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Wang W, Li D, Xu Q, Cheng J, Yu Z, Li G, Qiao S, Pan J, Wang H, Shi J, Zheng T, Sui G. G-quadruplexes promote the motility in MAZ phase-separated condensates to activate CCND1 expression and contribute to hepatocarcinogenesis. Nat Commun 2024; 15:1045. [PMID: 38316778 PMCID: PMC10844655 DOI: 10.1038/s41467-024-45353-5] [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: 05/03/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
G-quadruplexes (G4s) can recruit transcription factors to activate gene expression, but detailed mechanisms remain enigmatic. Here, we demonstrate that G4s in the CCND1 promoter propel the motility in MAZ phase-separated condensates and subsequently activate CCND1 transcription. Zinc finger (ZF) 2 of MAZ is a responsible for G4 binding, while ZF3-5, but not a highly disordered region, is critical for MAZ condensation. MAZ nuclear puncta overlaps with signals of G4s and various coactivators including BRD4, MED1, CDK9 and active RNA polymerase II, as well as gene activation histone markers. MAZ mutants lacking either G4 binding or phase separation ability did not form nuclear puncta, and showed deficiencies in promoting hepatocellular carcinoma cell proliferation and xenograft tumor formation. Overall, we unveiled that G4s recruit MAZ to the CCND1 promoter and facilitate the motility in MAZ condensates that compartmentalize coactivators to activate CCND1 expression and subsequently exacerbate hepatocarcinogenesis.
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Affiliation(s)
- Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Qingqing Xu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiahui Cheng
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhiwei Yu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Shiyao Qiao
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiasong Pan
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Hao Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jinming Shi
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Tongsen Zheng
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
- Key Laboratory of Molecular Oncology of Heilongjiang Province, Harbin, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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102
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Ingersoll S, Trouth A, Luo X, Espinoza A, Wen J, Tucker J, Astatike K, Phiel CJ, Kutateladze TG, Wu TP, Ramachandran S, Ren X. Sparse CBX2 nucleates many Polycomb proteins to promote facultative heterochromatinization of Polycomb target genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.578969. [PMID: 38370615 PMCID: PMC10871256 DOI: 10.1101/2024.02.05.578969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Facultative heterochromatinization of genomic regulators by Polycomb repressive complex (PRC) 1 and 2 is essential in development and differentiation; however, the underlying molecular mechanisms remain obscure. Using genetic engineering, molecular approaches, and live-cell single-molecule imaging, we quantify the number of proteins within condensates formed through liquid-liquid phase separation (LLPS) and find that in mouse embryonic stem cells (mESCs), approximately 3 CBX2 proteins nucleate many PRC1 and PRC2 subunits to form one non-stoichiometric condensate. We demonstrate that sparse CBX2 prevents Polycomb proteins from migrating to constitutive heterochromatin, demarcates the spatial boundaries of facultative heterochromatin, controls the deposition of H3K27me3, regulates transcription, and impacts cellular differentiation. Furthermore, we show that LLPS of CBX2 is required for the demarcation and deposition of H3K27me3 and is essential for cellular differentiation. Our findings uncover new functional roles of LLPS in the formation of facultative heterochromatin and unravel a new mechanism by which low-abundant proteins nucleate many other proteins to form compartments that enable them to execute their functions.
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Affiliation(s)
- Steven Ingersoll
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Abby Trouth
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xinlong Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Axel Espinoza
- Department of Integrative Biology, University of Colorado Denver, CO 80217-3364, USA
| | - Joey Wen
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Joseph Tucker
- Department of Integrative Biology, University of Colorado Denver, CO 80217-3364, USA
| | - Kalkidan Astatike
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Christopher J. Phiel
- Department of Integrative Biology, University of Colorado Denver, CO 80217-3364, USA
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Tao P. Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
- Department of Integrative Biology, University of Colorado Denver, CO 80217-3364, USA
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103
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Allyn BM, Hayer KE, Oyeniran C, Nganga V, Lee K, Mishra B, Sacan A, Oltz EM, Bassing CH. Locus folding mechanisms determine modes of antigen receptor gene assembly. J Exp Med 2024; 221:e20230985. [PMID: 38189780 PMCID: PMC10772921 DOI: 10.1084/jem.20230985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/12/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and bidirectional chromosome looping both contribute to structuring Tcrb for efficient long-range V(D)J recombination. Inactivation of the CTCF binding element (CBE) or promoter at the most 5'Vβ segment (Trbv1) impaired loop extrusion originating locally and extending to DβJβ CBEs at the opposite end of Tcrb. Promoter or CBE mutation nearly eliminated Trbv1 contacts and decreased RAG endonuclease-mediated Trbv1 recombination. Importantly, Trbv1 rearrangement can proceed independent of substrate orientation, ruling out scanning by DβJβ-bound RAG as the sole mechanism of Vβ recombination, distinguishing it from Igh. Our data indicate that CBE-dependent generation of loops cooperates with promoter-mediated activation of chromatin to juxtapose Vβ and DβJβ segments for recombination through diffusion-based synapsis. Thus, the mechanisms that fold a genomic region can influence molecular processes occurring in that space, which may include recombination, repair, and transcriptional programming.
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Affiliation(s)
- Brittney M. Allyn
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina E. Hayer
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Perelman School of Medicine, Philadelphia, PA, USA
| | - Clement Oyeniran
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Vincent Nganga
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Kyutae Lee
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bikash Mishra
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Ahmet Sacan
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Craig H. Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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104
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Udupa A, Kotha SR, Staller MV. Commonly asked questions about transcriptional activation domains. Curr Opin Struct Biol 2024; 84:102732. [PMID: 38056064 PMCID: PMC11193542 DOI: 10.1016/j.sbi.2023.102732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Eukaryotic transcription factors activate gene expression with their DNA-binding domains and activation domains. DNA-binding domains bind the genome by recognizing structurally related DNA sequences; they are structured, conserved, and predictable from protein sequences. Activation domains recruit chromatin modifiers, coactivator complexes, or basal transcriptional machinery via structurally diverse protein-protein interactions. Activation domains and DNA-binding domains have been called independent, modular units, but there are many departures from modularity, including interactions between these regions and overlap in function. Compared to DNA-binding domains, activation domains are poorly understood because they are poorly conserved, intrinsically disordered, and difficult to predict from protein sequences. This review, organized around commonly asked questions, describes recent progress that the field has made in understanding the sequence features that control activation domains and predicting them from sequence.
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Affiliation(s)
- Aditya Udupa
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA
| | - Sanjana R Kotha
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA; Center for Computational Biology, University of California, Berkeley, 94720, USA
| | - Max V Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA; Center for Computational Biology, University of California, Berkeley, 94720, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA.
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105
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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.
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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.
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106
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Lim F, Solvason JJ, Ryan GE, Le SH, Jindal GA, Steffen P, Jandu SK, Farley EK. Affinity-optimizing enhancer variants disrupt development. Nature 2024; 626:151-159. [PMID: 38233525 PMCID: PMC10830414 DOI: 10.1038/s41586-023-06922-8] [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: 01/11/2023] [Accepted: 11/30/2023] [Indexed: 01/19/2024]
Abstract
Enhancers control the location and timing of gene expression and contain the majority of variants associated with disease1-3. The ZRS is arguably the most well-studied vertebrate enhancer and mediates the expression of Shh in the developing limb4. Thirty-one human single-nucleotide variants (SNVs) within the ZRS are associated with polydactyly4-6. However, how this enhancer encodes tissue-specific activity, and the mechanisms by which SNVs alter the number of digits, are poorly understood. Here we show that the ETS sites within the ZRS are low affinity, and identify a functional ETS site, ETS-A, with extremely low affinity. Two human SNVs and a synthetic variant optimize the binding affinity of ETS-A subtly from 15% to around 25% relative to the strongest ETS binding sequence, and cause polydactyly with the same penetrance and severity. A greater increase in affinity results in phenotypes that are more penetrant and more severe. Affinity-optimizing SNVs in other ETS sites in the ZRS, as well as in ETS, interferon regulatory factor (IRF), HOX and activator protein 1 (AP-1) sites within a wide variety of enhancers, cause gain-of-function gene expression. The prevalence of binding sites with suboptimal affinity in enhancers creates a vulnerability in genomes whereby SNVs that optimize affinity, even slightly, can be pathogenic. Searching for affinity-optimizing SNVs in genomes could provide a mechanistic approach to identify causal variants that underlie enhanceropathies.
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Affiliation(s)
- Fabian Lim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Joe J Solvason
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Genevieve E Ryan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Sophia H Le
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Granton A Jindal
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Paige Steffen
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Simran K Jandu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emma K Farley
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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107
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Barral A, Zaret KS. Pioneer factors: roles and their regulation in development. Trends Genet 2024; 40:134-148. [PMID: 37940484 PMCID: PMC10873006 DOI: 10.1016/j.tig.2023.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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108
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Sipko EL, Chappell GF, Berlow RB. Multivalency emerges as a common feature of intrinsically disordered protein interactions. Curr Opin Struct Biol 2024; 84:102742. [PMID: 38096754 DOI: 10.1016/j.sbi.2023.102742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Intrinsically disordered proteins (IDPs) use their unique molecular properties and conformational plasticity to interact with cellular partners in a wide variety of biological contexts. Multivalency is an important feature of IDPs that allows for utilization of an expanded toolkit for interactions with other macromolecules and confers additional complexity to molecular recognition processes. Recent studies have offered insights into how multivalent interactions of IDPs enable responsive and sensitive regulation in the context of transcription and cellular signaling. Multivalency is also widely recognized as an important feature of IDP interactions that mediate formation of biomolecular condensates. We highlight recent examples of multivalent interactions of IDPs across diverse contexts to illustrate the breadth of biological processes that utilize multivalency in molecular interactions.
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Affiliation(s)
- Emily L Sipko
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garrett F Chappell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca B Berlow
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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109
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Zhang D, Ni QQ, Wang SY, He WF, Hong ZX, Liu HY, Chen XH, Chen LJ, Han FY, Zhang LJ, Li XM, Ding YQ, Jiao HL, Ye YP. APC mutations disrupt β-catenin destruction complex condensates organized by Axin phase separation. Cell Mol Life Sci 2024; 81:57. [PMID: 38279052 PMCID: PMC10817841 DOI: 10.1007/s00018-023-05068-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 01/28/2024]
Abstract
The Wnt/β-catenin pathway is critical to maintaining cell fate decisions. Recent study showed that liquid-liquid-phase separation (LLPS) of Axin organized the β-catenin destruction complex condensates in a normal cellular state. Mutations inactivating the APC gene are found in approximately 80% of all human colorectal cancer (CRC). However, the molecular mechanism of the formation of β-catenin destruction complex condensates organized by Axin phase separation and how APC mutations impact the condensates are still unclear. Here, we report that the β-catenin destruction complex, which is constructed by Axin, was assembled condensates via a phase separation process in CRC cells. The key role of wild-type APC is to stabilize destruction complex condensates. Surprisingly, truncated APC did not affect the formation of condensates, and GSK 3β and CK1α were unsuccessfully recruited, preventing β-catenin phosphorylation and resulting in accumulation in the cytoplasm of CRCs. Besides, we propose that the phase separation ability of Axin participates in the nucleus translocation of β-catenin and be incorporated and concentrated into transcriptional condensates, affecting the transcriptional activity of Wnt signaling pathway.
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Affiliation(s)
- Dan Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Qi-Qi Ni
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Shu-Yang Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Wen-Feng He
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ze-Xuan Hong
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Hui-Ye Liu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Xiao-Hong Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Li-Jie Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Fang-Yi Han
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ling-Jie Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Xiao-Ming Li
- Department of Pathology, The People's Hospital of Baoan Shenzhen, Shenzhen, Guangdong, China.
| | - Yan-Qing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
- Jinfeng Laboratory, Chongqing, China.
| | - Hong-Li Jiao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
| | - Ya-Ping Ye
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
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110
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Hannon CE, Eisen MB. Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors. eLife 2024; 12:RP88221. [PMID: 38275292 PMCID: PMC10945700 DOI: 10.7554/elife.88221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Abstract
Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early Drosophila embryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high-concentration clusters within nuclei. Here, we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in the Drosophila proteome, we generated a library of IDRs from transcription factors expressed in the early Drosophila embryo. We used this library to perform a high-throughput imaging screen in Drosophila Schneider-2 (S2) cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full-length transcription factors. These results are consistent in live Drosophila embryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.
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Affiliation(s)
- Colleen E Hannon
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Michael B Eisen
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
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111
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Martinez TC, McNerney ME. Haploinsufficient Transcription Factors in Myeloid Neoplasms. ANNUAL REVIEW OF PATHOLOGY 2024; 19:571-598. [PMID: 37906947 DOI: 10.1146/annurev-pathmechdis-051222-013421] [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] [Indexed: 11/02/2023]
Abstract
Many transcription factors (TFs) function as tumor suppressor genes with heterozygous phenotypes, yet haploinsufficiency generally has an underappreciated role in neoplasia. This is no less true in myeloid cells, which are normally regulated by a delicately balanced and interconnected transcriptional network. Detailed understanding of TF dose in this circuitry sheds light on the leukemic transcriptome. In this review, we discuss the emerging features of haploinsufficient transcription factors (HITFs). We posit that: (a) monoallelic and biallelic losses can have distinct cellular outcomes; (b) the activity of a TF exists in a greater range than the traditional Mendelian genetic doses; and (c) how a TF is deleted or mutated impacts the cellular phenotype. The net effect of a HITF is a myeloid differentiation block and increased intercellular heterogeneity in the course of myeloid neoplasia.
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Affiliation(s)
- Tanner C Martinez
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
- Medical Scientist Training Program, The University of Chicago, Chicago, Illinois, USA
| | - Megan E McNerney
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
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112
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Schütz S, Bergsdorf C, Hänni-Holzinger S, Lingel A, Renatus M, Gossert AD, Jahnke W. Intrinsically Disordered Regions in the Transcription Factor MYC:MAX Modulate DNA Binding via Intramolecular Interactions. Biochemistry 2024. [PMID: 38264995 DOI: 10.1021/acs.biochem.3c00608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor (TF) MYC is in large part an intrinsically disordered oncoprotein. In complex with its obligate heterodimerization partner MAX, MYC preferentially binds E-Box DNA sequences (CANNTG). At promoters containing these sequence motifs, MYC controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. A vast network of proteins in turn regulates MYC function via intermolecular interactions. In this work, we establish another layer of MYC regulation by intramolecular interactions. We used nuclear magnetic resonance (NMR) spectroscopy to identify and map multiple binding sites for the C-terminal MYC:MAX DNA-binding domain (DBD) on the intrinsically disordered regions (IDRs) in the MYC N-terminus. We find that these binding events in trans are driven by electrostatic attraction, that they have distinct affinities, and that they are competitive with DNA binding. Thereby, we observe the strongest effects for the N-terminal MYC box 0 (Mb0), a conserved motif involved in MYC transactivation and target gene induction. We prepared recombinant full-length MYC:MAX complex and demonstrate that the interactions identified in this work are also relevant in cis, i.e., as intramolecular interactions. These findings are supported by surface plasmon resonance (SPR) experiments, which revealed that intramolecular IDR:DBD interactions in MYC decelerate the association of MYC:MAX complexes to DNA. Our work offers new insights into how bHLH-LZ TFs are regulated by intramolecular interactions, which open up new possibilities for drug discovery.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra Hänni-Holzinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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113
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Fukute J, Maki K, Adachi T. The nucleolar shell provides anchoring sites for DNA untwisting. Commun Biol 2024; 7:83. [PMID: 38263258 PMCID: PMC10805735 DOI: 10.1038/s42003-023-05750-w] [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: 08/18/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024] Open
Abstract
DNA underwinding (untwisting) is a crucial step in transcriptional activation. DNA underwinding occurs between the site where torque is generated by RNA polymerase (RNAP) and the site where the axial rotation of DNA is constrained. However, what constrains DNA axial rotation in the nucleus is yet unknown. Here, we show that the anchorage to the nuclear protein condensates constrains DNA axial rotation for DNA underwinding in the nucleolus. In situ super-resolution imaging of underwound DNA reveal that underwound DNA accumulates in the nucleolus, a nuclear condensate with a core-shell structure. Specifically, underwound DNA is distributed in the nucleolar core owing to RNA polymerase I (RNAPI) activities. Furthermore, underwound DNA in the core decreases when nucleolar shell components are prevented from binding to their recognition structure, G-quadruplex (G4). Taken together, these results suggest that the nucleolar shell provides anchoring sites that constrain DNA axial rotation for RNAPI-driven DNA underwinding in the core. Our findings will contribute to understanding how nuclear protein condensates make up constraints for the site-specific regulation of DNA underwinding and transcription.
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Affiliation(s)
- Jumpei Fukute
- Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
- Laboratory of Biomechanics, Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, Japan
| | - Koichiro Maki
- Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan.
- Laboratory of Biomechanics, Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, Japan.
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Sakyo, Kyoto, Japan.
- Department of Medicine and Medical Science, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan.
| | - Taiji Adachi
- Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
- Laboratory of Biomechanics, Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, Japan
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Sakyo, Kyoto, Japan
- Department of Medicine and Medical Science, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
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114
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Ji D, Shao C, Yu J, Hou Y, Gao X, Wu Y, Wang L, Chen P. FOXA1 forms biomolecular condensates that unpack condensed chromatin to function as a pioneer factor. Mol Cell 2024; 84:244-260.e7. [PMID: 38101414 DOI: 10.1016/j.molcel.2023.11.020] [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: 06/12/2023] [Revised: 09/14/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Eukaryotic DNA is packaged into chromatin in the nucleus, restricting the binding of transcription factors (TFs) to their target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiate the opening of local chromatin for gene expression. However, the principles of FOXA1 recruitment and how it subsequently unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin. In addition, the DNA-binding capacity of FOXA1 contributes to its ability to both form condensates and dissolve condensed chromatin. Further genome-wide investigation showed that IDRs enable FOXA1 to bind and unpack the condensed chromatin to regulate the proliferation and migration of breast cancer cells. This work provides a principle of how pioneer TFs function to initiate competent chromatin states using their IDRs.
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Affiliation(s)
- Dengyu Ji
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Changrong Shao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoyao Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiao Gao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Yichuan Wu
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Liang Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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115
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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.
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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
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116
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Yang L, Lyu J, Li X, Guo G, Zhou X, Chen T, Lin Y, Li T. Phase separation as a possible mechanism for dosage sensitivity. Genome Biol 2024; 25:17. [PMID: 38225666 PMCID: PMC10789095 DOI: 10.1186/s13059-023-03128-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: 04/04/2023] [Accepted: 11/27/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Deletion of haploinsufficient genes or duplication of triplosensitive ones results in phenotypic effects in a concentration-dependent manner, and the mechanisms underlying these dosage-sensitive effects remain elusive. Phase separation drives functional compartmentalization of biomolecules in a concentration-dependent manner as well, which suggests a potential link between these two processes, and warrants further systematic investigation. RESULTS Here we provide bioinformatic and experimental evidence to show a close link between phase separation and dosage sensitivity. We first demonstrate that haploinsufficient or triplosensitive gene products exhibit a higher tendency to undergo phase separation. Assessing the well-established dosage-sensitive genes HNRNPK, PAX6, and PQBP1 with experiments, we show that these proteins undergo phase separation. Critically, pathogenic variations in dosage-sensitive genes disturb the phase separation process either through reduced protein levels, or loss of phase-separation-prone regions. Analysis of multi-omics data further demonstrates that loss-of-function genetic perturbations on phase-separating genes cause similar dysfunction phenotypes as dosage-sensitive gene perturbations. In addition, dosage-sensitive scores derived from population genetics data predict phase-separating proteins with much better performance than available sequence-based predictors, further illustrating close ties between these two parameters. CONCLUSIONS Together, our study shows that phase separation is functionally linked to dosage sensitivity and provides novel insights for phase-separating protein prediction from the perspective of population genetics data.
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Affiliation(s)
- Liang Yang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jiali Lyu
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xi Li
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Gaigai Guo
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xueya Zhou
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Taoyu Chen
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yi Lin
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Tingting Li
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191, China.
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117
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Lu F, Park BJ, Fujiwara R, Wilusz JE, Gilmour DS, Lehmann R, Lionnet T. Integrator-mediated clustering of poised RNA polymerase II synchronizes histone transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.07.561364. [PMID: 37873455 PMCID: PMC10592978 DOI: 10.1101/2023.10.07.561364] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Numerous components of the transcription machinery, including RNA polymerase II (Pol II), accumulate in regions of high local concentration known as clusters, which are thought to facilitate transcription. Using the histone locus of Drosophila nurse cells as a model, we find that Pol II forms long-lived, transcriptionally poised clusters distinct from liquid droplets, which contain unbound and paused Pol II. Depletion of the Integrator complex endonuclease module, but not its phosphatase module or Pol II pausing factors disperses these Pol II clusters. Consequently, histone transcription fails to reach peak levels during S-phase and aberrantly continues throughout the cell cycle. We propose that Pol II clustering is a regulatory step occurring near promoters that limits rapid gene activation to defined times. One Sentence Summary Using the Drosophila histone locus as a model, we show that clustered RNA polymerase II is poised for synchronous activation.
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118
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Irani S, Tan W, Li Q, Toy W, Jones C, Gadiya M, Marra A, Katzenellenbogen JA, Carlson KE, Katzenellenbogen BS, Karimi M, Segu Rajappachetty R, Del Priore IS, Reis-Filho JS, Shen Y, Chandarlapaty S. Somatic estrogen receptor α mutations that induce dimerization promote receptor activity and breast cancer proliferation. J Clin Invest 2024; 134:e163242. [PMID: 37883178 PMCID: PMC10760953 DOI: 10.1172/jci163242] [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: 07/06/2022] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
Physiologic activation of estrogen receptor α (ERα) is mediated by estradiol (E2) binding in the ligand-binding pocket of the receptor, repositioning helix 12 (H12) to facilitate binding of coactivator proteins in the unoccupied coactivator binding groove. In breast cancer, activation of ERα is often observed through point mutations that lead to the same H12 repositioning in the absence of E2. Through expanded genetic sequencing of breast cancer patients, we identified a collection of mutations located far from H12 but nonetheless capable of promoting E2-independent transcription and breast cancer cell growth. Using machine learning and computational structure analyses, this set of mutants was inferred to act distinctly from the H12-repositioning mutants and instead was associated with conformational changes across the ERα dimer interface. Through both in vitro and in-cell assays of full-length ERα protein and isolated ligand-binding domain, we found that these mutants promoted ERα dimerization, stability, and nuclear localization. Point mutations that selectively disrupted dimerization abrogated E2-independent transcriptional activity of these dimer-promoting mutants. The results reveal a distinct mechanism for activation of ERα function through enforced receptor dimerization and suggest dimer disruption as a potential therapeutic strategy to treat ER-dependent cancers.
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Affiliation(s)
- Seema Irani
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Qing Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Weiyi Toy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Catherine Jones
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mayur Gadiya
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Antonio Marra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John A. Katzenellenbogen
- Department of Chemistry and Molecular and Integrative Physiology, and the Cancer Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kathryn E. Carlson
- Department of Chemistry and Molecular and Integrative Physiology, and the Cancer Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Benita S. Katzenellenbogen
- Department of Chemistry and Molecular and Integrative Physiology, and the Cancer Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Ramya Segu Rajappachetty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Isabella S. Del Priore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
- Department of Computer Science and Engineering and
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
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119
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Zhang Q, Kim W, Panina S, Mayfield JE, Portz B, Zhang YJ. Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.01.573828. [PMID: 38260389 PMCID: PMC10802280 DOI: 10.1101/2024.01.01.573828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. Recent insights highlight the pivotal role of CTD in driving condensate formation on gene loci. Yet, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear. Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulatory proteins, forms distinct condensates from unphosphorylated CTD. Function studies demonstrate CTD variants with diverse condensation properties in vitro exhibit difference in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths lead to alternative splicing outcomes impacting cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.
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Affiliation(s)
- Qian Zhang
- Department of Molecular Biosciences, University of Texas, Austin, Texas, 78712
| | - Wantae Kim
- McKetta Department of Chemical Engineering, University of Texas, Austin, Texas, 78712
| | - Svetlana Panina
- Department of Molecular Biosciences, University of Texas, Austin, Texas, 78712
| | - Joshua E. Mayfield
- Department of Pharmacology, Chemistry, and Biochemistry, and Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093
| | - Bede Portz
- Dewpoint Therapeutics, 451 D Street, Boston, Massachusetts 02210
| | - Y. Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, Texas, 78712
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120
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Xing YH, Dong R, Lee L, Rengarajan S, Riggi N, Boulay G, Rivera MN. DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins. Nat Biotechnol 2024; 42:52-64. [PMID: 37037903 PMCID: PMC10791585 DOI: 10.1038/s41587-023-01737-4] [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: 07/06/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
Abstract
Intrinsically disordered regions (IDRs) in DNA-associated proteins are known to influence gene regulation, but their distribution and cooperative functions in genome-wide regulatory programs remain poorly understood. Here we describe DisP-seq (disordered protein precipitation followed by DNA sequencing), an antibody-independent chemical precipitation assay that can simultaneously map endogenous DNA-associated disordered proteins genome-wide through a combination of biotinylated isoxazole precipitation and next-generation sequencing. DisP-seq profiles are composed of thousands of peaks that are associated with diverse chromatin states, are enriched for disordered transcription factors (TFs) and are often arranged in large lineage-specific clusters with high local concentrations of disordered proteins and different combinations of histone modifications linked to regulatory potential. We use DisP-seq to analyze cancer cells and reveal how disordered protein-associated islands enable IDR-dependent mechanisms that control the binding and function of disordered TFs, including oncogene-dependent sequestration of TFs through long-range interactions and the reactivation of differentiation pathways upon loss of oncogenic stimuli in Ewing sarcoma.
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Affiliation(s)
- Yu-Hang Xing
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Rui Dong
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Lukuo Lee
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Shruthi Rengarajan
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Nicolò Riggi
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Gaylor Boulay
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Miguel N Rivera
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
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121
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Luo J, Huang R, Xiao P, Xu A, Dong Z, Zhang L, Wu R, Qiu Y, Zhu L, Zhang R, Tang L. Construction of hub transcription factor-microRNAs-messenger RNA regulatory network in recurrent implantation failure. J Assist Reprod Genet 2024; 41:3-13. [PMID: 37878219 PMCID: PMC10789703 DOI: 10.1007/s10815-023-02947-0] [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: 07/01/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
PURPOSE Recurrent implantation failure (RIF) affects up to 10% of in vitro fertilization (IVF) patients worldwide. However, the pathogenesis of RIF remains unclear. This study was aimed at identifying hub transcription factors (TFs) of RIF in bioinformatics approaches. METHODS The GSE111974 (mRNA), GSE71332 (miRNA), and GSE103465 (mRNA) datasets were downloaded from the Gene Expression Omnibus database from human endometrial tissue using R version 4.2.1 and used to identify differentially expressed TFs (DETFs), differentially expressed miRNAs, and differentially expressed genes for RIF, respectively. DETFs were subjected to functional enrichment analysis and the protein-protein interaction network analysis using the Search Tool for the Retrieval of Interacting Genes (version 11.5) database. Hub TFs were identified using the cytoHubb plug-in, after which a hub TF-miRNA-mRNA network was constructed using Cytoscape v3.8.2. RESULTS Fifty-seven DETFs were identified, in which Gene Ontology analysis revealed to be mainly involved in the regulation of transcription. Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that DETFs were enriched in transcriptional misregulation in cancer, aldosterone synthesis and secretion, AMPK signaling pathway, and cGMP-PKG signaling pathway. EOMES, NKX2-1, and POU5F1 were identified as hub TFs, and a hub TF-miRNA-mRNA regulatory network was constructed using these three hub TFs, four miRNAs, and four genes. CONCLUSION Collectively, we identified three promising molecular biomarkers for the diagnosis of RIF, which may further be potential therapeutic targets. This study provides novel insights into the molecular mechanisms underlying RIF. However, further experiments are required to verify these results.
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Affiliation(s)
- Jiahuan Luo
- Department of Reproductive Genetics, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Wuhua District, Kunming, China
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- First Clinical Medical College, Kunming Medical University, Kunming, China
| | - Rongxia Huang
- Department of Gynecology, Kunming Maternal and Child Health Hospital, Kunming, China
| | - Pengying Xiao
- Reproductive Medicine Center, Dongguan Songshan Lake Central Hospital, Dongguan, 523429, China
| | - Anli Xu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Zhaomei Dong
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Lirong Zhang
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Rui Wu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Yunlin Qiu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Li Zhu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China.
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China.
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China.
| | - Ruopeng Zhang
- Reproductive Medicine Center, Dongguan Songshan Lake Central Hospital, Dongguan, 523429, China.
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China.
| | - Li Tang
- Department of Reproductive Genetics, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Wuhua District, Kunming, China.
- First Clinical Medical College, Kunming Medical University, Kunming, China.
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Wang J, Chen Y, Xiao Z, Liu X, Liu C, Huang K, Chen H. Phase Separation of Chromatin Structure-related Biomolecules: A Driving Force for Epigenetic Regulations. Curr Protein Pept Sci 2024; 25:553-566. [PMID: 38551058 DOI: 10.2174/0113892037296216240301074253] [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: 01/03/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 07/25/2024]
Abstract
Intracellularly, membrane-less organelles are formed by spontaneous fusion and fission of macro-molecules in a process called phase separation, which plays an essential role in cellular activities. In certain disease states, such as cancers and neurodegenerative diseases, aberrant phase separations take place and participate in disease progression. Chromatin structure-related proteins, based on their characteristics and upon external stimuli, phase separate to exert functions like genome assembly, transcription regulation, and signal transduction. Moreover, many chromatin structure-related proteins, such as histones, histone-modifying enzymes, DNA-modifying enzymes, and DNA methylation binding proteins, are involved in epigenetic regulations through phase separation. This review introduces phase separation and how phase separation affects epigenetics with a focus on chromatin structure-related molecules.
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Affiliation(s)
- Jiao Wang
- Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Yuchen Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zixuan Xiao
- ISA Wenhua Wuhan High School, Fenglin Road, Junshan New Town, Wuhan Economics & Technological Development Zone, Wuhan, Hubei 430119, China
| | - Xikai Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chengyu Liu
- Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hong Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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123
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Salomone J, Farrow E, Gebelein B. Homeodomain complex formation and biomolecular condensates in Hox gene regulation. Semin Cell Dev Biol 2024; 152-153:93-100. [PMID: 36517343 PMCID: PMC10258226 DOI: 10.1016/j.semcdb.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Hox genes are a family of homeodomain transcription factors that regulate specialized morphological structures along the anterior-posterior axis of metazoans. Over the past few decades, researchers have focused on defining how Hox factors with similar in vitro DNA binding activities achieve sufficient target specificity to regulate distinct cell fates in vivo. In this review, we highlight how protein interactions with other transcription factors, many of which are also homeodomain proteins, result in the formation of transcription factor complexes with enhanced DNA binding specificity. These findings suggest that Hox-regulated enhancers utilize distinct combinations of homeodomain binding sites, many of which are low-affinity, to recruit specific Hox complexes. However, low-affinity sites can only yield reproducible responses with high transcription factor concentrations. To overcome this limitation, recent studies revealed how transcription factors, including Hox factors, use intrinsically disordered domains (IDRs) to form biomolecular condensates that increase protein concentrations. Moreover, Hox factors with altered IDRs have been associated with altered transcriptional activity and human disease states, demonstrating the importance of IDRs in mediating essential Hox output. Collectively, these studies highlight how Hox factors use their DNA binding domains, protein-protein interaction domains, and IDRs to form specific transcription factor complexes that yield accurate gene expression.
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Affiliation(s)
- Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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124
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Liu J, Fan H, Liang X, Chen Y. Polycomb repressor complex: Its function in human cancer and therapeutic target strategy. Biomed Pharmacother 2023; 169:115897. [PMID: 37981459 DOI: 10.1016/j.biopha.2023.115897] [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: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
The Polycomb Repressor Complex (PRC) plays a pivotal role in gene regulation during development and disease, with dysregulation contributing significantly to various human cancers. The intricate interplay between PRC and cellular signaling pathways sheds light on cancer complexity. PRC presents promising therapeutic opportunities, with inhibitors undergoing rigorous evaluation in preclinical and clinical studies. In this review, we emphasize the critical role of PRC complex in gene regulation, particularly PcG proteins mediated chromatin compaction through phase separation. We also highlight the pathological implications of PRC complex dysregulation in various tumors, elucidating underlying mechanisms driving cancer progression. The burgeoning field of therapeutic strategies targeting PRC complexes, notably EZH2 inhibitors, has advanced significantly. However, we explore the need for combination therapies to enhance PRC targeted treatments efficacy, providing a glimpse into the future of cancer therapeutics.
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Affiliation(s)
- Jingrong Liu
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Hongjie Fan
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Xinmiao Liang
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yang Chen
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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125
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Blayney JW, Francis H, Rampasekova A, Camellato B, Mitchell L, Stolper R, Cornell L, Babbs C, Boeke JD, Higgs DR, Kassouf M. Super-enhancers include classical enhancers and facilitators to fully activate gene expression. Cell 2023; 186:5826-5839.e18. [PMID: 38101409 PMCID: PMC10858684 DOI: 10.1016/j.cell.2023.11.030] [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: 08/08/2022] [Revised: 07/06/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Super-enhancers are compound regulatory elements that control expression of key cell identity genes. They recruit high levels of tissue-specific transcription factors and co-activators such as the Mediator complex and contact target gene promoters with high frequency. Most super-enhancers contain multiple constituent regulatory elements, but it is unclear whether these elements have distinct roles in activating target gene expression. Here, by rebuilding the endogenous multipartite α-globin super-enhancer, we show that it contains bioinformatically equivalent but functionally distinct element types: classical enhancers and facilitator elements. Facilitators have no intrinsic enhancer activity, yet in their absence, classical enhancers are unable to fully upregulate their target genes. Without facilitators, classical enhancers exhibit reduced Mediator recruitment, enhancer RNA transcription, and enhancer-promoter interactions. Facilitators are interchangeable but display functional hierarchy based on their position within a multipartite enhancer. Facilitators thus play an important role in potentiating the activity of classical enhancers and ensuring robust activation of target genes.
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Affiliation(s)
- Joseph W Blayney
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Helena Francis
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Alexandra Rampasekova
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Brendan Camellato
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Leslie Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Rosa Stolper
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Lucy Cornell
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA.
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Chinese Academy of Medical Sciences Oxford Institute, Oxford OX3 7BN, UK.
| | - Mira Kassouf
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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126
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Asante Y, Benischke K, Osman I, Ngo QA, Wurth J, Laubscher D, Kim H, Udhayakumar B, Khan MIH, Chin DH, Porch J, Chakraborty M, Sallari R, Delattre O, Zaidi S, Morice S, Surdez D, Danielli SG, Schäfer BW, Gryder BE, Wachtel M. PAX3-FOXO1 uses its activation domain to recruit CBP/P300 and shape RNA Pol2 cluster distribution. Nat Commun 2023; 14:8361. [PMID: 38102136 PMCID: PMC10724205 DOI: 10.1038/s41467-023-43780-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Activation of oncogenic gene expression from long-range enhancers is initiated by the assembly of DNA-binding transcription factors (TF), leading to recruitment of co-activators such as CBP/p300 to modify the local genomic context and facilitate RNA-Polymerase 2 (Pol2) binding. Yet, most TF-to-coactivator recruitment relationships remain unmapped. Here, studying the oncogenic fusion TF PAX3-FOXO1 (P3F) from alveolar rhabdomyosarcoma (aRMS), we show that a single cysteine in the activation domain (AD) of P3F is important for a small alpha helical coil that recruits CBP/p300 to chromatin. P3F driven transcription requires both this single cysteine and CBP/p300. Mutants of the cysteine reduce aRMS cell proliferation and induce cellular differentiation. Furthermore, we discover a profound dependence on CBP/p300 for clustering of Pol2 loops that connect P3F to its target genes. In the absence of CBP/p300, Pol2 long range enhancer loops collapse, Pol2 accumulates in CpG islands and fails to exit the gene body. These results reveal a potential novel axis for therapeutic interference with P3F in aRMS and clarify the molecular relationship of P3F and CBP/p300 in sustaining active Pol2 clusters essential for oncogenic transcription.
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Affiliation(s)
- Yaw Asante
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Katharina Benischke
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Issra Osman
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Quy A Ngo
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Jakob Wurth
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Dominik Laubscher
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Hyunmin Kim
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Md Imdadul H Khan
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Diana H Chin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jadon Porch
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | | | - Olivier Delattre
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sakina Zaidi
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sarah Morice
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Didier Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Sara G Danielli
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Beat W Schäfer
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland.
| | - Berkley E Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Marco Wachtel
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland.
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127
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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.
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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
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128
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Parra AS, Johnston CA. Phase Separation as a Driver of Stem Cell Organization and Function during Development. J Dev Biol 2023; 11:45. [PMID: 38132713 PMCID: PMC10743522 DOI: 10.3390/jdb11040045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
A properly organized subcellular composition is essential to cell function. The canonical organizing principle within eukaryotic cells involves membrane-bound organelles; yet, such structures do not fully explain cellular complexity. Furthermore, discrete non-membrane-bound structures have been known for over a century. Liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mode of cellular organization without the need for formal lipid membranes, with an ever-expanding and diverse list of cellular functions that appear to be regulated by this process. In comparison to traditional organelles, LLPS can occur across wider spatial and temporal scales and involves more distinct protein and RNA complexes. In this review, we discuss the impacts of LLPS on the organization of stem cells and their function during development. Specifically, the roles of LLPS in developmental signaling pathways, chromatin organization, and gene expression will be detailed, as well as its impacts on essential processes of asymmetric cell division. We will also discuss how the dynamic and regulated nature of LLPS may afford stem cells an adaptable mode of organization throughout the developmental time to control cell fate. Finally, we will discuss how aberrant LLPS in these processes may contribute to developmental defects and disease.
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129
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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.
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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
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130
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Titus KR, Simandi Z, Chandrashekar H, Paquet D, Phillips-Cremins JE. Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569731. [PMID: 38106199 PMCID: PMC10723365 DOI: 10.1101/2023.12.04.569731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
DNA is folded into higher-order structures that shape and are shaped by genome function. The role for long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNAPolII) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitors (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNAPolII initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops, promoter-promoter loops, or unlooped. Genes transitioning from repression to RNAPolII initiation exhibit slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNAPolII-mediated elongation during neural cell fate transitions.
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Affiliation(s)
- Katelyn R Titus
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | - Zoltan Simandi
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | - Harshini Chandrashekar
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | - Dominik Paquet
- Institute for Stroke and Dementia Research, Ludwig Maximilians Universitat, Munich, Germany
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
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131
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Abstract
The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid-liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric heterochromatin domains. In this review, we will describe our understanding of heterochromatin organization and LLPS. In addition, we will highlight the increasing importance of multivalent weak homo- and heteromolecular interactions in LLPS-mediated heterochromatin compartmentalization in the complex environment inside living cells.
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Affiliation(s)
- Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Hector Romero
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany,CONTACT M. Cristina Cardoso Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287Darmstadt, Germany
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Tsuji K, Kawata H, Kamiakito T, Nakaya T, Tanaka A. RNA-binding protein 14 promotes phase separation to sustain prostate specific antigen expression under androgen deprivation in human prostate cancer. J Steroid Biochem Mol Biol 2023; 235:106407. [PMID: 37806532 DOI: 10.1016/j.jsbmb.2023.106407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/01/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Castration-resistant prostate cancer (CRPC) is a big challenge in managing prostate cancer patients. The androgen receptor (AR) pathway is a major driver even in CRPC under androgen deprivation. The mechanism in maintaining of the AR pathway under androgen deprivation remains elusive. The recent discovery of biomolecular condensate, a membrane-less intracellular construct formed by liquid-liquid phase separation (LLPS), that facilitate molecular assembly, encouraged the re-screening of our previous microarray data list. We selected Rbm14 as a target molecule for further analysis because it works as a coactivator of nuclear receptors as well as it facilitates formation of biomolecular condensates via its intrinsically disordered region. GFP-tagged Rbm14 transfected into HEK293T cells formed droplet-like puncta, which diminished following treatment with 1,6-hexanediol. Droplet-like structures were also observed in immunofluorescence for endogenous RBM14 of PC-3 and DU145 cells. Luciferase assay revealed that Rbm14 enhanced androgen-responsive element (ARE)-mediated reporter activity in all conditions with or without testosterone and AR. Co-immunoprecipitation confirmed the Rbm14-AR interaction. Long non-coding RNAs, including NEAT1, SRA1, and HOTAIR, were also interacted with Rbm14. Small interfering RNAs of NEAT1 reduced ARE-mediated reporter activity, while transfection of SRA1 and HOTAIR enhance the reporter activity. Treatment with 1,6-hexanediol as well as transfection with a dominant-negative splice variant of Rbm14 reduced expression of prostate specific antigen (PSA), a prototype of androgen-regulated gene, in LNCaP, PC-3, and DU145 cells under androgen deprivation. Immunohistochemically, RBM14 expression was substantially upregulated in prostate cancer tissues after androgen deprivation therapy than in untreated tumors. In conclusion, RBM14 is a novel factor involved in maintenance of PSA expression via phase separation under androgen deprivation in prostate cancer.
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Affiliation(s)
- Kentaro Tsuji
- Department of Pathology, Division of Human Pathology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Hirotoshi Kawata
- Department of Pathology, Division of Human Pathology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Tomoko Kamiakito
- Department of Pathology, Division of Human Pathology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Takeo Nakaya
- Department of Pathology, Division of Human Pathology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Akira Tanaka
- Department of Pathology, Division of Human Pathology, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan.
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Mann R, Notani D. Transcription factor condensates and signaling driven transcription. Nucleus 2023; 14:2205758. [PMID: 37129580 PMCID: PMC10155639 DOI: 10.1080/19491034.2023.2205758] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023] Open
Abstract
Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the 3D nuclear space is believed to provide a fast response, which is on the same pace as the signaling cascade and yet ever-so-specific in the crowded environment of the nucleus. However, the current understanding of how TF-condensates can achieve these feet so quickly and efficiently is still unclear. In this review, we draw parallels with other protein condensates and share our speculations on how the nucleus uses these TF-condensates to achieve high transcriptional specificity and fidelity. We discuss the various constituents of TF-condensates, their properties, and the known and unknown functions of TF-condensates with a particular focus on steroid signaling-induced transcriptional programs.
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Affiliation(s)
- Rajat Mann
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Dimple Notani
- National Centre for Biological Sciences, TIFR, Bangalore, India
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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135
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Stossi F, Rivera Tostado A, Johnson HL, Mistry RM, Mancini MG, Mancini MA. Gene transcription regulation by ER at the single cell and allele level. Steroids 2023; 200:109313. [PMID: 37758052 PMCID: PMC10842394 DOI: 10.1016/j.steroids.2023.109313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/12/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023]
Abstract
In this short review we discuss the current view of how the estrogen receptor (ER), a pivotal member of the nuclear receptor superfamily of transcription factors, regulates gene transcription at the single cell and allele level, focusing on in vitro cell line models. We discuss central topics and new trends in molecular biology including phenotypic heterogeneity, single cell sequencing, nuclear phase separated condensates, single cell imaging, and image analysis methods, with particular focus on the methodologies and results that have been reported in the last few years using microscopy-based techniques. These observations augment the results from biochemical assays that lead to a much more complex and dynamic view of how ER, and arguably most transcription factors, act to regulate gene transcription.
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Affiliation(s)
- Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, United States.
| | | | - Hannah L Johnson
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, United States
| | - Ragini M Mistry
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, United States
| | - Maureen G Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, United States
| | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, United States; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States.
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136
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Cai L, Wang GG. Through the lens of phase separation: intrinsically unstructured protein and chromatin looping. Nucleus 2023; 14:2179766. [PMID: 36821650 PMCID: PMC9980480 DOI: 10.1080/19491034.2023.2179766] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The establishment, maintenance and dynamic regulation of three-dimensional (3D) chromatin structures provide an important means for partitioning of genome into functionally distinctive domains, which helps to define specialized gene expression programs associated with developmental stages and cell types. Increasing evidence supports critical roles for intrinsically disordered regions (IDRs) harbored within transcription factors (TFs) and chromatin-modulatory proteins in inducing phase separation, a phenomenon of forming membrane-less condensates through partitioning of biomolecules. Such a process is also critically involved in the establishment of high-order chromatin structures and looping. IDR- and phase separation-driven 3D genome (re)organization often goes wrong in disease such as cancer. This review discusses about recent advances in understanding how phase separation of intrinsically disordered proteins (IDPs) modulates chromatin looping and gene expression.
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Affiliation(s)
- Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Ling Cai Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,CONTACT Gang Greg Wang Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
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137
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Gao G, Sumrall ES, Pitchiaya S, Bitzer M, Alberti S, Walter NG. Biomolecular condensates in kidney physiology and disease. Nat Rev Nephrol 2023; 19:756-770. [PMID: 37752323 DOI: 10.1038/s41581-023-00767-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2023] [Indexed: 09/28/2023]
Abstract
The regulation and preservation of distinct intracellular and extracellular solute microenvironments is crucial for the maintenance of cellular homeostasis. In mammals, the kidneys control bodily salt and water homeostasis. Specifically, the urine-concentrating mechanism within the renal medulla causes fluctuations in extracellular osmolarity, which enables cells of the kidney to either conserve or eliminate water and electrolytes, depending on the balance between intake and loss. However, relatively little is known about the subcellular and molecular changes caused by such osmotic stresses. Advances have shown that many cells, including those of the kidney, rapidly (within seconds) and reversibly (within minutes) assemble membraneless, nano-to-microscale subcellular assemblies termed biomolecular condensates via the biophysical process of hyperosmotic phase separation (HOPS). Mechanistically, osmotic cell compression mediates changes in intracellular hydration, concentration and molecular crowding, rendering HOPS one of many related phase-separation phenomena. Osmotic stress causes numerous homo-multimeric proteins to condense, thereby affecting gene expression and cell survival. HOPS rapidly regulates specific cellular biochemical processes before appropriate protective or corrective action by broader stress response mechanisms can be initiated. Here, we broadly survey emerging evidence for, and the impact of, biomolecular condensates in nephrology, where initial concentration buffering by HOPS and its subsequent cellular escalation mechanisms are expected to have important implications for kidney physiology and disease.
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Affiliation(s)
- Guoming Gao
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily S Sumrall
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Markus Bitzer
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany
| | - Nils G Walter
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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138
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Basu S, Martínez-Cristóbal P, Frigolé-Vivas M, Pesarrodona M, Lewis M, Szulc E, Bañuelos CA, Sánchez-Zarzalejo C, Bielskutė S, Zhu J, Pombo-García K, Garcia-Cabau C, Zodi L, Dockx H, Smak J, Kaur H, Batlle C, Mateos B, Biesaga M, Escobedo A, Bardia L, Verdaguer X, Ruffoni A, Mawji NR, Wang J, Obst JK, Tam T, Brun-Heath I, Ventura S, Meierhofer D, García J, Robustelli P, Stracker TH, Sadar MD, Riera A, Hnisz D, Salvatella X. Rational optimization of a transcription factor activation domain inhibitor. Nat Struct Mol Biol 2023; 30:1958-1969. [PMID: 38049566 PMCID: PMC10716049 DOI: 10.1038/s41594-023-01159-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 10/23/2023] [Indexed: 12/06/2023]
Abstract
Transcription factors are among the most attractive therapeutic targets but are considered largely 'undruggable' in part due to the intrinsically disordered nature of their activation domains. Here we show that the aromatic character of the activation domain of the androgen receptor, a therapeutic target for castration-resistant prostate cancer, is key for its activity as transcription factor, allowing it to translocate to the nucleus and partition into transcriptional condensates upon activation by androgens. On the basis of our understanding of the interactions stabilizing such condensates and of the structure that the domain adopts upon condensation, we optimized the structure of a small-molecule inhibitor previously identified by phenotypic screening. The optimized compounds had more affinity for their target, inhibited androgen-receptor-dependent transcriptional programs, and had an antitumorigenic effect in models of castration-resistant prostate cancer in cells and in vivo. These results suggest that it is possible to rationally optimize, and potentially even to design, small molecules that target the activation domains of oncogenic transcription factors.
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Affiliation(s)
- Shaon Basu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Paula Martínez-Cristóbal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Frigolé-Vivas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mireia Pesarrodona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Michael Lewis
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elzbieta Szulc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - C Adriana Bañuelos
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Carolina Sánchez-Zarzalejo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stasė Bielskutė
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jiaqi Zhu
- Dartmouth College, Department of Chemistry, Hanover, NH, USA
| | - Karina Pombo-García
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Levente Zodi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Jordann Smak
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Harpreet Kaur
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Cristina Batlle
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Borja Mateos
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mateusz Biesaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Albert Escobedo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Xavier Verdaguer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Barcelona, Spain
| | - Alessandro Ruffoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nasrin R Mawji
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jun Wang
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jon K Obst
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Teresa Tam
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Facility, Berlin, Germany
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Paul Robustelli
- Dartmouth College, Department of Chemistry, Hanover, NH, USA
| | - Travis H Stracker
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Marianne D Sadar
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Barcelona, Spain.
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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139
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Liu J, Chen Y, Nong B, Luo X, Cui K, Li Z, Zhang P, Tan W, Yang Y, Ma W, Liang P, Songyang Z. CRISPR-assisted transcription activation by phase-separation proteins. Protein Cell 2023; 14:874-887. [PMID: 36905356 PMCID: PMC10691850 DOI: 10.1093/procel/pwad013] [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: 11/25/2022] [Accepted: 01/11/2023] [Indexed: 03/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been widely used for genome engineering and transcriptional regulation in many different organisms. Current CRISPR-activation (CRISPRa) platforms often require multiple components because of inefficient transcriptional activation. Here, we fused different phase-separation proteins to dCas9-VPR (dCas9-VP64-P65-RTA) and observed robust increases in transcriptional activation efficiency. Notably, human NUP98 (nucleoporin 98) and FUS (fused in sarcoma) IDR domains were best at enhancing dCas9-VPR activity, with dCas9-VPR-FUS IDR (VPRF) outperforming the other CRISPRa systems tested in this study in both activation efficiency and system simplicity. dCas9-VPRF overcomes the target strand bias and widens gRNA designing windows without affecting the off-target effect of dCas9-VPR. These findings demonstrate the feasibility of using phase-separation proteins to assist in the regulation of gene expression and support the broad appeal of the dCas9-VPRF system in basic and clinical applications.
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Affiliation(s)
- Jiaqi Liu
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuxi Chen
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Baoting Nong
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiao Luo
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kaixin Cui
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhan Li
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pengfei Zhang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | - Yue Yang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Puping Liang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
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140
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Barajas-Mora EM, Feeney AJ. Enhancers within the Ig V Gene Region Orchestrate Chromatin Topology and Regulate V Gene Rearrangement Frequency to Shape the B Cell Receptor Repertoire Specificities. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1613-1622. [PMID: 37983521 PMCID: PMC10662671 DOI: 10.4049/jimmunol.2300261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 11/22/2023]
Abstract
Effective Ab-mediated responses depend on a highly diverse Ab repertoire with the ability to bind a wide range of epitopes in disease-causing agents. The generation of this repertoire depends on the somatic recombination of the variable (V), diversity (D), and joining (J) genes in the Ig loci of developing B cells. It has been known for some time that individual V, D, and J gene segments rearrange at different frequencies, but the mechanisms behind this unequal V gene usage have not been well understood. However, recent work has revealed that newly described enhancers scattered throughout the V gene-containing portion of the Ig loci regulate the V gene recombination frequency in a regional manner. Deletion of three of these enhancers revealed that these elements exert many layers of control during V(D)J recombination, including long-range chromatin interactions, epigenetic milieu, chromatin accessibility, and compartmentalization.
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Affiliation(s)
- E. Mauricio Barajas-Mora
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA, Current address: Poseida Therapeutics, Inc. San Diego, CA
| | - Ann J. Feeney
- Scripps Research, Department of Immunology and Microbiology, La Jolla, CA 92014
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141
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Medwig-Kinney TN, Kinney BA, Martinez MAQ, Yee C, Sirota SS, Mullarkey AA, Somineni N, Hippler J, Zhang W, Shen K, Hammell C, Pani AM, Matus DQ. Dynamic compartmentalization of the pro-invasive transcription factor NHR-67 reveals a role for Groucho in regulating a proliferative-invasive cellular switch in C. elegans. eLife 2023; 12:RP84355. [PMID: 38038410 PMCID: PMC10691804 DOI: 10.7554/elife.84355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
A growing body of evidence suggests that cell division and basement membrane invasion are mutually exclusive cellular behaviors. How cells switch between proliferative and invasive states is not well understood. Here, we investigated this dichotomy in vivo by examining two cell types in the developing Caenorhabditis elegans somatic gonad that derive from equipotent progenitors, but exhibit distinct cell behaviors: the post-mitotic, invasive anchor cell and the neighboring proliferative, non-invasive ventral uterine (VU) cells. We show that the fates of these cells post-specification are more plastic than previously appreciated and that levels of NHR-67 are important for discriminating between invasive and proliferative behavior. Transcription of NHR-67 is downregulated following post-translational degradation of its direct upstream regulator, HLH-2 (E/Daughterless) in VU cells. In the nuclei of VU cells, residual NHR-67 protein is compartmentalized into discrete punctae that are dynamic over the cell cycle and exhibit liquid-like properties. By screening for proteins that colocalize with NHR-67 punctae, we identified new regulators of uterine cell fate maintenance: homologs of the transcriptional co-repressor Groucho (UNC-37 and LSY-22), as well as the TCF/LEF homolog POP-1. We propose a model in which the association of NHR-67 with the Groucho/TCF complex suppresses the default invasive state in non-invasive cells, which complements transcriptional regulation to add robustness to the proliferative-invasive cellular switch in vivo.
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Affiliation(s)
- Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Brian A Kinney
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Michael AQ Martinez
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford UniversityStanfordUnited States
| | - Sydney S Sirota
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Angelina A Mullarkey
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Neha Somineni
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Justin Hippler
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
- Science and Technology Research Program, Smithtown High School EastSt. JamesUnited States
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford UniversityStanfordUnited States
| | | | - Ariel M Pani
- Departments of Biology and Cell Biology, University of VirginiaCharlottesvilleUnited States
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
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142
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Moyers BA, Partridge EC, Mackiewicz M, Betti MJ, Darji R, Meadows SK, Newberry KM, Brandsmeier LA, Wold BJ, Mendenhall EM, Myers RM. Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells. Genome Res 2023; 33:1879-1892. [PMID: 37852782 PMCID: PMC10760452 DOI: 10.1101/gr.278205.123] [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] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
Transcription factors (TFs) are trans-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the human cancer cell line HepG2, for a total of 680 broadly termed DNA-associated proteins (DAPs). We used this deep collection to model each TF's impact on gene expression, and identified a cohort of 26 candidate transcriptional repressors. We examine high occupancy target (HOT) sites in the context of three-dimensional genome organization and show biased motif placement in distal-promoter connections involving HOT sites. We also found a substantial number of closed chromatin regions with multiple DAPs bound, and explored their properties, finding that a MAFF/MAFK TF pair correlates with transcriptional repression. Altogether, these analyses provide novel insights into the regulatory logic of the human cell line HepG2 genome and show the usefulness of large genomic analyses for elucidation of individual TF functions.
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Affiliation(s)
- Belle A Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Michael J Betti
- Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Roshan Darji
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sarah K Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | | | - Barbara J Wold
- Merkin Institute for Translational Research, California Institute of Technology, Pasadena, California 91125, USA
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
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143
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Ganser C, Staples MI, Dowell M, Frazer C, Dainis J, Sircaik S, Bennett RJ. Filamentation and biofilm formation are regulated by the phase-separation capacity of network transcription factors in Candida albicans. PLoS Pathog 2023; 19:e1011833. [PMID: 38091321 PMCID: PMC10718430 DOI: 10.1371/journal.ppat.1011833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
The ability of the fungus Candida albicans to filament and form biofilms contributes to its burden as a leading cause of hospital-acquired infections. Biofilm development involves an interconnected transcriptional regulatory network (TRN) consisting of nine transcription factors (TFs) that bind both to their own regulatory regions and to those of the other network TFs. Here, we show that seven of the nine TFs in the C. albicans biofilm network contain prion-like domains (PrLDs) that have been linked to the ability to form phase-separated condensates. Construction of PrLD mutants in four biofilm TFs reveals that these domains are essential for filamentation and biofilm formation in C. albicans. Moreover, biofilm PrLDs promote the formation of phase-separated condensates in the nuclei of live cells, and PrLD mutations that abolish phase separation (such as the removal of aromatic residues) also prevent biofilm formation. Biofilm TF condensates can selectively recruit other TFs through PrLD-PrLD interactions and can co-recruit RNA polymerase II, implicating condensate formation in the assembly of active transcriptional complexes. Finally, we show that PrLD mutations that block the phase separation of biofilm TFs also prevent filamentation in an in vivo model of gastrointestinal colonization. Together, these studies associate transcriptional condensates with the regulation of filamentation and biofilm formation in C. albicans, and highlight how targeting of PrLD-PrLD interactions could prevent pathogenesis by this species.
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Affiliation(s)
- Collin Ganser
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Mae I. Staples
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Maureen Dowell
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Corey Frazer
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Joseph Dainis
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Shabnam Sircaik
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
| | - Richard J. Bennett
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, United States of America
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144
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Demmerle J, Hao S, Cai D. Transcriptional condensates and phase separation: condensing information across scales and mechanisms. Nucleus 2023; 14:2213551. [PMID: 37218279 PMCID: PMC10208215 DOI: 10.1080/19491034.2023.2213551] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Transcription is the fundamental process of gene expression, which in eukaryotes occurs within the complex physicochemical environment of the nucleus. Decades of research have provided extreme detail in the molecular and functional mechanisms of transcription, but the spatial and genomic organization of transcription remains mysterious. Recent discoveries show that transcriptional components can undergo phase separation and create distinct compartments inside the nucleus, providing new models through which to view the transcription process in eukaryotes. In this review, we focus on transcriptional condensates and their phase separation-like behaviors. We suggest differentiation between physical descriptions of phase separation and the complex and dynamic biomolecular assemblies required for productive gene expression, and we discuss how transcriptional condensates are central to organizing the three-dimensional genome across spatial and temporal scales. Finally, we map approaches for therapeutic manipulation of transcriptional condensates and ask what technical advances are needed to understand transcriptional condensates more completely.
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Affiliation(s)
- Justin Demmerle
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Siyuan Hao
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
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145
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Ling YH, Ye Z, Liang C, Yu C, Park G, Corden JL, Wu C. Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551302. [PMID: 37577667 PMCID: PMC10418089 DOI: 10.1101/2023.07.31.551302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Efficient gene expression requires RNA Polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in 3D nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. Here, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is required for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation, and reduces transcription bursting. This study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression.
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Affiliation(s)
- Yick Hin Ling
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Ziyang Ye
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Chloe Liang
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Chuofan Yu
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Giho Park
- Department of Biology, Johns Hopkins University, Baltimore, USA
| | - Jeffry L Corden
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
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146
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Gao Y, Tong M, Wong TL, Ng KY, Xie YN, Wang Z, Yu H, Loh JJ, Li M, Ma S. Long Noncoding RNA URB1-Antisense RNA 1 (AS1) Suppresses Sorafenib-Induced Ferroptosis in Hepatocellular Carcinoma by Driving Ferritin Phase Separation. ACS NANO 2023; 17:22240-22258. [PMID: 37966480 DOI: 10.1021/acsnano.3c01199] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Sorafenib, a first-line molecular-target drug for advanced hepatocellular carcinoma (HCC), has been shown to be a potent ferroptosis inducer in HCC. However, we found that there was a lower level of ferroptosis in sorafenib-resistant HCC samples than in sorafenib-sensitive HCC samples, suggesting that sorafenib resistance in HCC may be a result of ferroptosis suppression. Recent reports have shown that long noncoding RNAs (lncRNAs) are involved in programmed cell death (PCD), including apoptosis and ferroptosis. This study aimed to investigate the roles and underlying molecular mechanisms of lncRNAs in sorafenib-induced ferroptosis in HCC cells. Using lncRNA sequencing, we identified a ferroptosis-related lncRNA, URB1-antisense RNA 1 (AS1), which was highly expressed in sorafenib-resistant HCC samples and predicted poor survival in HCC. Furthermore, URB1-AS1 mitigates sorafenib-induced ferroptosis by inducing ferritin phase separation and reducing the cellular free iron content. Hypoxia inducible factor (HIF)-1α was identified as a key factor promoting URB1-AS1 expression in sorafenib-resistant HCC cells. Notably, we found that specifically inhibiting the expression of URB1-AS1 with N-acetylgalactosamine (GalNAc)-small interfering (si)URB1-AS1 successfully enhanced the sensitivity of HCC cells to sorafenib in an in vivo tumor model. Our study uncovered a critical role for URB1-AS1 in the repression of ferroptosis, suggesting URB1-AS1 targeting may represent a potential approach to overcome sorafenib resistance in HCC.
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Affiliation(s)
- Yuan Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an 710000, China
| | - Man Tong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tin-Lok Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong SAR, China
| | - Kai-Yu Ng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yu-Nong Xie
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zhaowei Wang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an 710000, China
| | - Huajian Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jia-Jian Loh
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Meng Li
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an 710000, China
| | - Stephanie Ma
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong SAR, China
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147
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Shen P, Ye K, Xiang H, Zhang Z, He Q, Zhang X, Cai MC, Chen J, Sun Y, Lin L, Qi C, Zhang M, Cheung LWT, Shi T, Yin X, Li Y, Di W, Zang R, Tan L, Zhuang G. Therapeutic targeting of CPSF3-dependent transcriptional termination in ovarian cancer. SCIENCE ADVANCES 2023; 9:eadj0123. [PMID: 37992178 PMCID: PMC10664987 DOI: 10.1126/sciadv.adj0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Transcriptional dysregulation is a recurring pathogenic hallmark and an emerging therapeutic vulnerability in ovarian cancer. Here, we demonstrated that ovarian cancer exhibited a unique dependency on the regulatory machinery of transcriptional termination, particularly, cleavage and polyadenylation specificity factor (CPSF) complex. Genetic abrogation of multiple CPSF subunits substantially hampered neoplastic cell viability, and we presented evidence that their indispensable roles converged on the endonuclease CPSF3. Mechanistically, CPSF perturbation resulted in lengthened 3'-untranslated regions, diminished intronic polyadenylation and widespread transcriptional readthrough, and consequently suppressed oncogenic pathways. Furthermore, we reported the development of specific CPSF3 inhibitors building upon the benzoxaborole scaffold, which exerted potent antitumor activity. Notably, CPSF3 blockade effectively exacerbated genomic instability by down-regulating DNA damage repair genes and thus acted in synergy with poly(adenosine 5'-diphosphate-ribose) polymerase inhibition. These findings establish CPSF3-dependent transcriptional termination as an exploitable driving mechanism of ovarian cancer and provide a promising class of boron-containing compounds for targeting transcription-addicted human malignancies.
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Affiliation(s)
- Peiye Shen
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaiyan Ye
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaijiang Xiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenfeng Zhang
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qinyang He
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Mei-Chun Cai
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junfei Chen
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunheng Sun
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lifeng Lin
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunting Qi
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Meiying Zhang
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lydia W. T. Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tingyan Shi
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xia Yin
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wen Di
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rongyu Zang
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Tan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Guanglei Zhuang
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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148
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Shi G, Schweizer KS. Theory of the center-of-mass diffusion and viscosity of microstructured and variable sequence copolymer liquids. SOFT MATTER 2023; 19:8893-8910. [PMID: 37955602 DOI: 10.1039/d3sm01193c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Biomolecular condensates formed through the phase separation of proteins and nucleic acids are widely observed, offering a fundamental means of organizing intracellular materials in a membrane-less fashion. Traditionally, these condensates have been regarded as homogeneous isotropic liquids. However, in analogy with some synthetic copolymer systems, our recent theoretical research has demonstrated that model biomolecular condensates can exhibit a microemulsion-like internal structure, contingent upon the specific sequence, inter-chain site-site interactions, and concentrated phase polymer density. Motivated by these considerations, here we present a microscopic dynamical theory for the self-diffusion constant and viscosity of a simpler class of model systems - concentrated unentangled A/B regular multiblock copolymer solutions. Our approach integrates static equilibrium local and microdomain scale structural information obtained from PRISM integral equation theory and the time evolution of the autocorrelation function of monomer scale forces at the center-of-mass level to determine the polymer diffusion constant and viscosity in a weak caging regime far from a glass or gel transition. We focus on regular multi-block systems both for simplicity and for its relevance to synthetic macromolecular science. The impact of sequence and inter-chain attraction strength on the slowing down of copolymer mass transport and flow due to local clustering enhanced collisional friction and emergent microdomain scale ordering are established. Analytic analysis and metrics employed in the study of biomolecular condensates are employed to identify key order parameters that quantity how attractive forces, packing structure, multiblock sequence, and copolymer density determine dynamical slowing down above and below the crossover to a fluctuating polymeric microemulsion state.
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Affiliation(s)
- Guang Shi
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA.
| | - Kenneth S Schweizer
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA.
- Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA
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149
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Martinez-Yamout MA, Nasir I, Shnitkind S, Ellis JP, Berlow RB, Kroon G, Deniz AA, Dyson HJ, Wright PE. Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions. Proc Natl Acad Sci U S A 2023; 120:e2313835120. [PMID: 37971402 PMCID: PMC10666024 DOI: 10.1073/pnas.2313835120] [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: 08/14/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three subdomains, the glutamine-rich domains Q1 and Q2 and the kinase inducible activation domain (KID). NMR chemical shifts show that the isolated subdomains are intrinsically disordered but have a propensity to populate local elements of secondary structure. The Q1 and Q2 domains exhibit a propensity for formation of short β-hairpin motifs that function as binding sites for glutamine-rich sequences. These motifs mediate intramolecular interactions between the CREB Q1 and Q2 domains as well as intermolecular interactions with the glutamine-rich Q1 domain of the TATA-box binding protein associated factor 4 (TAF4) subunit of transcription factor IID (TFIID). Using small-angle X-ray scattering, NMR, and single-molecule Förster resonance energy transfer, we show that the Q1, Q2, and KID regions remain dynamically disordered in a full-length CREB transactivation domain (CREBTAD) construct. The CREBTAD polypeptide chain is largely extended although some compaction is evident in the KID and Q2 domains. Paramagnetic relaxation enhancement reveals transient long-range contacts both within and between the Q1 and Q2 domains while the intervening KID domain is largely devoid of intramolecular interactions. Phosphorylation results in expansion of the KID domain, presumably making it more accessible for binding the CBP/p300 transcriptional coactivators. Our study reveals the complex nature of the interactions within the intrinsically disordered transactivation domain of CREB and provides molecular-level insights into dynamic and transient interactions mediated by the glutamine-rich domains.
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Affiliation(s)
- Maria A. Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Irem Nasir
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Sergey Shnitkind
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Jamie P. Ellis
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Rebecca B. Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Gerard Kroon
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
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150
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Boone BA, Ichino L, Wang S, Gardiner J, Yun J, Jami-Alahmadi Y, Sha J, Mendoza CP, Steelman BJ, van Aardenne A, Kira-Lucas S, Trentchev I, Wohlschlegel JA, Jacobsen SE. ACD15, ACD21, and SLN regulate the accumulation and mobility of MBD6 to silence genes and transposable elements. SCIENCE ADVANCES 2023; 9:eadi9036. [PMID: 37967186 PMCID: PMC10651127 DOI: 10.1126/sciadv.adi9036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
DNA methylation mediates silencing of transposable elements and genes in part via recruitment of the Arabidopsis MBD5/6 complex, which contains the methyl-CpG binding domain (MBD) proteins MBD5 and MBD6, and the J-domain containing protein SILENZIO (SLN). Here, we characterize two additional complex members: α-crystalline domain (ACD) containing proteins ACD15 and ACD21. We show that they are necessary for gene silencing, bridge SLN to the complex, and promote higher-order multimerization of MBD5/6 complexes within heterochromatin. These complexes are also highly dynamic, with the mobility of MBD5/6 complexes regulated by the activity of SLN. Using a dCas9 system, we demonstrate that tethering the ACDs to an ectopic site outside of heterochromatin can drive a massive accumulation of MBD5/6 complexes into large nuclear bodies. These results demonstrate that ACD15 and ACD21 are critical components of the gene-silencing MBD5/6 complex and act to drive the formation of higher-order, dynamic assemblies at CG methylation (meCG) sites.
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Affiliation(s)
- Brandon A. Boone
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lucia Ichino
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Shuya Wang
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jason Gardiner
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jaewon Yun
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jihui Sha
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Cristy P. Mendoza
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bailey J. Steelman
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Aliya van Aardenne
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sophia Kira-Lucas
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Isabelle Trentchev
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Steven E. Jacobsen
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute (HHMI), University of California Los Angeles, Los Angeles, CA 90095, USA
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