the mechanism of how the integrated HPV genome and its transcribed RNAs exhibit transcription activation function has not been fully elucidated. In this study, we found that HPV18 transcripts contain an enhancer RNA-like function to activate proximal genes including CCAT1-5L and c-Myc. We showed that the human genome-integrated HPV18 genes are activated by transcription coregulators including BRD4 and Mediator. The transcribed HPV18 RNAs form a liquid-like condensate at chromosome 8q24.21 locus, which in turn accumulates RNA polymerase II. Moreover, we focused on a relatively uncharacterized transcript from the upstream region of CCAT1, named URC. The URC RNA is transcribed as a chimera RNA with HPV18 and is composed of the 3'-untranslated region of the HPV18 transcript. We experimentally showed that the URC contributes to stabilization of HPV18 RNAs by supplying a polyadenylation site for the HPV18 transcript. Our findings suggest that integrated HPV18 at 8q24.21 locus produces HPV18-URC chimera RNA and promotes tumorigenesis through RNA-based condensate formation.
Collapse
Affiliation(s)
- Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomonori Hirose
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| |
Collapse
|
4
|
Morelli C, Faltova L, Capasso Palmiero U, Makasewicz K, Papp M, Jacquat RPB, Pinotsi D, Arosio P. RNA modulates hnRNPA1A amyloid formation mediated by biomolecular condensates. Nat Chem 2024; 16:1052-1061. [PMID: 38472406 PMCID: PMC11230912 DOI: 10.1038/s41557-024-01467-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Several RNA binding proteins involved in membraneless organelles can form pathological amyloids associated with neurodegenerative diseases, but the mechanisms of how this aggregation is modulated remain elusive. Here we investigate how heterotypic protein-RNA interactions modulate the condensation and the liquid to amyloid transition of hnRNPA1A, a protein involved in amyothropic lateral sclerosis. In the absence of RNA, formation of condensates promotes hnRNPA1A aggregation and fibrils are localized at the interface of the condensates. Addition of RNA modulates the soluble to amyloid transition of hnRNPA1A according to different pathways depending on RNA/protein stoichiometry. At low RNA concentrations, RNA promotes both condensation and amyloid formation, and the catalytic effect of RNA adds to the role of the interface between the dense and dilute phases. At higher RNA concentrations, condensation is suppressed according to re-entrant phase behaviour but formation of hnRNPA1A amyloids is observed over longer incubation times. Our findings show how heterotypic nucleic acid-protein interactions affect the kinetics and molecular pathways of amyloid formation.
Collapse
Affiliation(s)
- Chiara Morelli
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Katarzyna Makasewicz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Marcell Papp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Raphaël P B Jacquat
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zürich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland.
| |
Collapse
|
5
|
Chen PT, Levo M, Zoller B, Gregor T. Gene activity fully predicts transcriptional bursting dynamics. ARXIV 2024:arXiv:2304.08770v3. [PMID: 37131882 PMCID: PMC10153294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Transcription commonly occurs in bursts, with alternating productive (ON) and quiescent (OFF) periods, governing mRNA production rates. Yet, how transcription is regulated through bursting dynamics remains unresolved. Here, we conduct real-time measurements of endogenous transcriptional bursting with single-mRNA sensitivity. Leveraging the diverse transcriptional activities in early fly embryos, we uncover stringent relationships between bursting parameters. Specifically, we find that the durations of ON and OFF periods are linked. Regardless of the developmental stage or body-axis position, gene activity levels predict individual alleles' average ON and OFF periods. Lowly transcribing alleles predominantly modulate OFF periods (burst frequency), while highly transcribing alleles primarily tune ON periods (burst size). These relationships persist even under perturbations of cis-regulatory elements or trans-factors and account for bursting dynamics measured in other species. Our results suggest a novel mechanistic constraint governing bursting dynamics rather than a modular control of distinct parameters by distinct regulatory processes.
Collapse
Affiliation(s)
- Po-Ta Chen
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Michal Levo
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Benjamin Zoller
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Stem Cell and Developmental Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - Thomas Gregor
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Stem Cell and Developmental Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| |
Collapse
|
6
|
Salari H, Fourel G, Jost D. Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization. Nat Commun 2024; 15:5393. [PMID: 38918438 PMCID: PMC11199603 DOI: 10.1038/s41467-024-49727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Although our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
Collapse
Affiliation(s)
- Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
- École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007, Lyon, France.
| | - Geneviève Fourel
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
| |
Collapse
|
7
|
Liang F, Jin J, Li Q, Duan J, Jiang A, Chen X, Geng H, Wu K, Yu F, Zhao X, Zhou Y, Hu D, Chen L. DOT1L/H3K79me2 represses HIV-1 reactivation via recruiting DCAF1. Cell Rep 2024; 43:114368. [PMID: 38905100 DOI: 10.1016/j.celrep.2024.114368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 06/23/2024] Open
Abstract
DOT1L mediates the methylation of histone H3 at lysine 79 and, in turn, the transcriptional activation or repression in a context-dependent manner, yet the regulatory mechanisms and functions of DOT1L/H3K79me remain to be fully explored. Following peptide affinity purification and proteomic analysis, we identified that DCAF1-a component of the E3 ligase complex involved in HIV regulation-is associated with H3K79me2 and DOT1L. Interestingly, blocking the expression or catalytic activity of DOT1L or repressing the expression of DCAF1 significantly enhances the tumor necrosis factor alpha (TNF-α)/nuclear factor κB (NF-κB)-induced reactivation of the latent HIV-1 genome. Mechanistically, upon TNF-α/NF-κB activation, DCAF1 is recruited to the HIV-1 long terminal repeat (LTR) by DOT1L and H3K79me2. Recruited DCAF1 subsequently induces the ubiquitination of NF-κB and restricts its accumulation at the HIV-1 LTR. Altogether, our findings reveal a feedback modulation of HIV reactivation by DOT1L-mediated histone modification regulation and highlight the potential of targeting the DOT1L/DCAF1 axis as a therapeutic strategy for HIV treatment.
Collapse
Affiliation(s)
- Fenfei Liang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiaxing Jin
- State Key Laboratory of Experimental Hematology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qiming Li
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiangkai Duan
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ao Jiang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoqing Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huichao Geng
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kai Wu
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fei Yu
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaolu Zhao
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Zhou
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Deqing Hu
- State Key Laboratory of Experimental Hematology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Cancer Institute and Hospital of Tianjin Medical University, Tianjin 300060, China.
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
8
|
Chen F, Li X, Guo W, Wang Y, Guo M, Shum HC. Size Scaling of Condensates in Multicomponent Phase Separation. J Am Chem Soc 2024; 146:16000-16009. [PMID: 38809420 DOI: 10.1021/jacs.4c02906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Constant proportionalities between cells and their intracellular organelles have been widely observed in various types of cells, known as intracellular size scaling. However, the mechanism underlying the size scaling and its modulation by environmental factors in multicomponent systems remain poorly understood. Here, we study the size scaling of membrane-less condensates using microdroplet-encapsulated minimalistic condensates formed by droplet microfluidics and mean-field theory. We demonstrate that the size scaling of condensates is an inherent characteristic of liquid-liquid phase separation. This concept is supported by experiments showing the occurrence of size scaling phenomena in various condensate systems and a generic lever rule acquired from mean-field theory. Moreover, it is found that the condensate-to-microdroplet scaling ratio can be affected by the solute and salt concentrations, with good agreement between experiments and predictions by theory. Notably, we identify a noise buffering mechanism whereby condensates composed of large macromolecules effectively maintain constant volumes and counteract concentration fluctuations of small molecules. This mechanism is achieved through the dynamic rearrangement of small molecules in and out of membrane-free interfaces. Our work provides crucial insights into understanding mechanistic principles that govern the size of cells and intracellular organelles as well as associated biological functions.
Collapse
Affiliation(s)
- Feipeng Chen
- Department of Mechanical Engineering, the University of Hong Kong, Pokfulam Road, Hong Kong (SAR) 999077, China
| | - Xiufeng Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR) 999077, China
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Wei Guo
- Department of Mechanical Engineering, the University of Hong Kong, Pokfulam Road, Hong Kong (SAR) 999077, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR) 999077, China
| | - Yuchao Wang
- Department of Mechanical Engineering, the University of Hong Kong, Pokfulam Road, Hong Kong (SAR) 999077, China
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ho Cheung Shum
- Department of Mechanical Engineering, the University of Hong Kong, Pokfulam Road, Hong Kong (SAR) 999077, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR) 999077, China
| |
Collapse
|
9
|
Kodan N, Hussaini R, Weber SC, Kondev J, Mohapatra L. Transcription templated assembly of the nucleolus in the C. elegans embryo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597440. [PMID: 38895351 PMCID: PMC11185672 DOI: 10.1101/2024.06.06.597440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The nucleolus is a multicomponent structure made of RNA and proteins that serves as the site of ribosome biogenesis within the nucleus. It has been extensively studied as a prototype of a biomolecular condensate whose assembly is driven by phase separation. While the steady-state size of the nucleolus is quantitatively accounted for by the thermodynamics of phase separation, we show that experimental measurements of the assembly dynamics are inconsistent with a simple model of a phase-separating system relaxing to its equilibrium state. Instead, we show that the dynamics are well described by a model in which the transcription of ribosomal RNA actively drives nucleolar assembly. We find that our model of active transcription-templated assembly quantitatively accounts for the rapid kinetics observed in early embryos at different developmental stages, and for different RNAi perturbations of embryo size. Our model predicts a scaling of the time to assembly with the volume of the nucleus to the one-third power, which is confirmed by experimental data. Our study highlights the role of active processes such as transcription in controlling the placement and timing of assembly of membraneless organelles.
Collapse
Affiliation(s)
- Nishant Kodan
- School of Physics and Astronomy, College of Science, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Rabeya Hussaini
- Department of Physics, New York University, New York, NY 10003, USA
| | - Stephanie C Weber
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Lishibanya Mohapatra
- School of Physics and Astronomy, College of Science, Rochester Institute of Technology, Rochester, NY 14623, USA
| |
Collapse
|
10
|
Papadopoulos D, Ha SA, Fleischhauer D, Uhl L, Russell TJ, Mikicic I, Schneider K, Brem A, Valanju OR, Cossa G, Gallant P, Schuelein-Voelk C, Maric HM, Beli P, Büchel G, Vos SM, Eilers M. The MYCN oncoprotein is an RNA-binding accessory factor of the nuclear exosome targeting complex. Mol Cell 2024; 84:2070-2086.e20. [PMID: 38703770 DOI: 10.1016/j.molcel.2024.04.007] [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: 09/05/2023] [Revised: 02/28/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
The MYCN oncoprotein binds active promoters in a heterodimer with its partner protein MAX. MYCN also interacts with the nuclear exosome, a 3'-5' exoribonuclease complex, suggesting a function in RNA metabolism. Here, we show that MYCN forms stable high-molecular-weight complexes with the exosome and multiple RNA-binding proteins. MYCN binds RNA in vitro and in cells via a conserved sequence termed MYCBoxI. In cells, MYCN associates with thousands of intronic transcripts together with the ZCCHC8 subunit of the nuclear exosome targeting complex and enhances their processing. Perturbing exosome function results in global re-localization of MYCN from promoters to intronic RNAs. On chromatin, MYCN is then replaced by the MNT(MXD6) repressor protein, inhibiting MYCN-dependent transcription. RNA-binding-deficient alleles show that RNA-binding limits MYCN's ability to activate cell growth-related genes but is required for MYCN's ability to promote progression through S phase and enhance the stress resilience of neuroblastoma cells.
Collapse
Affiliation(s)
- Dimitrios Papadopoulos
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany
| | - Stefanie Anh Ha
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Daniel Fleischhauer
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Leonie Uhl
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Timothy J Russell
- Massachusetts Institute of Technology, Department of Biology, 31 Ames Street, Cambridge, MA 02142, USA
| | - Ivan Mikicic
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Ackermannweg 4, 55128 Mainz, Germany; Institute of Molecular Biology (IMB), Johannes Gutenberg University, Ackermannweg 4, 55128 Mainz, Germany
| | - Katharina Schneider
- Massachusetts Institute of Technology, Department of Biology, 31 Ames Street, Cambridge, MA 02142, USA
| | - Annika Brem
- Massachusetts Institute of Technology, Department of Biology, 31 Ames Street, Cambridge, MA 02142, USA
| | - Omkar Rajendra Valanju
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, Building D15, 97080 Würzburg, Germany
| | - Giacomo Cossa
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Peter Gallant
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christina Schuelein-Voelk
- Theodor Boveri Institute, Core Unit High-Content Microscopy, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Hans Michael Maric
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, Building D15, 97080 Würzburg, Germany
| | - Petra Beli
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Ackermannweg 4, 55128 Mainz, Germany; Institute of Molecular Biology (IMB), Johannes Gutenberg University, Ackermannweg 4, 55128 Mainz, Germany
| | - Gabriele Büchel
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany
| | - Seychelle M Vos
- Massachusetts Institute of Technology, Department of Biology, 31 Ames Street, Cambridge, MA 02142, USA.
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| |
Collapse
|
11
|
Chauhan G, Bremer A, Dar F, Mittag T, Pappu RV. Crowder titrations enable the quantification of driving forces for macromolecular phase separation. Biophys J 2024; 123:1376-1392. [PMID: 37717144 PMCID: PMC11163301 DOI: 10.1016/j.bpj.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023] Open
Abstract
Macromolecular solubility is an important contributor to the driving forces for phase separation. Formally, the driving forces in a binary mixture comprising a macromolecule dissolved in a solvent can be quantified in terms of the saturation concentration, which is the threshold macromolecular concentration above which the mixture separates into coexisting dense and dilute phases. In addition, the second virial coefficient, which measures the effective strength of solvent-mediated intermolecular interactions provides direct assessments of solvent quality. The sign and magnitude of second virial coefficients will be governed by a combination of solution conditions and the nature of the macromolecule of interest. Here, we show, using a combination of theory, simulation, and in vitro experiments, that titrations of crowders, providing they are true depletants, can be used to extract the intrinsic driving forces for macromolecular phase separation. This refers to saturation concentrations in the absence of crowders and the second virial coefficients that quantify the magnitude of the incompatibility between macromolecules and the solvent. Our results show how the depletion-mediated attractions afforded by crowders can be leveraged to obtain comparative assessments of macromolecule-specific, intrinsic driving forces for phase separation.
Collapse
Affiliation(s)
- Gaurav Chauhan
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Anne Bremer
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri.
| |
Collapse
|
12
|
Mathias KM, Liu Y, Wan L. Dysregulation of transcriptional condensates in human disease: mechanisms, biological functions, and open questions. Curr Opin Genet Dev 2024; 86:102203. [PMID: 38788489 PMCID: PMC11162900 DOI: 10.1016/j.gde.2024.102203] [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: 10/30/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
Precise gene expression, crucial for normal development and health, depends on the co-ordinated assembly and function of various factors within the crowded nucleus. Recent evidence suggests that this process is in part regulated by mesoscale compartmentalization and concentration of transcriptional components within condensates, offering a new perspective on gene regulation. Dysregulation of transcriptional condensates is increasingly associated with diseases, indicating a potential role in pathogenesis. In this mini-review, we provide a concise overview of the current understanding of the formation and function of transcriptional condensates, with a specific focus on recent advances in their dysregulation and implications in diseases, notably cancer. We also address limitations in the field and highlight open questions for future research.
Collapse
Affiliation(s)
- Kaeli M Mathias
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry Biophysics Chemical Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yiman Liu
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Liling Wan
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
13
|
Hayward-Lara G, Fischer MD, Mir M. Dynamic microenvironments shape nuclear organization and gene expression. Curr Opin Genet Dev 2024; 86:102177. [PMID: 38461773 PMCID: PMC11162947 DOI: 10.1016/j.gde.2024.102177] [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: 12/05/2023] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Live imaging has revealed that the regulation of gene expression is largely driven by transient interactions. For example, many regulatory proteins bind chromatin for just seconds, and loop-like genomic contacts are rare and last only minutes. These discoveries have been difficult to reconcile with our canonical models that are predicated on stable and hierarchical interactions. Proteomic microenvironments that concentrate nuclear factors may explain how brief interactions can still mediate gene regulation by creating conditions where reactions occur more frequently. Here, we summarize new imaging technologies and recent discoveries implicating microenvironments as a potential driver of nuclear function. Finally, we propose that key properties of proteomic microenvironments, such as their size, enrichment, and lifetimes, are directly linked to regulatory function.
Collapse
Affiliation(s)
- Gabriela Hayward-Lara
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
- Developmental, Stem Cell, and Regenerative Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
| | - Matthew D. Fischer
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
| | - Mustafa Mir
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Howard Hughes Medical Institute, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
| |
Collapse
|
14
|
Sandoval R, Dilsavor CN, Grishanina NR, Patel V, Zamudio JR. Mammalian RNAi represses pericentromeric lncRNAs to maintain genome stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593425. [PMID: 38765997 PMCID: PMC11100815 DOI: 10.1101/2024.05.09.593425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Mammalian pericentromeric tandem repeats produce long noncoding RNAs (lncRNAs) that are dysregulated in cancer and linked to genomic instability. Identifying the basic molecular characteristics of these lncRNAs and their regulation is important to understanding their biological function. Here, we determine that the Argonaute (Ago) proteins of the RNA interference (RNAi) pathway directly and uniformly repress bidirectional pericentromeric lncRNAs in a Dicer-dependent manner in mouse embryonic and adult stem cells. Ago-dependent and Dicer-dependent autoregulatory small RNAs were identified within pericentromeric lncRNA degradation intermediates. We develop an RNase H cleavage assay to determine the relative proportions and lengths of the pericentromeric lncRNA targets. We find that 5'-phosphate and non-polyadenylated bidirectional pericentromeric lncRNAs are expressed at similar proportions. These lncRNAs can span up to 9 repeats, with transcription from the reverse strand template yielding the longer products. Using pericentromeric repeat RNA reporters, we determine that Ago represses pericentromeric lncRNAs after S phase transcription. Upon loss of Ago, pericentromeric lncRNA dysregulation results in delayed cell cycle progression, a defective mitotic spindle assembly checkpoint (SAC) and genomic instability. These results show that an evolutionarily conserved Ago activity at pericentromeres contributes to mammalian genome stability.
Collapse
|
15
|
He J, Huo X, Pei G, Jia Z, Yan Y, Yu J, Qu H, Xie Y, Yuan J, Zheng Y, Hu Y, Shi M, You K, Li T, Ma T, Zhang MQ, Ding S, Li P, Li Y. Dual-role transcription factors stabilize intermediate expression levels. Cell 2024; 187:2746-2766.e25. [PMID: 38631355 DOI: 10.1016/j.cell.2024.03.023] [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: 06/09/2023] [Revised: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Precise control of gene expression levels is essential for normal cell functions, yet how they are defined and tightly maintained, particularly at intermediate levels, remains elusive. Here, using a series of newly developed sequencing, imaging, and functional assays, we uncover a class of transcription factors with dual roles as activators and repressors, referred to as condensate-forming level-regulating dual-action transcription factors (TFs). They reduce high expression but increase low expression to achieve stable intermediate levels. Dual-action TFs directly exert activating and repressing functions via condensate-forming domains that compartmentalize core transcriptional unit selectively. Clinically relevant mutations in these domains, which are linked to a range of developmental disorders, impair condensate selectivity and dual-action TF activity. These results collectively address a fundamental question in expression regulation and demonstrate the potential of level-regulating dual-action TFs as powerful effectors for engineering controlled expression levels.
Collapse
Affiliation(s)
- Jinnan He
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiangru Huo
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Zeran Jia
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yiming Yan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Yu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Haozhi Qu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yunxin Xie
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Junsong Yuan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yuan Zheng
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yanyan Hu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Minglei Shi
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kaiqiang You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianhua Ma
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Michael Q Zhang
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China; Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas, TX 75080-3021, USA
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
| | - Yinqing Li
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
16
|
Kar M, Vogel LT, Chauhan G, Felekyan S, Ausserwöger H, Welsh TJ, Dar F, Kamath AR, Knowles TPJ, Hyman AA, Seidel CAM, Pappu RV. Solutes unmask differences in clustering versus phase separation of FET proteins. Nat Commun 2024; 15:4408. [PMID: 38782886 PMCID: PMC11116469 DOI: 10.1038/s41467-024-48775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Phase separation and percolation contribute to phase transitions of multivalent macromolecules. Contributions of percolation are evident through the viscoelasticity of condensates and through the formation of heterogeneous distributions of nano- and mesoscale pre-percolation clusters in sub-saturated solutions. Here, we show that clusters formed in sub-saturated solutions of FET (FUS-EWSR1-TAF15) proteins are affected differently by glutamate versus chloride. These differences on the nanoscale, gleaned using a suite of methods deployed across a wide range of protein concentrations, are prevalent and can be unmasked even though the driving forces for phase separation remain unchanged in glutamate versus chloride. Strikingly, differences in anion-mediated interactions that drive clustering saturate on the micron-scale. Beyond this length scale the system separates into coexisting phases. Overall, we find that sequence-encoded interactions, mediated by solution components, make synergistic and distinct contributions to the formation of pre-percolation clusters in sub-saturated solutions, and to the driving forces for phase separation.
Collapse
Affiliation(s)
- Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Gaurav Chauhan
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Hannes Ausserwöger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Anjana R Kamath
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Anthony A Hyman
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany.
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| |
Collapse
|
17
|
Jiang Y, Sun S, Liu X, Su K, Zhang C, Zhang P, Zhao Z, Su Y, Wang C, Du X. U3 snoRNA inter-regulates with DDX21 in the perichromosomal region to control mitosis. Cell Death Dis 2024; 15:342. [PMID: 38760378 PMCID: PMC11101645 DOI: 10.1038/s41419-024-06725-3] [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: 12/05/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
U3 snoRNA is essential for ribosome biogenesis during interphase. Upon mitotic onset, the nucleolus disassembles and U3 snoRNA relocates to the perichromosomal region (PR) to be considered as a chromosome passenger. Whether U3 controls mitosis remains unknown. Here, we demonstrate that U3 snoRNA is required for mitotic progression. We identified DDX21 as the predominant U3-binding protein during mitosis and confirmed that U3 snoRNA colocalizes with DDX21 in the PR. DDX21 knockdown induces mitotic catastrophe and similar mitotic defects caused by U3 snoRNA depletion. Interestingly, the uniform PR distribution of U3 snoRNA and DDX21 is interdependent. DDX21 functions in mitosis depending on its PR localization. Mechanistically, U3 snoRNA regulates DDX21 PR localization through maintaining its mobility. Moreover, Cy5-U3 snoRNA downsizes the fibrous condensates of His-DDX21 at proper molecular ratios in vitro. This work highlights the importance of the equilibrium between U3 snoRNA and DDX21 in PR formation and reveals the potential relationship between the PR assembly and mitotic regulation.
Collapse
Affiliation(s)
- Yang Jiang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Shiqi Sun
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Xiaofeng Liu
- Hepatopancreatobiliary Surgery Department I, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Cancer Hospital & Institute, Peking University, Beijing, 100142, China
| | - Kunqi Su
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Chunfeng Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Peipei Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Zhuochen Zhao
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Ya Su
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Chang Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Xiaojuan Du
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China.
| |
Collapse
|
18
|
Saha D, Animireddy S, Lee J, Thommen A, Murvin MM, Lu Y, Calabrese JM, Bartholomew B. Enhancer switching in cell lineage priming is linked to eRNA, Brg1's AT-hook, and SWI/SNF recruitment. Mol Cell 2024; 84:1855-1869.e5. [PMID: 38593804 PMCID: PMC11104297 DOI: 10.1016/j.molcel.2024.03.013] [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: 05/08/2023] [Revised: 11/24/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
RNA transcribed from enhancers, i.e., eRNA, has been suggested to directly activate transcription by recruiting transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find that the AT-hook of SWI/SNF preferentially binds RNA and, as part of the esBAF complex, associates with eRNA transcribed from intronic and intergenic regions. Our data suggest that SWI/SNF is globally recruited in cis by eRNA to cell-type-specific enhancers, representative of two distinct stages that mimic early mammalian development, and not at enhancers that are shared between the two stages. In this manner, SWI/SNF facilitates recruitment and/or activation of MLL3/4, p300/CBP, and Mediator to stage-specific enhancers and super-enhancers that regulate the transcription of metabolic and cell lineage priming-related genes. These findings highlight a connection between ATP-dependent chromatin remodeling and eRNA in cell identity and typical- and super-enhancer activation.
Collapse
Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Junwoo Lee
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Anna Thommen
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - McKenzie M Murvin
- Department of Pharmacology, RNA Discovery Center, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA; Curriculum in Mechanistic, Interdisciplinary Studies in Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA
| | - J Mauro Calabrese
- Department of Pharmacology, RNA Discovery Center, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA; Curriculum in Mechanistic, Interdisciplinary Studies in Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA.
| |
Collapse
|
19
|
Shelkovnikova TA, Hautbergue GM. RNP granules in ALS and neurodegeneration: From multifunctional membraneless organelles to therapeutic opportunities. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:455-479. [PMID: 38802180 DOI: 10.1016/bs.irn.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and related neurodegenerative diseases are characterised by dysfunction of a host of RNA-binding proteins (RBPs) and a severely disrupted RNA metabolism. Recently, RBP-harbouring phase-separated complexes, ribonucleoprotein (RNP) granules, have come into the limelight as "crucibles" of neuronal pathology in ALS. RNP granules are indispensable for the multitude of regulatory processes underlying cellular RNA metabolism and serve as critical organisers of cellular biochemistry. Neurons, highly specialised cells, heavily rely on RNP granules for efficient trafficking, signalling and stress responses. Multiple RNP granule components, primarily RBPs such as TDP-43 and FUS, are affected by ALS mutations. However, even in the absence of mutations, RBP proteinopathies represent pathophysiological hallmarks of ALS. Given the high local concentrations of RBPs and RNAs, their weakened or enhanced interactions within RNP granules disrupt their homeostasis. Thus, the physiological process of phase separation and RNP granule formation, vital for maintaining the high-functioning state of neuronal cells, becomes their Achilles heel. Here, we will review the recent literature on the causes and consequences of abnormal RNP granule functioning in ALS and related disorders. In particular, we will summarise the evidence for the network-level dysfunction of RNP granules in these conditions and discuss considerations for therapeutic interventions to target RBPs, RNP granules and their network as a whole.
Collapse
Affiliation(s)
- Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom; Healthy Lifespan Institute (HELSI), University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
| |
Collapse
|
20
|
Lerra L, Panatta M, Bär D, Zanini I, Tan JY, Pisano A, Mungo C, Baroux C, Panse VG, Marques AC, Santoro R. An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains. Mol Cell 2024; 84:1667-1683.e10. [PMID: 38599210 PMCID: PMC11065421 DOI: 10.1016/j.molcel.2024.03.015] [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: 02/23/2023] [Revised: 10/19/2023] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
The nucleus is composed of functionally distinct membraneless compartments that undergo phase separation (PS). However, whether different subnuclear compartments are connected remains elusive. We identified a type of nuclear body with PS features composed of BAZ2A that associates with active chromatin. BAZ2A bodies depend on RNA transcription and BAZ2A non-disordered RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space, BAZ2A bodies contact H3K27me3 bodies. BAZ2A-body disruption promotes BAZ2A invasion into H3K27me3 domains, causing H3K27me3-body loss and gene upregulation. Weak BAZ2A-RNA interactions, such as with nascent transcripts, promote BAZ2A bodies, whereas the strong binder long non-coding RNA (lncRNA) Malat1 impairs them while mediating BAZ2A association to chromatin at nuclear speckles. In addition to unraveling a direct connection between nuclear active and repressive compartments through PS mechanisms, the results also showed that the strength of RNA-protein interactions regulates this process, contributing to nuclear organization and the regulation of chromatin and gene expression.
Collapse
Affiliation(s)
- Luigi Lerra
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Dominik Bär
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Isabella Zanini
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Jennifer Yihong Tan
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Agnese Pisano
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Chiara Mungo
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8057, Switzerland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Ana C Marques
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland.
| |
Collapse
|
21
|
Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol 2024; 25:396-415. [PMID: 38242953 PMCID: PMC11045326 DOI: 10.1038/s41580-023-00694-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets.
Collapse
Affiliation(s)
- Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
| |
Collapse
|
22
|
Lee M, Moon HC, Jeong H, Kim DW, Park HY, Shin Y. Optogenetic control of mRNA condensation reveals an intimate link between condensate material properties and functions. Nat Commun 2024; 15:3216. [PMID: 38622120 PMCID: PMC11018775 DOI: 10.1038/s41467-024-47442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Biomolecular condensates, often assembled through phase transition mechanisms, play key roles in organizing diverse cellular activities. The material properties of condensates, ranging from liquid droplets to solid-like glasses or gels, are key features impacting the way resident components associate with one another. However, it remains unclear whether and how different material properties would influence specific cellular functions of condensates. Here, we combine optogenetic control of phase separation with single-molecule mRNA imaging to study relations between phase behaviors and functional performance of condensates. Using light-activated condensation, we show that sequestering target mRNAs into condensates causes translation inhibition. Orthogonal mRNA imaging reveals highly transient nature of interactions between individual mRNAs and condensates. Tuning condensate composition and material property towards more solid-like states leads to stronger translational repression, concomitant with a decrease in molecular mobility. We further demonstrate that β-actin mRNA sequestration in neurons suppresses spine enlargement during chemically induced long-term potentiation. Our work highlights how the material properties of condensates can modulate functions, a mechanism that may play a role in fine-tuning the output of condensate-driven cellular activities.
Collapse
Affiliation(s)
- Min Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea
| | - Hyungseok C Moon
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hyeonjeong Jeong
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, USA
| | - Dong Wook Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea.
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, USA.
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea.
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea.
| |
Collapse
|
23
|
Chandrasekaran A, Graham K, Stachowiak JC, Rangamani P. Kinetic trapping organizes actin filaments within liquid-like protein droplets. Nat Commun 2024; 15:3139. [PMID: 38605007 PMCID: PMC11009352 DOI: 10.1038/s41467-024-46726-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
Several actin-binding proteins (ABPs) phase separate to form condensates capable of curating the actin network shapes. Here, we use computational modeling to understand the principles of actin network organization within VASP condensate droplets. Our simulations reveal that the different actin shapes, namely shells, rings, and mixture states are highly dependent on the kinetics of VASP-actin interactions, suggesting that they arise from kinetic trapping. Specifically, we show that reducing the residence time of VASP on actin filaments reduces degree of bundling, thereby promoting assembly of shells rather than rings. We validate the model predictions experimentally using a VASP-mutant with decreased bundling capability. Finally, we investigate the ring opening within deformed droplets and found that the sphere-to-ellipsoid transition is favored under a wide range of filament lengths while the ellipsoid-to-rod transition is only permitted when filaments have a specific range of lengths. Our findings highlight key mechanisms of actin organization within phase-separated ABPs.
Collapse
Affiliation(s)
- Aravind Chandrasekaran
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093-0411, USA
| | - Kristin Graham
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093-0411, USA.
| |
Collapse
|
24
|
Fischer AAM, Robertson HB, Kong D, Grimm MM, Grether J, Groth J, Baltes C, Fliegauf M, Lautenschläger F, Grimbacher B, Ye H, Helms V, Weber W. Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in Mammalian Cells and Mice. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2311834. [PMID: 38573961 DOI: 10.1002/smll.202311834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/22/2024] [Indexed: 04/06/2024]
Abstract
Phase separation of biomolecules into condensates is a key mechanism in the spatiotemporal organization of biochemical processes in cells. However, the impact of the material properties of biomolecular condensates on important processes, such as the control of gene expression, remains largely elusive. Here, the material properties of optogenetically induced transcription factor condensates are systematically tuned, and probed for their impact on the activation of target promoters. It is demonstrated that transcription factors in rather liquid condensates correlate with increased gene expression levels, whereas stiffer transcription factor condensates correlate with the opposite effect, reduced activation of gene expression. The broad nature of these findings is demonstrated in mammalian cells and mice, as well as by using different synthetic and natural transcription factors. These effects are observed for both transgenic and cell-endogenous promoters. The findings provide a novel materials-based layer in the control of gene expression, which opens novel opportunities in optogenetic engineering and synthetic biology.
Collapse
Affiliation(s)
- Alexandra A M Fischer
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 21a, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Hanah B Robertson
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123, Saarbrücken, Germany
| | - Deqiang Kong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Merlin M Grimm
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Jakob Grether
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Biberach University of Applied Sciences, Karlstraße 6-11, 88400, Biberach an der Riß, Germany
| | - Johanna Groth
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Carsten Baltes
- Department of Experimental Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Manfred Fliegauf
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstr. 115, 79106, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Franziska Lautenschläger
- Department of Experimental Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstr. 115, 79106, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- DZIF - German Center for Infection Research, Deutsches Zentrum für Infektionsforschung e.V., Inhoffenstr. 7, 38124, Braunschweig, Germany
- RESIST - Cluster of Excellence 2155 to Hanover Medical School, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123, Saarbrücken, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 21a, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Department of Materials Science and Engineering, Campus D2 2, Saarland University, 66123, Saarbrücken, Germany
| |
Collapse
|
25
|
Chin KY, Ishida S, Sasaki Y, Terayama K. Predicting condensate formation of protein and RNA under various environmental conditions. BMC Bioinformatics 2024; 25:143. [PMID: 38566033 PMCID: PMC10988968 DOI: 10.1186/s12859-024-05764-z] [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: 12/01/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Liquid-liquid phase separation (LLPS) by biomolecules plays a central role in various biological phenomena and has garnered significant attention. The behavior of LLPS is strongly influenced by the characteristics of RNAs and environmental factors such as pH and temperature, as well as the properties of proteins. Recently, several databases recording LLPS-related biomolecules have been established, and prediction models of LLPS-related phenomena have been explored using these databases. However, a prediction model that concurrently considers proteins, RNAs, and experimental conditions has not been developed due to the limited information available from individual experiments in public databases. RESULTS To address this challenge, we have constructed a new dataset, RNAPSEC, which serves each experiment as a data point. This dataset was accomplished by manually collecting data from public literature. Utilizing RNAPSEC, we developed two prediction models that consider a protein, RNA, and experimental conditions. The first model can predict the LLPS behavior of a protein and RNA under given experimental conditions. The second model can predict the required conditions for a given protein and RNA to undergo LLPS. CONCLUSIONS RNAPSEC and these prediction models are expected to accelerate our understanding of the roles of proteins, RNAs, and environmental factors in LLPS.
Collapse
Affiliation(s)
- Ka Yin Chin
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Shoichi Ishida
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yukio Sasaki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kei Terayama
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- RIKEN Center for Advanced Intelligence Project, 1-4-1, Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.
- MDX Research Center for Element Strategy, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
| |
Collapse
|
26
|
Ryu K, Park G, Cho WK. Emerging insights into transcriptional condensates. Exp Mol Med 2024; 56:820-826. [PMID: 38658705 PMCID: PMC11059374 DOI: 10.1038/s12276-024-01228-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Eukaryotic transcription, a fundamental process that governs cell-specific gene expression, has long been the subject of extensive investigations in the fields of molecular biology, biochemistry, and structural biology. Recent advances in microscopy techniques have led to a fascinating concept known as "transcriptional condensates." These dynamic assemblies are the result of a phenomenon called liquid‒liquid phase separation, which is driven by multivalent interactions between the constituent proteins in cells. The essential proteins associated with transcription are concentrated in transcriptional condensates. Recent studies have shed light on the temporal dynamics of transcriptional condensates and their potential role in enhancing the efficiency of transcription. In this article, we explore the properties of transcriptional condensates, investigate how they evolve over time, and evaluate the significant impact they have on the process of transcription. Furthermore, we highlight innovative techniques that allow us to manipulate these condensates, thus demonstrating their responsiveness to cellular signals and their connection to transcriptional bursting. As our understanding of transcriptional condensates continues to grow, they are poised to revolutionize our understanding of eukaryotic gene regulation.
Collapse
Affiliation(s)
- Kwangmin Ryu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Gunhee Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Won-Ki Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
- KAIST Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), 291 Deahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
| |
Collapse
|
27
|
Friedman MJ, Wagner T, Lee H, Rosenfeld MG, Oh S. Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations. Exp Mol Med 2024; 56:772-787. [PMID: 38658702 PMCID: PMC11058250 DOI: 10.1038/s12276-024-01233-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
Collapse
Affiliation(s)
- Meyer J Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Wagner
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haram Lee
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Michael G Rosenfeld
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Soohwan Oh
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
| |
Collapse
|
28
|
Valyaeva AA, Sheval EV. Nonspecific Interactions in Transcription Regulation and Organization of Transcriptional Condensates. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:688-700. [PMID: 38831505 DOI: 10.1134/s0006297924040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 06/05/2024]
Abstract
Eukaryotic cells are characterized by a high degree of compartmentalization of their internal contents, which ensures precise and controlled regulation of intracellular processes. During many processes, including different stages of transcription, dynamic membraneless compartments termed biomolecular condensates are formed. Transcription condensates contain various transcription factors and RNA polymerase and are formed by high- and low-specificity interactions between the proteins, DNA, and nearby RNA. This review discusses recent data demonstrating important role of nonspecific multivalent protein-protein and RNA-protein interactions in organization and regulation of transcription.
Collapse
Affiliation(s)
- Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
29
|
Xie S, Yue C, Ye S, Li Z. Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complexes through fuzzy interaction and mesoscale condensation. Phys Chem Chem Phys 2024; 26:10408-10418. [PMID: 38502252 DOI: 10.1039/d3cp05957j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Nuclear transition protein TNP1 is a crucial player mediating histone-protamine exchange in condensing spermatids. A unique combination of intrinsic disorder and multivalent properties turns TNP1 into an ideal agent for orchestrating the formation of versatile TNP-DNA assemblies. Despite its significance, the physicochemical property and the molecular mechanism followed by TNP1 for histone replacement and DNA condensation are still poorly understood. This study reports the first-time in vitro expression and purification of human TNP1 and investigates the hierarchical dynamics of TNP1-DNA interaction using a combination of computational simulations, biochemical assays, fluorescence imaging, and atomic force microscopy. We explored three crucial facets of TNP1-DNA interactions. Initially, we delve into the molecular binding process that entails fuzzy interactions between TNP1 and DNA at the atomistic scale. Subsequently, we analyze how TNP1 binding affects the electrostatic and mechanical characteristics of DNA and influences its morphology. Finally, we study the biomolecular condensation of TNP1-DNA when subjected to high concentrations. The findings of our study set the foundation for comprehending the potential involvement of TNP1 in histone replacement and DNA condensation in spermatogenesis.
Collapse
Affiliation(s)
- Shangqiang Xie
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Congran Yue
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Sheng Ye
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Zhenlu Li
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| |
Collapse
|
30
|
Shin S, Shi G, Cho HW, Thirumalai D. Transcription-induced active forces suppress chromatin motion. Proc Natl Acad Sci U S A 2024; 121:e2307309121. [PMID: 38489381 PMCID: PMC10963020 DOI: 10.1073/pnas.2307309121] [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: 05/02/2023] [Accepted: 02/06/2024] [Indexed: 03/17/2024] Open
Abstract
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of chromatin. Some experiments have shown that the motility of individual loci in human interphase chromosome decreases during transcription and increases upon inhibiting transcription. This is a counterintuitive finding because it is thought that the active mechanical force (F) on the order of ten piconewtons, generated by RNA polymerase II (RNAPII) that is presumably transmitted to the gene-rich region of the chromatin, would render it more open, thus enhancing the mobility. We developed a minimal active copolymer model for interphase chromosomes to investigate how F affects the dynamical properties of chromatin. The movements of the loci in the gene-rich region are suppressed in an intermediate range of F and are enhanced at small F values, which has also been observed in experiments. In the intermediate F, the bond length between consecutive loci increases, becoming commensurate with the distance at the minimum of the attractive interaction between nonbonded loci. This results in a transient disorder-to-order transition, leading to a decreased mobility during transcription. Strikingly, the F-dependent change in the locus dynamics preserves the organization of the chromosome at [Formula: see text]. Transient ordering of the loci, which is not found in the polymers with random epigenetic profiles, in the gene-rich region might be a plausible mechanism for nucleating a dynamic network involving transcription factors, RNAPII, and chromatin.
Collapse
Affiliation(s)
- Sucheol Shin
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
| | - Guang Shi
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
- Department of Materials Science, University of Illinois, Urbana, IL61801
| | - Hyun Woo Cho
- Department of Fine Chemistry and Center for Functional Biomaterials, Seoul National University of Science and Technology, Seoul01811, Republic of Korea
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
- Department of Physics, The University of Texas at Austin, Austin, TX78712
| |
Collapse
|
31
|
Meng L, Mao S, Lin J. Heterogeneous elasticity drives ripening and controls bursting kinetics of transcriptional condensates. Proc Natl Acad Sci U S A 2024; 121:e2316610121. [PMID: 38489385 PMCID: PMC10962985 DOI: 10.1073/pnas.2316610121] [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: 09/24/2023] [Accepted: 02/10/2024] [Indexed: 03/17/2024] Open
Abstract
Many biomolecular condensates, including transcriptional condensates, are formed in elastic mediums. In this work, we study the nonequilibrium condensate dynamics in a chromatin-like environment modeled as a heterogeneous elastic medium. We demonstrate that the ripening process in such an elastic medium exhibits a temporal power-law scaling of the average condensate radius, depending on the local stiffness distribution and different from Ostwald ripening. Moreover, we incorporate an active process to model the dissolution of transcriptional condensates upon RNA accumulation. Intriguingly, three types of kinetics of condensate growth emerge, corresponding to constitutively expressed, transcriptional-bursting, and silenced genes. Furthermore, the simulated burst frequency decreases exponentially with the local stiffness, through which we infer a lognormal distribution of local stiffness in living cells using the transcriptome-wide distribution of burst frequency. Under the inferred stiffness distribution, the simulated distributions of bursting kinetic parameters agree reasonably well with the experimental data. Our findings reveal the interplay between biomolecular condensates and elastic mediums, yielding far-reaching implications for gene expression.
Collapse
Affiliation(s)
- Lingyu Meng
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Sheng Mao
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing100871, China
| | - Jie Lin
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| |
Collapse
|
32
|
Lee G, Kim S, Hwang DE, Eom YG, Jang G, Park HY, Choi JM, Ko J, Shin Y. Thermodynamic modulation of gephyrin condensation by inhibitory synapse components. Proc Natl Acad Sci U S A 2024; 121:e2313236121. [PMID: 38466837 PMCID: PMC10963017 DOI: 10.1073/pnas.2313236121] [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: 08/08/2023] [Accepted: 02/05/2024] [Indexed: 03/13/2024] Open
Abstract
Phase separation drives compartmentalization of intracellular contents into various biomolecular condensates. Individual condensate components are thought to differentially contribute to the organization and function of condensates. However, how intermolecular interactions among constituent biomolecules modulate the phase behaviors of multicomponent condensates remains unclear. Here, we used core components of the inhibitory postsynaptic density (iPSD) as a model system to quantitatively probe how the network of intra- and intermolecular interactions defines the composition and cellular distribution of biomolecular condensates. We found that oligomerization-driven phase separation of gephyrin, an iPSD-specific scaffold, is critically modulated by an intrinsically disordered linker region exhibiting minimal homotypic attractions. Other iPSD components, such as neurotransmitter receptors, differentially promote gephyrin condensation through distinct binding modes and affinities. We further demonstrated that the local accumulation of scaffold-binding proteins at the cell membrane promotes the nucleation of gephyrin condensates in neurons. These results suggest that in multicomponent systems, the extent of scaffold condensation can be fine-tuned by scaffold-binding factors, a potential regulatory mechanism for self-organized compartmentalization in cells.
Collapse
Affiliation(s)
- Gyehyun Lee
- Department of Mechanical Engineering, Seoul National University, Seoul08826, Republic of Korea
| | - Seungjoon Kim
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu42988, Republic of Korea
- Center for Synapse Diversity and Specificity, Daegu Gyeongbuk Institute of Science and Technology, Daegu42988, Republic of Korea
| | - Da-Eun Hwang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan46241, Republic of Korea
| | - Yu-Gon Eom
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan46241, Republic of Korea
| | - Gyubin Jang
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu42988, Republic of Korea
- Center for Synapse Diversity and Specificity, Daegu Gyeongbuk Institute of Science and Technology, Daegu42988, Republic of Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul08826, Republic of Korea
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN55455
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan46241, Republic of Korea
| | - Jaewon Ko
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu42988, Republic of Korea
- Center for Synapse Diversity and Specificity, Daegu Gyeongbuk Institute of Science and Technology, Daegu42988, Republic of Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul08826, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Republic of Korea
| |
Collapse
|
33
|
Tang G, Xia H, Huang Y, Guo Y, Chen Y, Ma Z, Liu W. Liquid-liquid phase separation of H3K27me3 reader BP1 regulates transcriptional repression. Genome Biol 2024; 25:67. [PMID: 38468348 PMCID: PMC10926671 DOI: 10.1186/s13059-024-03209-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Bromo-adjacent homology-plant homeodomain domain containing protein 1 (BP1) is a reader of histone post-translational modifications in fungi. BP1 recognizes trimethylation of lysine 27 in histone H3 (H3K27me3), an epigenetic hallmark of gene silencing. However, whether and how BP1 participates in transcriptional repression remains poorly understood. RESULTS We report that BP1 forms phase-separated liquid condensates to modulate its biological function in Fusarium graminearum. Deletion assays reveal that intrinsically disordered region 2 (IDR2) of BP1 mediates its liquid-liquid phase separation. The phase separation of BP1 is indispensable for its interaction with suppressor of Zeste 12, a component of polycomb repressive complex 2. Furthermore, IDR2 deletion abolishes BP1-H3K27me3 binding and alleviates the transcriptional repression of secondary metabolism-related genes, especially deoxynivalenol mycotoxin biosynthesis genes. CONCLUSIONS BP1 maintains transcriptional repression by forming liquid-liquid phase-separated condensates, expanding our understanding of the relationship between post-translational modifications and liquid-liquid phase separation.
Collapse
Affiliation(s)
- Guangfei Tang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haoxue Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yufei Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuanwen Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
34
|
Xu M, Senanayaka D, Zhao R, Chigumira T, Tripathi A, Tones J, Lackner RM, Wondisford AR, Moneysmith LN, Hirschi A, Craig S, Alishiri S, O'Sullivan RJ, Chenoweth DM, Reiter NJ, Zhang H. TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells. Nat Commun 2024; 15:2165. [PMID: 38461301 PMCID: PMC10925046 DOI: 10.1038/s41467-024-46509-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/28/2024] [Indexed: 03/11/2024] Open
Abstract
The telomere repeat-containing RNA (TERRA) forms R-loops to promote homology-directed DNA synthesis in the alternative lengthening of telomere (ALT) pathway. Here we report that TERRA contributes to ALT via interacting with the lysine-specific demethylase 1A (LSD1 or KDM1A). We show that LSD1 localizes to ALT telomeres in a TERRA dependent manner and LSD1 function in ALT is largely independent of its demethylase activity. Instead, LSD1 promotes TERRA recruitment to ALT telomeres via RNA binding. In addition, LSD1 and TERRA undergo phase separation, driven by interactions between the RNA binding properties of LSD1 and the G-quadruplex structure of TERRA. Importantly, the formation of TERRA-LSD1 condensates enriches the R-loop stimulating protein Rad51AP1 and increases TERRA-containing R-loops at telomeres. Our findings suggest that LSD1-TERRA phase separation enhances the function of R-loop regulatory molecules for ALT telomere maintenance, providing a mechanism for how the biophysical properties of histone modification enzyme-RNA interactions impact chromatin function.
Collapse
Affiliation(s)
- Meng Xu
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Dulmi Senanayaka
- Klingler College of Arts and Sciences, Department of Chemistry, Marquette University, Milwaukee, WI, 53233, USA
| | - Rongwei Zhao
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Tafadzwa Chigumira
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Astha Tripathi
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Jason Tones
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Rachel M Lackner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19014, USA
| | - Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Laurel N Moneysmith
- Klingler College of Arts and Sciences, Department of Chemistry, Marquette University, Milwaukee, WI, 53233, USA
| | - Alexander Hirschi
- Cepheid Diagnostics, 904 E. Caribbean Dr., Sunnyvale, California, 94089, USA
| | - Sara Craig
- Klingler College of Arts and Sciences, Department of Chemistry, Marquette University, Milwaukee, WI, 53233, USA
| | - Sahar Alishiri
- Klingler College of Arts and Sciences, Department of Chemistry, Marquette University, Milwaukee, WI, 53233, USA
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19014, USA
| | - Nicholas J Reiter
- Klingler College of Arts and Sciences, Department of Chemistry, Marquette University, Milwaukee, WI, 53233, USA
| | - Huaiying Zhang
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
| |
Collapse
|
35
|
de Vries T, Novakovic M, Ni Y, Smok I, Inghelram C, Bikaki M, Sarnowski CP, Han Y, Emmanouilidis L, Padroni G, Leitner A, Allain FHT. Specific protein-RNA interactions are mostly preserved in biomolecular condensates. SCIENCE ADVANCES 2024; 10:eadm7435. [PMID: 38446881 PMCID: PMC10917357 DOI: 10.1126/sciadv.adm7435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.
Collapse
Affiliation(s)
- Tebbe de Vries
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Mihajlo Novakovic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Yinan Ni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Izabela Smok
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Clara Inghelram
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Maria Bikaki
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Chris P. Sarnowski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Yaning Han
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | - Giacomo Padroni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | |
Collapse
|
36
|
Guo X, Peng K, He Y, Xue L. Mechanistic regulation of FOXO transcription factors in the nucleus. Biochim Biophys Acta Rev Cancer 2024; 1879:189083. [PMID: 38309444 DOI: 10.1016/j.bbcan.2024.189083] [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: 10/18/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/05/2024]
Abstract
FOXO proteins represent evolutionarily conserved transcription factors (TFs) that play critical roles in responding to various physiological signals or pathological stimuli, either through transcription-dependent or -independent mechanisms. Dysfunction of these proteins have been implicated in numerous diseases, including cancer. Although the regulation of FOXO TFs shuttling between the cytoplasm and the nucleus has been extensively studied and reviewed, there's still a lack of a comprehensive review focusing on the intricate interactions between FOXO, DNA, and cofactors in the regulation of gene expression. In this review, we aim to summarize recent advances and provide a detailed understanding of the mechanism underlying FOXO proteins binding to target DNA. Additionally, we will discuss the challenges associated with pharmacological approaches in modulating FOXO function, and explore the dynamic association between TF, DNA, and RNA on chromatin. This review will contribute to a better understanding of mechanistic regulations of eukaryotic TFs within the nucleus.
Collapse
Affiliation(s)
- Xiaowei Guo
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Changsha, China.
| | - Kai Peng
- Institute of Intervention Vessel, Shanghai 10th People's Hospital, Shanghai Key Laboratory of Signaling and Diseases Research, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Yanwen He
- Changsha Stomatological Hospital, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Lei Xue
- Institute of Intervention Vessel, Shanghai 10th People's Hospital, Shanghai Key Laboratory of Signaling and Diseases Research, School of Life Science and Technology, Tongji University, Shanghai, China.
| |
Collapse
|
37
|
Zheng H, Zhang H. More than a bystander: RNAs specify multifaceted behaviors of liquid-liquid phase-separated biomolecular condensates. Bioessays 2024; 46:e2300203. [PMID: 38175843 DOI: 10.1002/bies.202300203] [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: 10/24/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
Cells contain a myriad of membraneless ribonucleoprotein (RNP) condensates with distinct compositions of proteins and RNAs. RNP condensates participate in different cellular activities, including RNA storage, mRNA translation or decay, stress response, etc. RNP condensates are assembled via liquid-liquid phase separation (LLPS) driven by multivalent interactions. Transition of RNP condensates into bodies with abnormal material properties, such as solid-like amyloid structures, is associated with the pathogenesis of various diseases. In this review, we focus on how RNAs regulate multiple aspects of RNP condensates, such as dynamic assembly and/or disassembly and biophysical properties. RNA properties - including concentration, sequence, length and structure - also determine the phase behaviors of RNP condensates. RNA is also involved in specifying autophagic degradation of RNP condensates. Unraveling the role of RNA in RNPs provides novel insights into pathological accumulation of RNPs in various diseases. This new understanding can potentially be harnessed to develop therapeutic strategies.
Collapse
Affiliation(s)
- Hui Zheng
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
| |
Collapse
|
38
|
Dumelie JG, Chen Q, Miller D, Attarwala N, Gross SS, Jaffrey SR. Biomolecular condensates create phospholipid-enriched microenvironments. Nat Chem Biol 2024; 20:302-313. [PMID: 37973889 PMCID: PMC10922641 DOI: 10.1038/s41589-023-01474-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/08/2023] [Indexed: 11/19/2023]
Abstract
Proteins and RNA can phase separate from the aqueous cellular environment to form subcellular compartments called condensates. This process results in a protein-RNA mixture that is chemically different from the surrounding aqueous phase. Here, we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and extracts of cellular metabolites and identified metabolites enriched in the condensate phase. Among the most condensate-enriched metabolites were phospholipids, due primarily to the hydrophobicity of their fatty acyl moieties. We found that phospholipids can alter the number and size of phase-separated condensates and in some cases alter their morphology. Finally, we found that phospholipids partition into a diverse set of endogenous condensates as well as artificial condensates expressed in cells. Overall, these data show that many condensates are protein-RNA-lipid mixtures with chemical microenvironments that are ideally suited to facilitate phospholipid biology and signaling.
Collapse
Affiliation(s)
- Jason G Dumelie
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Dawson Miller
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Nabeel Attarwala
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA.
| |
Collapse
|
39
|
Wang X, Liu J, Mao C, Mao Y. Phase separation-mediated biomolecular condensates and their relationship to tumor. Cell Commun Signal 2024; 22:143. [PMID: 38383403 PMCID: PMC10880379 DOI: 10.1186/s12964-024-01518-9] [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: 09/29/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Phase separation is a cellular phenomenon where macromolecules aggregate or segregate, giving rise to biomolecular condensates resembling "droplets" and forming distinct, membrane-free compartments. This process is pervasive in biological cells, contributing to various essential cellular functions. However, when phase separation goes awry, leading to abnormal molecular aggregation, it can become a driving factor in the development of diseases, including tumor. Recent investigations have unveiled the intricate connection between dysregulated phase separation and tumor pathogenesis, highlighting its potential as a novel therapeutic target. This article provides an overview of recent phase separation research, with a particular emphasis on its role in tumor, its therapeutic implications, and outlines avenues for further exploration in this intriguing field.
Collapse
Affiliation(s)
- Xi Wang
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Jiameng Liu
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Chaoming Mao
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
| | - Yufei Mao
- Department of Ultrasound Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
| |
Collapse
|
40
|
Stortz M, Presman DM, Levi V. Transcriptional condensates: a blessing or a curse for gene regulation? Commun Biol 2024; 7:187. [PMID: 38365945 PMCID: PMC10873363 DOI: 10.1038/s42003-024-05892-5] [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: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Whether phase-separation is involved in the organization of the transcriptional machinery and if it aids or inhibits the transcriptional process is a matter of intense debate. In this Mini Review, we will cover the current knowledge regarding the role of transcriptional condensates on gene expression regulation. We will summarize the latest discoveries on the relationship between condensate formation, genome organization, and transcriptional activity, focusing on the strengths and weaknesses of the experimental approaches used to interrogate these aspects of transcription in living cells. Finally, we will discuss the challenges for future research.
Collapse
Grants
- PICT 2020-00818 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT-2018-1921 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT 2019-0397 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- 20020190100101BA University of Buenos Aires | Secretaría de Ciencia y Técnica, Universidad de Buenos Aires (Secretaría de Ciencia y Técnica de la Universidad de Buenos Aires)
- 2022-11220210100212CO Consejo Nacional de Investigaciones Científicas y Técnicas (National Scientific and Technical Research Council)
Collapse
Affiliation(s)
- Martin Stortz
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EGA, Argentina.
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
| |
Collapse
|
41
|
Kawasaki K, Fukaya T. Regulatory landscape of enhancer-mediated transcriptional activation. Trends Cell Biol 2024:S0962-8924(24)00020-5. [PMID: 38355349 DOI: 10.1016/j.tcb.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/21/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Enhancers are noncoding regulatory elements that instruct spatial and temporal specificity of gene transcription in response to a variety of intrinsic and extrinsic signals during development. Although it has long been postulated that enhancers physically interact with target promoters through the formation of stable loops, recent studies have changed this static view: sequence-specific transcription factors (TFs) and coactivators are dynamically recruited to enhancers and assemble so-called transcription hubs. Dynamic assembly of transcription hubs appears to serve as a key scaffold to integrate regulatory information encoded by surrounding genome and biophysical properties of transcription machineries. In this review, we outline emerging new models of transcriptional regulation by enhancers and discuss future perspectives.
Collapse
Affiliation(s)
- Koji Kawasaki
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
| |
Collapse
|
42
|
Meeussen JVW, Lenstra TL. Time will tell: comparing timescales to gain insight into transcriptional bursting. Trends Genet 2024; 40:160-174. [PMID: 38216391 PMCID: PMC10860890 DOI: 10.1016/j.tig.2023.11.003] [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: 09/13/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
Recent imaging studies have captured the dynamics of regulatory events of transcription inside living cells. These events include transcription factor (TF) DNA binding, chromatin remodeling and modification, enhancer-promoter (E-P) proximity, cluster formation, and preinitiation complex (PIC) assembly. Together, these molecular events culminate in stochastic bursts of RNA synthesis, but their kinetic relationship remains largely unclear. In this review, we compare the timescales of upstream regulatory steps (input) with the kinetics of transcriptional bursting (output) to generate mechanistic models of transcription dynamics in single cells. We highlight open questions and potential technical advances to guide future endeavors toward a quantitative and kinetic understanding of transcription regulation.
Collapse
Affiliation(s)
- Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands.
| |
Collapse
|
43
|
Willemin A, Szabó D, Pombo A. Epigenetic regulatory layers in the 3D nucleus. Mol Cell 2024; 84:415-428. [PMID: 38242127 PMCID: PMC10872226 DOI: 10.1016/j.molcel.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of sequence information transfer from DNA to RNAs and proteins. We have since learned that gene expression is finely tuned in time and space, due to the activities of RNAs and proteins on regulatory DNA elements, and through cell-type-specific three-dimensional conformations of the genome. Here, we review major advances in genome biology and discuss a set of ideas on gene regulation and highlight how various biomolecular assemblies lead to the formation of structural and regulatory features within the nucleus, with roles in transcriptional control. We conclude by suggesting further developments that will help capture the complex, dynamic, and often spatially restricted events that govern gene expression in mammalian cells.
Collapse
Affiliation(s)
- Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
| | - Dominik Szabó
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
| |
Collapse
|
44
|
Ramos-Alonso L, Chymkowitch P. Maintaining transcriptional homeostasis during cell cycle. Transcription 2024; 15:1-21. [PMID: 37655806 PMCID: PMC11093055 DOI: 10.1080/21541264.2023.2246868] [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: 06/21/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
The preservation of gene expression patterns that define cellular identity throughout the cell division cycle is essential to perpetuate cellular lineages. However, the progression of cells through different phases of the cell cycle severely disrupts chromatin accessibility, epigenetic marks, and the recruitment of transcriptional regulators. Notably, chromatin is transiently disassembled during S-phase and undergoes drastic condensation during mitosis, which is a significant challenge to the preservation of gene expression patterns between cell generations. This article delves into the specific gene expression and chromatin regulatory mechanisms that facilitate the preservation of transcriptional identity during replication and mitosis. Furthermore, we emphasize our recent findings revealing the unconventional role of yeast centromeres and mitotic chromosomes in maintaining transcriptional fidelity beyond mitosis.
Collapse
Affiliation(s)
- Lucía Ramos-Alonso
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Pierre Chymkowitch
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| |
Collapse
|
45
|
Brumbaugh-Reed EH, Aoki K, Toettcher JE. Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575860. [PMID: 38293146 PMCID: PMC10827175 DOI: 10.1101/2024.01.16.575860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Biomolecular condensates are broadly implicated in both normal cellular regulation and disease. Consequently, several chemical biology and optogenetic approaches have been developed to induce phase separation of a protein of interest. However, few tools are available to perform the converse function-dissolving a condensate of interest on demand. Such a tool would aid in testing whether the condensate plays specific functional roles, a major question in cell biology and drug development. Here we report an optogenetic approach to selectively dissolve a condensate of interest in a reversible and spatially controlled manner. We show that light-gated recruitment of maltose-binding protein (MBP), a commonly used solubilizing domain in protein purification, results in rapid and controlled dissolution of condensates formed from proteins of interest. Our optogenetic MBP-based dissolution strategy (OptoMBP) is rapid, reversible, and can be spatially controlled with subcellular precision. We also provide a proof-of-principle application of OptoMBP, showing that disrupting condensation of the oncogenic fusion protein FUS-CHOP results in reversion of FUS-CHOP driven transcriptional changes. We envision that the OptoMBP system could be broadly useful for disrupting constitutive protein condensates to probe their biological functions.
Collapse
Affiliation(s)
- Ellen H Brumbaugh-Reed
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton NJ 08544
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
| | - Kazuhiro Aoki
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
- Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8315, Japan
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton NJ 08544
| |
Collapse
|
46
|
Chick BY, Hargreaves DC. RNA polymerase II promoter-proximal pausing promotes BAF chromatin binding and remodeling. Nat Genet 2024; 56:19-20. [PMID: 38129539 DOI: 10.1038/s41588-023-01628-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- Brent Y Chick
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California at San Diego, La Jolla, CA, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
| |
Collapse
|
47
|
Qi L, Zhang J, Liu Q, Gao X. Ligand "switching on" fluorescence of HIV-1 RNA-templated copper nanoclusters for ligand-RNA interaction assays. Int J Biol Macromol 2024; 256:127779. [PMID: 37981280 DOI: 10.1016/j.ijbiomac.2023.127779] [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: 08/09/2023] [Revised: 09/15/2023] [Accepted: 10/27/2023] [Indexed: 11/21/2023]
Abstract
Ligand-RNA interaction assay provides the basis for developing new RNA-binding small molecules. In this study, fluorescent copper nanoclusters (CuNCs) were first prepared using two kinds of HIV-1 RNA targets, rev-responsive element (RRE) and transactivator response element (TAR) RNA, as new templates, and it was found that the fluorescence of the single RNA-templated CuNCs was negligible. Using neomycin as a model drug, the fluorescence could be augmented (approximately 6 times) for the neomycin/RNA-templated CuNCs. Thus, a novel method was developed for ligand-RNA interactions by observing the fluorescence changes in CuNCs prepared using RNA before and after the addition of ligands. The preparation parameters of neomycin/RNA-CuNCs were optimized. The as-prepared CuNCs were characterized using UV-vis spectroscopy, fluorescence spectroscopy, and high-resolution transmission electron microscope. Circular dichroism spectral analysis showed that RRE and TAR were inclined to form a double-stranded structure after interaction with neomycin, which was more conducive to the formation of CuNCs. The interactions of neomycin and three test drugs (amikacin, gentamicin, and tobramycin) with RNA were investigated using the proposed method, and the binding constants and number of binding sites were obtained through theoretical calculations. This study provides a novel approach for ligand-RNA interaction assays.
Collapse
Affiliation(s)
- Liang Qi
- School of Biomedical and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an 710021, China.
| | - Jiayun Zhang
- School of Biomedical and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Qiaoning Liu
- School of Biomedical and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Xiang Gao
- School of Biomedical and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an 710021, China.
| |
Collapse
|
48
|
Abrhámová K, Groušlová M, Valentová A, Hao X, Liu B, Převorovský M, Gahura O, Půta F, Sunnerhagen P, Folk P. Truncating the spliceosomal 'rope protein' Prp45 results in Htz1 dependent phenotypes. RNA Biol 2024; 21:1-17. [PMID: 38711165 PMCID: PMC11085953 DOI: 10.1080/15476286.2024.2348896] [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] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
Spliceosome assembly contributes an important but incompletely understood aspect of splicing regulation. Prp45 is a yeast splicing factor which runs as an extended fold through the spliceosome, and which may be important for bringing its components together. We performed a whole genome analysis of the genetic interaction network of the truncated allele of PRP45 (prp45(1-169)) using synthetic genetic array technology and found chromatin remodellers and modifiers as an enriched category. In agreement with related studies, H2A.Z-encoding HTZ1, and the components of SWR1, INO80, and SAGA complexes represented prominent interactors, with htz1 conferring the strongest growth defect. Because the truncation of Prp45 disproportionately affected low copy number transcripts of intron-containing genes, we prepared strains carrying intronless versions of SRB2, VPS75, or HRB1, the most affected cases with transcription-related function. Intron removal from SRB2, but not from the other genes, partly repaired some but not all the growth phenotypes identified in the genetic screen. The interaction of prp45(1-169) and htz1Δ was detectable even in cells with SRB2 intron deleted (srb2Δi). The less truncated variant, prp45(1-330), had a synthetic growth defect with htz1Δ at 16°C, which also persisted in the srb2Δi background. Moreover, htz1Δ enhanced prp45(1-330) dependent pre-mRNA hyper-accumulation of both high and low efficiency splicers, genes ECM33 and COF1, respectively. We conclude that while the expression defects of low expression intron-containing genes contribute to the genetic interactome of prp45(1-169), the genetic interactions between prp45 and htz1 alleles demonstrate the sensitivity of spliceosome assembly, delayed in prp45(1-169), to the chromatin environment.
Collapse
Affiliation(s)
- Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Martina Groušlová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Anna Valentová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| |
Collapse
|
49
|
Hudaiberdiev S, Ovcharenko I. Sequence characteristics and an accurate model of abundant hyperactive loci in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.05.527203. [PMID: 36945558 PMCID: PMC10028745 DOI: 10.1101/2023.02.05.527203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Enhancers and promoters are classically considered to be bound by a small set of TFs in a sequence-specific manner. This assumption has come under increasing skepticism as the datasets of ChIP-seq assays of TFs have expanded. In particular, high-occupancy target (HOT) loci attract hundreds of TFs with seemingly no detectable correlation between ChIP-seq peaks and DNA-binding motif presence. Here, we used a set of 1,003 TF ChIP-seq datasets (HepG2, K562, H1) to analyze the patterns of ChIP-seq peak co-occurrence in combination with functional genomics datasets. We identified 43,891 HOT loci forming at the promoter (53%) and enhancer (47%) regions. HOT promoters regulate housekeeping genes, whereas HOT enhancers are involved in tissue-specific process regulation. HOT loci form the foundation of human super-enhancers and evolve under strong negative selection, with some of these loci being located in ultraconserved regions. Sequence-based classification analysis of HOT loci suggested that their formation is driven by the sequence features, and the density of mapped ChIP-seq peaks across TF-bound loci correlates with sequence features and the expression level of flanking genes. Based on the affinities to bind to promoters and enhancers we detected 5 distinct clusters of TFs that form the core of the HOT loci. We report an abundance of HOT loci in the human genome and a commitment of 51% of all TF ChIP-seq binding events to HOT locus formation thus challenging the classical model of enhancer activity and propose a model of HOT locus formation based on the existence of large transcriptional condensates.
Collapse
Affiliation(s)
- Sanjarbek Hudaiberdiev
- National Institute for Biotechnology and Information, National Library of Medicine, National Institutes of Health. Bethesda, MD
| | - Ivan Ovcharenko
- National Institute for Biotechnology and Information, National Library of Medicine, National Institutes of Health. Bethesda, MD
| |
Collapse
|
50
|
Yoo W, Song YW, Kim J, Ahn J, Kim J, Shin Y, Ryu JK, Kim KK. Molecular basis for SOX2-dependent regulation of super-enhancer activity. Nucleic Acids Res 2023; 51:11999-12019. [PMID: 37930832 PMCID: PMC10711550 DOI: 10.1093/nar/gkad908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/22/2023] [Accepted: 10/06/2023] [Indexed: 11/08/2023] Open
Abstract
Pioneer transcription factors (TFs) like SOX2 are vital for stemness and cancer through enhancing gene expression within transcriptional condensates formed with coactivators, RNAs and mediators on super-enhancers (SEs). Despite their importance, how these factors work together for transcriptional condensation and activation remains unclear. SOX2, a pioneer TF found in SEs of pluripotent and cancer stem cells, initiates SE-mediated transcription by binding to nucleosomes, though the mechanism isn't fully understood. To address SOX2's role in SEs, we identified mSE078 as a model SOX2-enriched SE and p300 as a coactivator through bioinformatic analysis. In vitro and cell assays showed SOX2 forms condensates with p300 and SOX2-binding motifs in mSE078. We further proved that SOX2 condensation is highly correlated with mSE078's enhancer activity in cells. Moreover, we successfully demonstrated that p300 not only elevated transcriptional activity but also triggered chromatin acetylation via its direct interaction with SOX2 within these transcriptional condensates. Finally, our validation of SOX2-enriched SEs showcased their contribution to target gene expression in both stem cells and cancer cells. In its entirety, this study imparts valuable mechanistic insights into the collaborative interplay of SOX2 and its coactivator p300, shedding light on the regulation of transcriptional condensation and activation within SOX2-enriched SEs.
Collapse
Affiliation(s)
- Wanki Yoo
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Yi Wei Song
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Jihyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jihye Ahn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Je-Kyung Ryu
- Department of Physics & Astronomy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| |
Collapse
|