1
|
Ukmar‐Godec T, Yu T, de Opakua AI, Pantoja CF, Munari F, Zweckstetter M. Conformational diversity of human HP1α. Protein Sci 2024; 33:e5079. [PMID: 38895997 PMCID: PMC11187854 DOI: 10.1002/pro.5079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
Heterochromatin protein 1 alpha (HP1α) is an evolutionarily conserved protein that binds chromatin and is important for gene silencing. The protein comprises 191 residues arranged into three disordered regions and two structured domains, the chromo and chromoshadow domain, which associates into a homodimer. While high-resolution structures of the isolated domains of HP1 proteins are known, the structural properties of full-length HP1α remain largely unknown. Using a combination of NMR spectroscopy and structure predictions by AlphaFold2 we provide evidence that the chromo and chromoshadow domain of HP1α engage in direct contacts resulting in a compact chromo/chromoshadow domain arrangement. We further show that HP1β and HP1γ have increased interdomain dynamics when compared to HP1α which may contribute to the distinct roles of different Hp1 isoforms in gene silencing and activation.
Collapse
Affiliation(s)
- Tina Ukmar‐Godec
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
| | - Taekyung Yu
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
| | - Alain Ibanez de Opakua
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
| | - Christian F. Pantoja
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
| | | | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
- Department of NMR‐based Structural BiologyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| |
Collapse
|
2
|
Zhang J, Sun P, Wu Z, Wu J, Jia J, Zou H, Mo Y, Zhou Z, Liu B, Ao Y, Wang Z. Targeting CK2 eliminates senescent cells and prolongs lifespan in Zmpste24-deficient mice. Cell Death Dis 2024; 15:380. [PMID: 38816370 PMCID: PMC11139886 DOI: 10.1038/s41419-024-06760-0] [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: 12/22/2023] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024]
Abstract
Senescent cell clearance is emerging as a promising strategy for treating age-related diseases. Senolytics are small molecules that promote the clearance of senescent cells; however, senolytics are uncommon and their underlying mechanisms remain largely unknown. Here, we investigated whether genomic instability is a potential target for senolytic. We screened small-molecule kinase inhibitors involved in the DNA damage response (DDR) in Zmpste24-/- mouse embryonic fibroblasts, a progeroid model characterized with impaired DDR and DNA repair. 4,5,6,7-tetrabromo-2-azabenzamidazole (TBB), which specifically inhibits casein kinase 2 (CK2), was selected and discovered to preferentially trigger apoptosis in Zmpste24-/- cells. Mechanistically, inhibition of CK2 abolished the phosphorylation of heterochromatin protein 1α (HP1α), which retarded the dynamic HP1α dissociation from repressive histone mark H3K9me3 and its relocalization with γH2AX to DNA damage sites, suggesting that disrupting heterochromatin remodeling in the initiation of DDR accelerates apoptosis in senescent cells. Furthermore, feeding Zmpste24-deficient mice with TBB alleviated progeroid features and extended their lifespan. Our study identified TBB as a new class senolytic compound that can reduce age-related symptoms and prolong lifespan in progeroid mice.
Collapse
Affiliation(s)
- Jie Zhang
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, 518060, China
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University, Shenzhen, 518055, China
| | - Pengfei Sun
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Zhuping Wu
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Jie Wu
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Jiali Jia
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Haoman Zou
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Yanzhen Mo
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
| | - Zhongjun Zhou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Baohua Liu
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University, Shenzhen, 518055, China
| | - Ying Ao
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China.
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University, Shenzhen, 518055, China.
| | - Zimei Wang
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Carson International Cancer Center, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518055, China.
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University, Shenzhen, 518055, China.
| |
Collapse
|
3
|
Phan TM, Kim YC, Debelouchina GT, Mittal J. Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization. eLife 2024; 12:RP90820. [PMID: 38592759 PMCID: PMC11003746 DOI: 10.7554/elife.90820] [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: 04/10/2024] Open
Abstract
The heterochromatin protein 1 (HP1) family is a crucial component of heterochromatin with diverse functions in gene regulation, cell cycle control, and cell differentiation. In humans, there are three paralogs, HP1α, HP1β, and HP1γ, which exhibit remarkable similarities in their domain architecture and sequence properties. Nevertheless, these paralogs display distinct behaviors in liquid-liquid phase separation (LLPS), a process linked to heterochromatin formation. Here, we employ a coarse-grained simulation framework to uncover the sequence features responsible for the observed differences in LLPS. We highlight the significance of the net charge and charge patterning along the sequence in governing paralog LLPS propensities. We also show that both highly conserved folded and less-conserved disordered domains contribute to the observed differences. Furthermore, we explore the potential co-localization of different HP1 paralogs in multicomponent assemblies and the impact of DNA on this process. Importantly, our study reveals that DNA can significantly reshape the stability of a minimal condensate formed by HP1 paralogs due to competitive interactions of HP1α with HP1β and HP1γ versus DNA. In conclusion, our work highlights the physicochemical nature of interactions that govern the distinct phase-separation behaviors of HP1 paralogs and provides a molecular framework for understanding their role in chromatin organization.
Collapse
Affiliation(s)
- Tien M Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M UniversityCollege StationUnited States
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research LaboratoryWashingtonUnited States
| | - Galia T Debelouchina
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M UniversityCollege StationUnited States
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M UniversityCollege StationUnited States
| |
Collapse
|
4
|
Abasi LS, Elathram N, Movva M, Deep A, Corbett KD, Debelouchina GT. Phosphorylation regulates tau's phase separation behavior and interactions with chromatin. Commun Biol 2024; 7:251. [PMID: 38429335 PMCID: PMC10907630 DOI: 10.1038/s42003-024-05920-4] [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: 12/21/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
Tau is a microtubule-associated protein often found in neurofibrillary tangles (NFTs) in the brains of patients with Alzheimer's disease. Beyond this context, mounting evidence suggests that tau localizes into the nucleus, where it may play a role in DNA protection and heterochromatin regulation. The molecular mechanisms behind these observations are currently unclear. Using in vitro biophysical experiments, here we demonstrate that tau can undergo liquid-liquid phase separation (LLPS) with DNA, mononucleosomes, and reconstituted nucleosome arrays under low salt conditions. Low concentrations of tau promote chromatin compaction and protect DNA from digestion. While the material state of samples at physiological salt is dominated by chromatin oligomerization, tau can still associate strongly and reversibly with nucleosome arrays. These properties are driven by tau's strong interactions with linker and nucleosomal DNA. In addition, tau co-localizes into droplets formed by nucleosome arrays and phosphorylated HP1α, a key heterochromatin constituent thought to function through an LLPS mechanism. Importantly, LLPS and chromatin interactions are disrupted by aberrant tau hyperphosphorylation. These biophysical properties suggest that tau may directly impact DNA and chromatin accessibility and that loss of these interactions could contribute to the aberrant nuclear effects seen in tau pathology.
Collapse
Affiliation(s)
- Lannah S Abasi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Manasi Movva
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Galia T Debelouchina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
5
|
Deshpande P, Prentice E, Ceballos AV, Casaccia P, Elbaum-Garfinkle S. Modified histone peptides uniquely tune the material properties of HP1α condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579285. [PMID: 38370661 PMCID: PMC10871333 DOI: 10.1101/2024.02.07.579285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Biomolecular condensates have emerged as a powerful new paradigm in cell biology with broad implications to human health and disease, particularly in the nucleus where phase separation is thought to underly elements of chromatin organization and regulation. Specifically, it has been recently reported that phase separation of heterochromatin protein 1alpha (HP1α) with DNA contributes to the formation of condensed chromatin states. HP1α localization to heterochromatic regions is mediated by its binding to specific repressive marks on the tail of histone H3, such as trimethylated lysine 9 on histone H3 (H3K9me3). However, whether epigenetic marks play an active role in modulating the material properties of HP1α and dictating emergent functions of its condensates, remains only partially understood. Here, we leverage a reductionist system, comprised of modified and unmodified histone H3 peptides, HP1α and DNA to examine the contribution of specific epigenetic marks to phase behavior of HP1α. We show that the presence of histone peptides bearing the repressive H3K9me3 is compatible with HP1α condensates, while peptides containing unmodified residues or bearing the transcriptional activation mark H3K4me3 are incompatible with HP1α phase separation. In addition, inspired by the decreased ratio of nuclear H3K9me3 to HP1α detected in cells exposed to uniaxial strain, using fluorescence microscopy and rheological approaches we demonstrate that H3K9me3 histone peptides modulate the dynamics and network properties of HP1α condensates in a concentration dependent manner. These data suggest that HP1α-DNA condensates are viscoelastic materials, whose properties may provide an explanation for the dynamic behavior of heterochromatin in cells in response to mechanostimulation.
Collapse
Affiliation(s)
- Priyasha Deshpande
- Ph.D. Program in Biochemistry, Graduate Center of the City University of New York, NY
- Ph.D. Program in Biology, Graduate Center of the City University of New York, NY
- Structural Biology Initiative, Advanced Science Research Center, CUNY, New York, NY
| | - Emily Prentice
- Ph.D. Program in Biology, Graduate Center of the City University of New York, NY
- Neuroscience Initiative, Advanced Science Research Center, CUNY, New York, NY
| | | | - Patrizia Casaccia
- Ph.D. Program in Biochemistry, Graduate Center of the City University of New York, NY
- Ph.D. Program in Biology, Graduate Center of the City University of New York, NY
- Neuroscience Initiative, Advanced Science Research Center, CUNY, New York, NY
| | - Shana Elbaum-Garfinkle
- Ph.D. Program in Biochemistry, Graduate Center of the City University of New York, NY
- Ph.D. Program in Biology, Graduate Center of the City University of New York, NY
- Structural Biology Initiative, Advanced Science Research Center, CUNY, New York, NY
- Ph.D. Program in Chemistry, Graduate Center of the City University of New York, NY
| |
Collapse
|
6
|
Willemin A, Szabó D, Pombo A. Epigenetic regulatory layers in the 3D nucleus. Mol Cell 2024; 84:415-428. [PMID: 38242127 PMCID: PMC10872226 DOI: 10.1016/j.molcel.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of sequence information transfer from DNA to RNAs and proteins. We have since learned that gene expression is finely tuned in time and space, due to the activities of RNAs and proteins on regulatory DNA elements, and through cell-type-specific three-dimensional conformations of the genome. Here, we review major advances in genome biology and discuss a set of ideas on gene regulation and highlight how various biomolecular assemblies lead to the formation of structural and regulatory features within the nucleus, with roles in transcriptional control. We conclude by suggesting further developments that will help capture the complex, dynamic, and often spatially restricted events that govern gene expression in mammalian cells.
Collapse
Affiliation(s)
- Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
| | - Dominik Szabó
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
| |
Collapse
|
7
|
Abasi LS, Elathram N, Movva M, Deep A, Corbett KD, Debelouchina GT. Phosphorylation regulates tau's phase separation behavior and interactions with chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572911. [PMID: 38187700 PMCID: PMC10769318 DOI: 10.1101/2023.12.21.572911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Tau is a microtubule-associated protein often found in neurofibrillary tangles (NFTs) in the brains of patients with Alzheimer's disease (AD). Beyond this context, mounting evidence suggests that tau localizes into the nucleus, where it may play a role in DNA protection and heterochromatin regulation. Models of tau depletion or pathology show loss of genetically silent heterochromatin, aberrant expression of heterochromatic genes, and transposable element activation. The molecular mechanisms behind these observations are currently unclear. Using in vitro biophysical experiments, here we demonstrate that tau can undergo liquid-liquid phase separation (LLPS) with DNA, mononucleosomes, and reconstituted nucleosome arrays under low salt conditions. Low concentrations of tau promote chromatin compaction and protect DNA from digestion. While the material state of samples at physiological salt is dominated by chromatin oligomerization, tau can still associate strongly and reversibly with nucleosome arrays. These properties are driven by tau's strong interactions with linker and nucleosomal DNA, while magic angle spinning (MAS) solid-state NMR experiments show that tau binding does not drastically alter nucleosome structure and dynamics. In addition, tau co-localizes into droplets formed by nucleosome arrays and phosphorylated HP1α, a key heterochromatin constituent thought to function through an LLPS mechanism. Importantly, LLPS and chromatin interactions are disrupted by aberrant tau hyperphosphorylation. These biophysical properties suggest that tau may directly impact DNA and chromatin accessibility and that loss of these interactions could contribute to the aberrant nuclear effects seen in tau pathology.
Collapse
Affiliation(s)
- Lannah S. Abasi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Manasi Movva
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin D. Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
8
|
Phan TM, Kim YC, Debelouchina GT, Mittal J. Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.28.542535. [PMID: 37398008 PMCID: PMC10312469 DOI: 10.1101/2023.05.28.542535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The heterochromatin protein 1 (HP1) family is a crucial component of heterochromatin with diverse functions in gene regulation, cell cycle control, and cell differentiation. In humans, there are three paralogs, HP1α, HP1β, and HP1γ, which exhibit remarkable similarities in their domain architecture and sequence properties. Nevertheless, these paralogs display distinct behaviors in liquid-liquid phase separation (LLPS), a process linked to heterochromatin formation. Here, we employ a coarse-grained simulation framework to uncover the sequence features responsible for the observed differences in LLPS. We highlight the significance of the net charge and charge patterning along the sequence in governing paralog LLPS propensities. We also show that both highly conserved folded and less-conserved disordered domains contribute to the observed differences. Furthermore, we explore the potential co-localization of different HP1 paralogs in multicomponent assemblies and the impact of DNA on this process. Importantly, our study reveals that DNA can significantly reshape the stability of a minimal condensate formed by HP1 paralogs due to competitive interactions of HP1α with HP1β and HP1γ versus DNA. In conclusion, our work highlights the physicochemical nature of interactions that govern the distinct phase-separation behaviors of HP1 paralogs and provides a molecular framework for understanding their role in chromatin organization.
Collapse
Affiliation(s)
- Tien M. Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Young C. Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
- Department of Chemistry, Texas A&M University, College Station, TX, USA
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| |
Collapse
|
9
|
Chou MC, Wang YH, Chen FY, Kung CY, Wu KP, Kuo JC, Chan SJ, Cheng ML, Lin CY, Chou YC, Ho MC, Firestine S, Huang JR, Chen RH. PAICS ubiquitination recruits UBAP2 to trigger phase separation for purinosome assembly. Mol Cell 2023; 83:4123-4140.e12. [PMID: 37848033 DOI: 10.1016/j.molcel.2023.09.028] [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: 01/16/2023] [Revised: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
Purinosomes serve as metabolons to enhance de novo purine synthesis (DNPS) efficiency through compartmentalizing DNPS enzymes during stressed conditions. However, the mechanism underpinning purinosome assembly and its pathophysiological functions remains elusive. Here, we show that K6-polyubiquitination of the DNPS enzyme phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase (PAICS) by cullin-5/ankyrin repeat and SOCS box containing 11 (Cul5/ASB11)-based ubiquitin ligase plays a driving role in purinosome assembly. Upon several purinosome-inducing cues, ASB11 is upregulated by relieving the H3K9me3/HP1α-mediated transcriptional silencing, thus stimulating PAICS polyubiquitination. The polyubiquitinated PAICS recruits ubiquitin-associated protein 2 (UBAP2), a ubiquitin-binding protein with multiple stretches of intrinsically disordered regions, thereby inducing phase separation to trigger purinosome assembly for enhancing DNPS pathway flux. In human melanoma, ASB11 is highly expressed to facilitate a constitutive purinosome formation to which melanoma cells are addicted for supporting their proliferation, viability, and tumorigenesis in a xenograft model. Our study identifies a driving mechanism for purinosome assembly in response to cellular stresses and uncovers the impact of purinosome formation on human malignancies.
Collapse
Affiliation(s)
- Ming-Chieh Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Hsuan Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Fei-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Ying Kung
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Jean-Cheng Kuo
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Shu-Jou Chan
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Mei-Ling Cheng
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Chih-Yu Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Steven Firestine
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan.
| |
Collapse
|
10
|
Elathram N, Ackermann BE, Clark ET, Dunn SR, Debelouchina GT. Phosphorylated HP1α-Nucleosome Interactions in Phase Separated Environments. J Am Chem Soc 2023; 145:23994-24004. [PMID: 37870432 PMCID: PMC10636758 DOI: 10.1021/jacs.3c06481] [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: 06/19/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
In the nucleus, transcriptionally silent genes are sequestered into heterochromatin compartments comprising nucleosomes decorated with histone H3 Lys9 trimethylation and a protein called HP1α. This protein can form liquid-liquid droplets in vitro and potentially organize heterochromatin through a phase separation mechanism that is promoted by phosphorylation. Elucidating the molecular interactions that drive HP1α phase separation and its consequences on nucleosome structure and dynamics has been challenging due to the viscous and heterogeneous nature of such assemblies. Here, we tackle this problem by a combination of solution and solid-state NMR spectroscopy, which allows us to dissect the interactions of phosphorylated HP1α with nucleosomes in the context of phase separation. Our experiments indicate that phosphorylated human HP1α does not cause any major rearrangements to the nucleosome core, in contrast to the yeast homologue Swi6. Instead, HP1α interacts specifically with the methylated H3 tails and slows the dynamics of the H4 tails. Our results shed light on how phosphorylated HP1α proteins may regulate the heterochromatin landscape, while our approach provides an atomic resolution view of a heterogeneous and dynamic biological system regulated by a complex network of interactions and post-translational modifications.
Collapse
Affiliation(s)
- Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Evan T. Clark
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Shelby R. Dunn
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
11
|
Rahayu AF, Hayashi A, Yoshimura Y, Nakagawa R, Arita K, Nakayama JI. Cooperative DNA-binding activities of Chp2 are critical for its function in heterochromatin assembly. J Biochem 2023; 174:371-382. [PMID: 37400983 DOI: 10.1093/jb/mvad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Heterochromatin protein 1 (HP1) is an evolutionarily conserved protein that plays a critical role in heterochromatin assembly. HP1 proteins share a basic structure consisting of an N-terminal chromodomain (CD) and a C-terminal chromoshadow domain (CSD) linked by a disordered hinge region. The CD recognizes histone H3 lysine 9 methylation, a hallmark of heterochromatin, while the CSD forms a dimer to recruit other chromosomal proteins. HP1 proteins have been shown to bind DNA or RNA primarily through the hinge region. However, how DNA or RNA binding contributes to their function remains elusive. Here, we focus on Chp2, one of the two HP1 proteins in fission yeast, and investigate how Chp2's DNA-binding ability contributes to its function. Similar to other HP1 proteins, the Chp2 hinge exhibits clear DNA-binding activity. Interestingly, the Chp2 CSD also shows robust DNA-binding activity. Mutational analysis revealed that basic residues in the Chp2 hinge and at the N-terminus of the CSD are essential for DNA binding, and the combined amino acid substitutions of these residues alter Chp2 stability, impair Chp2 heterochromatin localization and lead to a silencing defect. These results demonstrate that the cooperative DNA-binding activities of Chp2 play an important role in heterochromatin assembly in fission yeast.
Collapse
Affiliation(s)
- Anisa Fitri Rahayu
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Aki Hayashi
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Yuriko Yoshimura
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Reiko Nakagawa
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kyohei Arita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Kanagawa 230-0045, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| |
Collapse
|
12
|
Her C, Phan TM, Jovic N, Kapoor U, Ackermann BE, Rizuan A, Kim Y, Mittal J, Debelouchina G. Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding. Nucleic Acids Res 2022; 50:12702-12722. [PMID: 36537242 PMCID: PMC9825191 DOI: 10.1093/nar/gkac1194] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Heterochromatin protein 1α (HP1α) is a crucial element of chromatin organization. It has been proposed that HP1α functions through liquid-liquid phase separation (LLPS), which allows it to compact chromatin into transcriptionally repressed heterochromatin regions. In vitro, HP1α can undergo phase separation upon phosphorylation of its N-terminus extension (NTE) and/or through interactions with DNA and chromatin. Here, we combine computational and experimental approaches to elucidate the molecular interactions that drive these processes. In phosphorylation-driven LLPS, HP1α can exchange intradimer hinge-NTE interactions with interdimer contacts, which also leads to a structural change from a compacted to an extended HP1α dimer conformation. This process can be enhanced by the presence of positively charged HP1α peptide ligands and disrupted by the addition of negatively charged or neutral peptides. In DNA-driven LLPS, both positively and negatively charged peptide ligands can perturb phase separation. Our findings demonstrate the importance of electrostatic interactions in HP1α LLPS where binding partners can modulate the overall charge of the droplets and screen or enhance hinge region interactions through specific and non-specific effects. Our study illuminates the complex molecular framework that can fine-tune the properties of HP1α and that can contribute to heterochromatin regulation and function.
Collapse
Affiliation(s)
| | | | - Nina Jovic
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Utkarsh Kapoor
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Bryce E Ackermann
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, WA, DC, USA
| | | | | |
Collapse
|
13
|
Okuda M, Tsunaka Y, Nishimura Y. Dynamic structures of intrinsically disordered proteins related to the general transcription factor TFIIH, nucleosomes, and histone chaperones. Biophys Rev 2022; 14:1449-1472. [PMID: 36659983 PMCID: PMC9842849 DOI: 10.1007/s12551-022-01014-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/06/2022] [Indexed: 11/19/2022] Open
Abstract
Advances in structural analysis by cryogenic electron microscopy (cryo-EM) and X-ray crystallography have revealed the tertiary structures of various chromatin-related proteins, including transcription factors, RNA polymerases, nucleosomes, and histone chaperones; however, the dynamic structures of intrinsically disordered regions (IDRs) in these proteins remain elusive. Recent studies using nuclear magnetic resonance (NMR), together with molecular dynamics (MD) simulations, are beginning to reveal dynamic structures of the general transcription factor TFIIH complexed with target proteins including the general transcription factor TFIIE, the tumor suppressor p53, the cell cycle protein DP1, the DNA repair factors XPC and UVSSA, and three RNA polymerases, in addition to the dynamics of histone tails in nucleosomes and histone chaperones. In complexes of TFIIH, the PH domain of the p62 subunit binds to an acidic string formed by the IDR in TFIIE, p53, XPC, UVSSA, DP1, and the RPB6 subunit of three RNA polymerases by a common interaction mode, namely extended string-like binding of the IDR on the positively charged surface of the PH domain. In the nucleosome, the dynamic conformations of the N-tails of histones H2A and H2B are correlated, while the dynamic conformations of the N-tails of H3 and H4 form a histone tail network dependent on their modifications and linker DNA. The acidic IDRs of the histone chaperones of FACT and NAP1 play important roles in regulating the accessibility to histone proteins in the nucleosome.
Collapse
Affiliation(s)
- Masahiko Okuda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045 Japan
| | - Yasuo Tsunaka
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045 Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045 Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, 739-8528 Japan
| |
Collapse
|
14
|
Mohanty P, Kapoor U, Sundaravadivelu Devarajan D, Phan TM, Rizuan A, Mittal J. Principles Governing the Phase Separation of Multidomain Proteins. Biochemistry 2022; 61:2443-2455. [PMID: 35802394 PMCID: PMC9669140 DOI: 10.1021/acs.biochem.2c00210] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A variety of membraneless organelles, often termed "biological condensates", play an important role in the regulation of cellular processes such as gene transcription, translation, and protein quality control. On the basis of experimental and theoretical investigations, liquid-liquid phase separation (LLPS) has been proposed as a possible mechanism for the origin of biological condensates. LLPS requires multivalent macromolecules that template the formation of long-range, intermolecular interaction networks and results in the formation of condensates with defined composition and material properties. Multivalent interactions driving LLPS exhibit a wide range of modes from highly stereospecific to nonspecific and involve both folded and disordered regions. Multidomain proteins serve as suitable macromolecules for promoting phase separation and achieving disparate functions due to their potential for multivalent interactions and regulation. Here, we aim to highlight the influence of the domain architecture and interdomain interactions on the phase separation of multidomain protein condensates. First, the general principles underlying these interactions are illustrated on the basis of examples of multidomain proteins that are predominantly associated with nucleic acid binding and protein quality control and contain both folded and disordered regions. Next, the examples showcase how LLPS properties of folded and disordered regions can be leveraged to engineer multidomain constructs that form condensates with the desired assembly and functional properties. Finally, we highlight the need for improvements in coarse-grained computational models that can provide molecular-level insights into multidomain protein condensates in conjunction with experimental efforts.
Collapse
Affiliation(s)
- Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Utkarsh Kapoor
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | | | - Tien Minh Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| |
Collapse
|
15
|
Abstract
Virtually all cell types have the same DNA, yet each type exhibits its own cell-specific pattern of gene expression. During the brief period of mitosis, the chromosomes exhibit changes in protein composition and modifications, a marked condensation, and a consequent reduction in transcription. Yet as cells exit mitosis, they reactivate their cell-specific programs with high fidelity. Initially, the field focused on the subset of transcription factors that are selectively retained in, and hence bookmark, chromatin in mitosis. However, recent studies show that many transcription factors can be retained in mitotic chromatin and that, surprisingly, such retention can be due to nonspecific chromatin binding. Here, we review the latest studies focusing on low-level transcription via promoters, rather than enhancers, as contributing to mitotic memory, as well as new insights into chromosome structure dynamics, histone modifications, cell cycle signaling, and nuclear envelope proteins that together ensure the fidelity of gene expression through a round of mitosis.
Collapse
Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | | |
Collapse
|
16
|
Biswas S, Chen Z, Karslake JD, Farhat A, Ames A, Raiymbek G, Freddolino PL, Biteen JS, Ragunathan K. HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization. SCIENCE ADVANCES 2022; 8:eabk0793. [PMID: 35857444 PMCID: PMC9269880 DOI: 10.1126/sciadv.abk0793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 05/24/2022] [Indexed: 05/31/2023]
Abstract
HP1 proteins traverse a complex and crowded chromatin landscape to bind with low affinity but high specificity to histone H3K9 methylation (H3K9me) and form transcriptionally inactive genomic compartments called heterochromatin. Here, we visualize single-molecule dynamics of an HP1 homolog, the fission yeast Swi6, in its native chromatin environment. By tracking single Swi6 molecules, we identify mobility states that map to discrete biochemical intermediates. Using Swi6 mutants that perturb H3K9me recognition, oligomerization, or nucleic acid binding, we determine how each biochemical property affects protein dynamics. We estimate that Swi6 recognizes H3K9me3 with ~94-fold specificity relative to unmodified nucleosomes in living cells. While nucleic acid binding competes with Swi6 oligomerization, as few as four tandem chromodomains can overcome these inhibitory effects to facilitate Swi6 localization at heterochromatin formation sites. Our studies indicate that HP1 oligomerization is essential to form dynamic, higher-order complexes that outcompete nucleic acid binding to enable specific H3K9me recognition.
Collapse
Affiliation(s)
- Saikat Biswas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104, USA
| | - Joshua D. Karslake
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104, USA
| | - Ali Farhat
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amanda Ames
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gulzhan Raiymbek
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Julie S. Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48104, USA
| | - Kaushik Ragunathan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
17
|
Latham AP, Zhang B. On the stability and layered organization of protein-DNA condensates. Biophys J 2022; 121:1727-1737. [PMID: 35364104 PMCID: PMC9117872 DOI: 10.1016/j.bpj.2022.03.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/02/2021] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Multi-component phase separation is emerging as a key mechanism for the formation of biological condensates that play essential roles in signal sensing and transcriptional regulation. The molecular factors that dictate these condensates' stability and spatial organization are not fully understood, and it remains challenging to predict their microstructures. Using a near-atomistic, chemically accurate force field, we studied the phase behavior of chromatin regulators that are crucial for heterochromatin organization and their interactions with DNA. Our computed phase diagrams recapitulated previous experimental findings on different proteins. They revealed a strong dependence of condensate stability on the protein-DNA mixing ratio as a result of balancing protein-protein interactions and charge neutralization. Notably, a layered organization was observed in condensates formed by mixing HP1, histone H1, and DNA. This layered organization may be of biological relevance, as it enables cooperative DNA packaging between the two chromatin regulators: histone H1 softens the DNA to facilitate the compaction induced by HP1 droplets. Our study supports near-atomistic models as a valuable tool for characterizing the structure and stability of biological condensates.
Collapse
Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
| |
Collapse
|
18
|
Guidotti N, Eördögh Á, Mivelaz M, Rivera-Fuentes P, Fierz B. Multivalent Peptide Ligands To Probe the Chromocenter Microenvironment in Living Cells. ACS Chem Biol 2022; 18:1066-1075. [PMID: 35447032 DOI: 10.1021/acschembio.2c00203] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin is spatially organized into functional states that are defined by both the presence of specific histone post-translational modifications (PTMs) and a defined set of chromatin-associated "reader" proteins. Different models for the underlying mechanism of such compartmentalization have been proposed, including liquid-liquid phase separation (LLPS) of chromatin-associated proteins to drive spatial organization. Heterochromatin, characterized by lysine 9 methylation on histone H3 (H3K9me3) and the presence of heterochromatin protein 1 (HP1) as a multivalent reader, represents a prime example of a spatially defined chromatin state. Heterochromatin foci exhibit features of protein condensates driven by LLPS; however, the exact nature of the physicochemical environment within heterochromatin in different cell types is not completely understood. Here we present tools to interrogate the environment of chromatin subcompartments in the form of modular, cell-permeable, multivalent, and fluorescent peptide probes. These probes can be tuned to target specific chromatin states by providing binding sites to reader proteins and can thereby integrate into the PTM-reader interaction network. Here we generate probes specific to HP1, directing them to heterochromatin at chromocenters in mouse fibroblasts. Moreover, we use a polarity-sensing photoactivatable probe that photoconverts to a fluorescent state in phase-separated protein droplets and thereby reports on the local microenvironment. Equipped with this dye, our probes indeed turn fluorescent in murine chromocenters. Image analysis and single-molecule tracking experiments reveal that the compartments are less dense and more dynamic than HP1 condensates obtained in vitro. Our results thus demonstrate that the local organization of heterochromatin in chromocenters is internally more complex than an HP1 condensate.
Collapse
Affiliation(s)
- Nora Guidotti
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland
| | - Ádám Eördögh
- EPFL, SB ISIC LOCBP, Station 6, CH-1015 Lausanne, Switzerland
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Maxime Mivelaz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland
| | | | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland
| |
Collapse
|
19
|
Nakamura R, Nakayama JI. Multiple interfaces to recognize nucleosomal targets. J Biochem 2021; 171:257-259. [PMID: 34967395 DOI: 10.1093/jb/mvab139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/14/2022] Open
Abstract
In eukaryotic cells, DNA is tightly compacted as chromatin. Chromatin states must be dynamically changed to increase the accessibility of transcription factors to chromatin or to stably silence genes by higher-order chromatin structures known as heterochromatin. The regulation of chromatin needs cooperative action performed by a variety of proteins. Specific binding of transcription factors to target DNA is the initial step of chromatin regulation, and promotes changes in the post-translational modifications of histone tails, which themselves are recognized by a set of histone reader proteins. Recent biochemical studies have revealed that some transcription factors that recognize specific DNA sequences can also interact with histones. Furthermore, histone reader proteins that recognize specific histone tail modifications have been shown to have the ability to directly bind to DNA. In this commentary, we introduce recent advances in the elucidation of how chromatin regulating factors recognize nucleosomal targets.
Collapse
Affiliation(s)
- Rinko Nakamura
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| |
Collapse
|
20
|
Abstract
Biomolecular condensates are membrane-less compartments that are formed through an assembly of proteins and nucleic acids in the cell. Dysregulation of biological condensates has been implicated in diseases such as neurodegeneration and cancer. Ribonucleic acid (RNA) is known to affect the assembly of proteins in vitro, if and how RNA is involved in regulating biomolecular condensates in cells is not well investigated. Here we examined two nuclear proteins, FUS and HP1α, in which RNA was found to have an opposite contribution for the assembly of these proteins. Reduction of nuclear RNA, by inhibiting the transcription, triggered assembly of FUS that had been distributed in the nucleoplasm, whereas it dispersed spontaneously formed HP1α assembly. Notably, the cell cycle-dependent phosphorylation-mimicking substitutions in HP1α promoted its assembly formation. These transcription inhibitor experiments are versatile to examine diverse roles of nuclear RNA in regulating biomolecular condensates, in both physiological and pathological conditions.
Collapse
Affiliation(s)
- Saho Matsui
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR)
| | - Ryu-Suke Nozawa
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR)
| |
Collapse
|
21
|
Bjarnason S, Ruidiaz SF, McIvor J, Mercadante D, Heidarsson PO. Protein intrinsic disorder on a dynamic nucleosomal landscape. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:295-354. [PMID: 34656332 DOI: 10.1016/bs.pmbts.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The complex nucleoprotein landscape of the eukaryotic cell nucleus is rich in dynamic proteins that lack a stable three-dimensional structure. Many of these intrinsically disordered proteins operate directly on the first fundamental level of genome compaction: the nucleosome. Here we give an overview of how disordered interactions with and within nucleosomes shape the dynamics, architecture, and epigenetic regulation of the genetic material, controlling cellular transcription patterns. We highlight experimental and computational challenges in the study of protein disorder and illustrate how integrative approaches are increasingly unveiling the fine details of nuclear interaction networks. We finally dissect sequence properties encoded in disordered regions and assess common features of disordered nucleosome-binding proteins. As drivers of many critical biological processes, disordered proteins are integral to a comprehensive molecular view of the dynamic nuclear milieu.
Collapse
Affiliation(s)
- Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Sarah F Ruidiaz
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Jordan McIvor
- School of Chemical Science, University of Auckland, Auckland, New Zealand
| | - Davide Mercadante
- School of Chemical Science, University of Auckland, Auckland, New Zealand.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland.
| |
Collapse
|
22
|
Casale AM, Cappucci U, Piacentini L. Unravelling HP1 functions: post-transcriptional regulation of stem cell fate. Chromosoma 2021; 130:103-111. [PMID: 34128099 PMCID: PMC8426308 DOI: 10.1007/s00412-021-00760-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Heterochromatin protein 1 (HP1) is a non-histone chromosomal protein first identified in Drosophila as a major component of constitutive heterochromatin, required for stable epigenetic gene silencing in many species including humans. Over the years, several studies have highlighted additional roles of HP1 in different cellular processes including telomere maintenance, DNA replication and repair, chromosome segregation and, surprisingly, positive regulation of gene expression. In this review, we briefly summarize past research and recent results supporting the unexpected and emerging role of HP1 in activating gene expression. In particular, we discuss the role of HP1 in post-transcriptional regulation of mRNA processing because it has proved decisive in the control of germline stem cells homeostasis in Drosophila and has certainly added a new dimension to our understanding on HP1 targeting and functions in epigenetic regulation of stem cell behaviour.
Collapse
Affiliation(s)
- Assunta Maria Casale
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.
| | - Ugo Cappucci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Lucia Piacentini
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.
| |
Collapse
|
23
|
trans-Acting Factors and cis Elements Involved in the Human Inactive X Chromosome Organization and Compaction. Genet Res (Camb) 2021; 2021:6683460. [PMID: 34035662 PMCID: PMC8121581 DOI: 10.1155/2021/6683460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/06/2021] [Accepted: 04/30/2021] [Indexed: 11/23/2022] Open
Abstract
During X chromosome inactivation, many chromatin changes occur on the future inactive X chromosome, including acquisition of a variety of repressive covalent histone modifications, heterochromatin protein associations, and DNA methylation of promoters. Here, we summarize trans-acting factors and cis elements that have been shown to be involved in the human inactive X chromosome organization and compaction.
Collapse
|
24
|
Oki M, Masai H. Regulation of HP1 protein by phosphorylation during transcriptional repression and cell cycle. J Biochem 2021; 169:629-632. [PMID: 33772590 DOI: 10.1093/jb/mvab040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 11/12/2022] Open
Abstract
HP1 (Heterochromatin Protein 1), a key factor for the formation of heterochromatin, binds to the methylated lysine 9 of histone H3 (H3K9me), and represses transcription. While the H3K9me mark and HP1 binding are thought to be faithfully propagated to daughter cells, the heterochromatin structure could be dynamically regulated during cell cycle. As evidenced by the well-known phenomenon called Position Effect Variegation (PEV), heterochromatin structure is dynamically and stochastically altered during developmental processes, and thus the expression of genes within or in the vicinity of heterochromatin could be affected by mutations in factors regulating DNA replication as well as by other epigenetic factors. Recent reports show that HP1 also plays an important role in the maintenance and transmission of chromosomes. Like many other factors ensuring faithful chromosome segregation, HP1 family proteins are subjected to posttranslational modifications, most notably phosphorylation, in a cell-cycle dependent manner. Recent studies identified a conserved phosphorylation site that profoundly affects the functions of HP1 during mitotic phase. In this commentary, we discuss dynamic regulation of HP1 protein by phosphorylation during transcriptional repression and cell cycle.
Collapse
Affiliation(s)
- Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, JAPAN
| | - Hisao Masai
- Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, JAPAN, Tel: 81-3-5316-3220
| |
Collapse
|
25
|
Keenen MM, Brown D, Brennan LD, Renger R, Khoo H, Carlson CR, Huang B, Grill SW, Narlikar GJ, Redding S. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains. eLife 2021; 10:e64563. [PMID: 33661100 PMCID: PMC7932698 DOI: 10.7554/elife.64563] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
In mammals, HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, and HP1γ, display rapid on-off dynamics. Here, we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1β. Finally, we find that differences in each HP1 paralog's DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale.
Collapse
Affiliation(s)
- Madeline M Keenen
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - David Brown
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Lucy D Brennan
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Roman Renger
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Harrison Khoo
- Department of Mechanical Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Christopher R Carlson
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Physiology, University of California, San FranciscoSan FranciscoUnited States
| | - Bo Huang
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Cluster of Excellence Physics of Life, Technische Universität DresdenDresdenGermany
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Marine Biological LaboratoryWoods HoleUnited States
| |
Collapse
|
26
|
Lobbia VR, Trueba Sanchez MC, van Ingen H. Beyond the Nucleosome: Nucleosome-Protein Interactions and Higher Order Chromatin Structure. J Mol Biol 2021; 433:166827. [PMID: 33460684 DOI: 10.1016/j.jmb.2021.166827] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/20/2022]
Abstract
The regulation of chromatin biology ultimately depends on the manipulation of its smallest subunit, the nucleosome. The proteins that bind and operate on the nucleosome do so, while their substrate is part of a polymer embedded in the dense nuclear environment. Their molecular interactions must in some way be tuned to deal with this complexity. Due to the rapid increase in the number of high-resolution structures of nucleosome-protein complexes and the increasing understanding of the cellular chromatin structure, it is starting to become clearer how chromatin factors operate in this complex environment. In this review, we analyze the current literature on the interplay between nucleosome-protein interactions and higher-order chromatin structure. We examine in what way nucleosomes-protein interactions can affect and can be affected by chromatin organization at the oligonucleosomal level. In addition, we review the characteristics of nucleosome-protein interactions that can cause phase separation of chromatin. Throughout, we hope to illustrate the exciting challenges in characterizing nucleosome-protein interactions beyond the nucleosome.
Collapse
Affiliation(s)
- Vincenzo R Lobbia
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Maria Cristina Trueba Sanchez
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| |
Collapse
|
27
|
Kamo N, Kujirai T, Kurumizaka H, Murakami H, Hayashi G, Okamoto A. Organoruthenium-catalyzed chemical protein synthesis to elucidate the functions of epigenetic modifications on heterochromatin factors. Chem Sci 2021; 12:5926-5937. [PMID: 35342540 PMCID: PMC8872386 DOI: 10.1039/d1sc00731a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/21/2021] [Indexed: 12/21/2022] Open
Abstract
The application of organometallic compounds for protein science has received attention. Recently, total chemical protein synthesis using transition metal complexes has been developed to produce various proteins bearing site-specific posttranslational modifications (PTMs). However, in general, significant amounts of metal complexes were required to achieve chemical reactions of proteins bearing a large number of nucleophilic functional groups. Moreover, syntheses of medium-size proteins (>20 kDa) were plagued by time-consuming procedures due to cumbersome purification and isolation steps, which prevented access to variously decorated proteins. Here, we report a one-pot multiple peptide ligation strategy assisted by an air-tolerant organoruthenium catalyst that showed more than 50-fold activity over previous palladium complexes, leading to rapid and quantitative deprotection on a protein with a catalytic amount (20 mol%) of the metal complex even in the presence of excess thiol moieties. Utilizing the organoruthenium catalyst, heterochromatin factors above 20 kDa, such as linker histone H1.2 and heterochromatin protein 1α (HP1α), bearing site-specific PTMs including phosphorylation, ubiquitination, citrullination, and acetylation have been synthesized. The biochemical assays using synthetic proteins revealed that the citrullination at R53 in H1.2 resulted in the reduced electrostatic interaction with DNA and the reduced binding affinity to nucleosomes. Furthermore, we identified a key phosphorylation region in HP1α to control its DNA-binding ability. The ruthenium chemistry developed here will facilitate the preparation of a variety of biologically and medically significant proteins containing PTMs and non-natural amino acids. Chemical protein synthesis assisted by an organoruthenium catalyst streamlined the production of heterochromatin factors bearing various patterns of epigenetic modifications, and their biological significance was elucidated.![]()
Collapse
Affiliation(s)
- Naoki Kamo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| |
Collapse
|
28
|
Feng Y, Endo M, Sugiyama H. Nucleosomes and Epigenetics from a Chemical Perspective. Chembiochem 2020; 22:595-612. [PMID: 32864867 DOI: 10.1002/cbic.202000332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/26/2020] [Indexed: 12/19/2022]
Abstract
Nucleosomes, which are the fundamental building blocks of chromatin, are highly dynamic, they play vital roles in the formation of higher-order chromatin structures and orchestrate gene regulation. Nucleosome structures, histone modifications, nucleosome-binding proteins, and their functions are being gradually unravelled with the development of epigenetics. With the continuous development of research approaches such as cryo-EM, FRET and next-generation sequencing for genome-wide analysis of nucleosomes, the understanding of nucleosomes is getting wider and deeper. Herein, we review recent progress in research on nucleosomes and epigenetics, from nucleosome structure to chromatin formation, with a focus on chemical aspects. Basic knowledge of the nucleosome (nucleosome structure, nucleosome position sequence, nucleosome assembly and remodeling), epigenetic modifications, chromatin structure, chemical biology methods and nucleosome, observation nucleosome by AFM, phase separation and nucleosomes are described in this review.
Collapse
Affiliation(s)
- Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
| |
Collapse
|
29
|
Shi G, Hu Y, Zhu X, Jiang Y, Pang J, Wang C, Huang W, Zhao Y, Ma W, Liu D, Huang J, Songyang Z. A critical role of telomere chromatin compaction in ALT tumor cell growth. Nucleic Acids Res 2020; 48:6019-6031. [PMID: 32379321 PMCID: PMC7293046 DOI: 10.1093/nar/gkaa224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/17/2020] [Accepted: 04/18/2020] [Indexed: 01/15/2023] Open
Abstract
ALT tumor cells often contain abundant DNA damage foci at telomeres and rely on the alternative lengthening of telomeres (ALT) mechanism to maintain their telomeres. How the telomere chromatin is regulated and maintained in these cells remains largely unknown. In this study, we present evidence that heterochromatin protein 1 binding protein 3 (HP1BP3) can localize to telomeres and is particularly enriched on telomeres in ALT cells. HP1BP3 inhibition led to preferential growth inhibition of ALT cells, which was accompanied by telomere chromatin decompaction, increased presence of C-circles, more pronounced ALT-associated phenotypes and elongated telomeres. Furthermore, HP1BP3 appeared to participate in regulating telomere histone H3K9me3 epigenetic marks. Taken together, our data suggest that HP1BP3 functions on telomeres to maintain telomere chromatin and represents a novel target for inhibiting ALT cancer cells.
Collapse
Affiliation(s)
- Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yang Hu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xing Zhu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanling Jiang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Pang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chuanle Wang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenjun Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Dan Liu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA 77030
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA 77030.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| |
Collapse
|
30
|
Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. SCIENCE CHINA. LIFE SCIENCES 2020; 63:953-985. [PMID: 32548680 DOI: 10.1007/s11427-020-1702-x] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
Cells are compartmentalized by numerous membrane-enclosed organelles and membraneless compartments to ensure that a wide variety of cellular activities occur in a spatially and temporally controlled manner. The molecular mechanisms underlying the dynamics of membrane-bound organelles, such as their fusion and fission, vesicle-mediated trafficking and membrane contactmediated inter-organelle interactions, have been extensively characterized. However, the molecular details of the assembly and functions of membraneless compartments remain elusive. Mounting evidence has emerged recently that a large number of membraneless compartments, collectively called biomacromolecular condensates, are assembled via liquid-liquid phase separation (LLPS). Phase-separated condensates participate in various biological activities, including higher-order chromatin organization, gene expression, triage of misfolded or unwanted proteins for autophagic degradation, assembly of signaling clusters and actin- and microtubule-based cytoskeletal networks, asymmetric segregations of cell fate determinants and formation of pre- and post-synaptic density signaling assemblies. Biomacromolecular condensates can transition into different material states such as gel-like structures and solid aggregates. The material properties of condensates are crucial for fulfilment of their distinct functions, such as biochemical reaction centers, signaling hubs and supporting architectures. Cells have evolved multiple mechanisms to ensure that biomacromolecular condensates are assembled and disassembled in a tightly controlled manner. Aberrant phase separation and transition are causatively associated with a variety of human diseases such as neurodegenerative diseases and cancers. This review summarizes recent major progress in elucidating the roles of LLPS in various biological pathways and diseases.
Collapse
|
31
|
Lerner J, Gomez-Garcia PA, McCarthy RL, Liu Z, Lakadamyali M, Zaret KS. Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin. Mol Cell 2020; 79:677-688.e6. [PMID: 32574554 DOI: 10.1016/j.molcel.2020.05.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 04/06/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Abstract
Enzymatic probes of chromatin structure reveal accessible versus inaccessible chromatin states, while super-resolution microscopy reveals a continuum of chromatin compaction states. Characterizing histone H2B movements by single-molecule tracking (SMT), we resolved chromatin domains ranging from low to high mobility and displaying different subnuclear localizations patterns. Heterochromatin constituents correlated with the lowest mobility chromatin, whereas transcription factors varied widely with regard to their respective mobility with low- or high-mobility chromatin. Pioneer transcription factors, which bind nucleosomes, can access the low-mobility chromatin domains, whereas weak or non-nucleosome binding factors are excluded from the domains and enriched in higher mobility domains. Nonspecific DNA and nucleosome binding accounted for most of the low mobility of strong nucleosome interactor FOXA1. Our analysis shows how the parameters of the mobility of chromatin-bound factors, but not their diffusion behaviors or SMT-residence times within chromatin, distinguish functional characteristics of different chromatin-interacting proteins.
Collapse
Affiliation(s)
- Jonathan Lerner
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Pablo Aurelio Gomez-Garcia
- Center for Genomic Regulation, Barcelona Biomedical Research Park, 08003 Barcelona, Spain; ICFO-Institute of Photonics Sciences, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ryan L McCarthy
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Zhe Liu
- HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Melike Lakadamyali
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA; University of Pennsylvania, Department of Physiology, Philadelphia, PA 19104-6058, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA.
| |
Collapse
|
32
|
How HP1 Post-Translational Modifications Regulate Heterochromatin Formation and Maintenance. Cells 2020; 9:cells9061460. [PMID: 32545538 PMCID: PMC7349378 DOI: 10.3390/cells9061460] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Heterochromatin Protein 1 (HP1) is a highly conserved protein that has been used as a classic marker for heterochromatin. HP1 binds to di- and tri-methylated histone H3K9 and regulates heterochromatin formation, functions and structure. Besides the well-established phosphorylation of histone H3 Ser10 that has been shown to modulate HP1 binding to chromatin, several studies have recently highlighted the importance of HP1 post-translational modifications and additional epigenetic features for the modulation of HP1-chromatin binding ability and heterochromatin formation. In this review, we summarize the recent literature of HP1 post-translational modifications that have contributed to understand how heterochromatin is formed, regulated and maintained.
Collapse
|
33
|
Sanulli S, Gross JD, Narlikar GJ. Biophysical Properties of HP1-Mediated Heterochromatin. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:217-225. [PMID: 32493764 PMCID: PMC9128075 DOI: 10.1101/sqb.2019.84.040360] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Heterochromatin is a classic context for studying the mechanisms of chromatin organization. At the core of a highly conserved type of heterochromatin is the complex formed between chromatin methylated on histone H3 lysine 9 and HP1 proteins. This type of heterochromatin plays central roles in gene repression, genome stability, and nuclear mechanics. Systematic studies over the last several decades have provided insight into the biophysical mechanisms by which the HP1-chromatin complex is formed. Here, we discuss these studies together with recent findings indicating a role for phase separation in heterochromatin organization and function. We suggest that the different functions of HP1-mediated heterochromatin may rely on the increasing diversity being uncovered in the biophysical properties of HP1-chromatin complexes.
Collapse
Affiliation(s)
- Serena Sanulli
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
| |
Collapse
|
34
|
Kumar A, Kono H. Heterochromatin protein 1 (HP1): interactions with itself and chromatin components. Biophys Rev 2020; 12:387-400. [PMID: 32144738 PMCID: PMC7242596 DOI: 10.1007/s12551-020-00663-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/23/2020] [Indexed: 12/12/2022] Open
Abstract
Isoforms of heterochromatin protein 1 (HP1) have been known to perform a multitude of functions ranging from gene silencing, gene activation to cell cycle regulation, and cell differentiation. This functional diversity arises from the dissimilarities coded in protein sequence which confers different biophysical and biochemical properties to individual structural elements of HP1 and thereby different behavior and interaction patterns. Hence, an understanding of various interactions of the structural elements of HP1 will be of utmost importance to better elucidate chromatin dynamics in its presence. In this review, we have gathered available information about interactions of HP1 both within and with itself as well as with chromatin elements. Also, the possible implications of these interactions are discussed.
Collapse
Affiliation(s)
- Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan.
| |
Collapse
|
35
|
Roach RJ, Garavís M, González C, Jameson GB, Filichev VV, Hale TK. Heterochromatin protein 1α interacts with parallel RNA and DNA G-quadruplexes. Nucleic Acids Res 2020; 48:682-693. [PMID: 31799602 PMCID: PMC6954420 DOI: 10.1093/nar/gkz1138] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
The eukaryotic genome is functionally organized into domains of transcriptionally active euchromatin and domains of highly compact transcriptionally silent heterochromatin. Heterochromatin is constitutively assembled at repetitive elements that include the telomeres and centromeres. The histone code model proposes that HP1α forms and maintains these domains of heterochromatin through the interaction of its chromodomain with trimethylated lysine 9 of histone 3, although this interaction is not the sole determinant. We show here that the unstructured hinge domain, necessary for the targeting of HP1α to constitutive heterochromatin, recognizes parallel G-quadruplex (G4) assemblies formed by the TElomeric Repeat-containing RNA (TERRA) transcribed from the telomere. This provides a mechanism by which TERRA can lead to the enrichment of HP1α at telomeres to maintain heterochromatin. Furthermore, we show that HP1α binds with a faster association rate to DNA G4s of parallel topology compared to antiparallel G4s that bind slowly or not at all. Such G4–DNAs are found in the regulatory regions of several oncogenes. This implicates specific non-canonical nucleic acid structures as determinants of HP1α function and thus RNA and DNA G4s need to be considered as contributors to chromatin domain organization and the epigenome.
Collapse
Affiliation(s)
- Ruby J Roach
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Miguel Garavís
- Instituto de Química Física 'Rocasolano', CSIC, Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, Serrano 119, 28006 Madrid, Spain
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.,Maurice Wilkins Centre, Private Bag 92019, Auckland, New Zealand
| | - Vyacheslav V Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.,Maurice Wilkins Centre, Private Bag 92019, Auckland, New Zealand
| | - Tracy K Hale
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.,Maurice Wilkins Centre, Private Bag 92019, Auckland, New Zealand
| |
Collapse
|
36
|
Murakami Y. Phosphorylation of repressive histone code readers by casein kinase 2 plays diverse roles in heterochromatin regulation. J Biochem 2019; 166:3-6. [PMID: 31198932 DOI: 10.1093/jb/mvz045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/07/2019] [Indexed: 12/30/2022] Open
Abstract
Heterochromatin is a condensed and transcriptionally silent chromatin structure and that plays important roles in epigenetic regulation of the genome. Two types of heterochromatin exist: constitutive heterochromatin is primarily associated with trimethylation of histone H3 at lysine 9 (H3K9me3), and facultative heterochromatin with trimethylation of H3 at lysine 27 (H3K27me3). The methylated histones are bound by the chromodomain of histone code 'reader' proteins: HP1 family proteins for H3K9me3 and Polycomb family proteins for H3K27me3. Each repressive reader associates with various 'effector' proteins that provide the functional basis of heterochromatin. Heterochromatin regulation is primarily achieved by controlling histone modifications. However, recent studies have revealed that the repressive readers are phosphorylated, like other regulatory proteins, suggesting that phosphorylation also participates in heterochromatin regulation. Detailed studies have shown that phosphorylation of readers affects the binding specificities of chromodomains for methylated histone H3, as well as the binding of effector proteins. Thus, phosphorylation adds another layer to heterochromatin regulation. Interestingly, casein kinase 2, a strong and predominant kinase within the cell, is responsible for phosphorylation of repressive readers. In this commentary, I summarize the regulation of repressive readers by casein kinase 2-dependent phosphorylation and discuss the functional meaning of this modification.
Collapse
Affiliation(s)
- Yota Murakami
- Department of Chemistry, Faculty of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, Hokkaido, Japan
| |
Collapse
|
37
|
Hiragami-Hamada K, Nakayama JI. Do the charges matter?-balancing the charges of the chromodomain proteins on the nucleosome. J Biochem 2019; 165:455-458. [PMID: 30649341 PMCID: PMC6537122 DOI: 10.1093/jb/mvz004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/11/2019] [Indexed: 02/06/2023] Open
Abstract
The chromodomain (CD) is a member of the Royal family of conserved chromatin-binding motifs with methylated substrate binding ability, and is often found in ‘readers’ or ‘writers’ of repressive histone marks. The regions upstream or downstream of the CD are generally highly charged. Several previous studies suggested that these charged regions modulate the CD’s chromatin-binding activity. Considering the relatively weak interaction between the CD and a modified histone tail, it is puzzling how the highly charged CD-flanking regions are ‘balanced’ on the highly charged nucleosomes to mediate a modification-dependent interaction. Interestingly, the charge distributions along the CD and surrounding regions appear to be distinct among different types of readers and writers, indicating their functional relevance. Here, we describe and discuss the current understanding of the highly charged CD-flanking regions and the potential experimental concerns caused by the regions.
Collapse
Affiliation(s)
- Kyoko Hiragami-Hamada
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| |
Collapse
|
38
|
Chemical and biophysical methods to explore dynamic mechanisms of chromatin silencing. Curr Opin Chem Biol 2019; 51:1-10. [PMID: 30825740 DOI: 10.1016/j.cbpa.2019.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/15/2019] [Accepted: 01/25/2019] [Indexed: 12/19/2022]
Abstract
Chromatin, the nucleoprotein complex organizing the genome, is central in regulating gene expression and genome organization. Chromatin conformational dynamics, controlled by histone post-translational modifications (PTM) and effector proteins, play a key role in this regulatory function. Recent developments in chemical biology, cell biology, and biophysics sparked important new studies, which probe direct causal connections between histone PTMs, chromatin effector proteins that write or read these modifications, and the involved functional chromatin states. In particular, the mechanisms of heterochromatin silencing have been explored in great detail in recent years. These studies revealed the highly dynamic nature of this chromatin state, its conformational heterogeneity, and different mechanisms of its formation. Here, we review how chemical biology and biophysics shaped our current understanding of the dynamic processes observed in heterochromatin and discuss the emerging technologies to detect chromatin organization directly in the cellular environment.
Collapse
|
39
|
Leopold K, Stirpe A, Schalch T. Transcriptional gene silencing requires dedicated interaction between HP1 protein Chp2 and chromatin remodeler Mit1. Genes Dev 2019; 33:565-577. [PMID: 30808655 PMCID: PMC6499331 DOI: 10.1101/gad.320440.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/05/2019] [Indexed: 11/25/2022]
Abstract
Heterochromatin protein 1 (HP1) proteins are key factors of eukaryotic heterochromatin that coordinate chromatin compaction and transcriptional gene silencing. Through their multivalency they act as adaptors between histone H3 Lys9 di/trimethyl marks in chromatin and effector complexes that bind to the HP1 chromoshadow domain. Most organisms encode for multiple HP1 isoforms and the molecular mechanisms that underpin their diverse functions in genome regulation remain poorly understood. In fission yeast, the two HP1 proteins Chp2 and Swi6 assume distinct roles and Chp2 is tightly associated with the nucleosome remodeling and deacetylation complex SHREC. Here we show that Chp2 directly engages the SHREC nucleosome remodeler subunit Mit1. The crystal structure of the interaction interface reveals an extraordinarily extensive and specific interaction between the chromoshadow domain of Chp2 and the N terminus of Mit1. The integrity of this interface is critical for high affinity binding and for heterochromatin formation. Comparison with Swi6 shows that the Chp2-Mit1 interface is highly selective and thereby provides the molecular basis for the functional specialization of an HP1 isoform.
Collapse
Affiliation(s)
- Karoline Leopold
- Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Alessandro Stirpe
- Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Thomas Schalch
- Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland.,Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, United Kingdom
| |
Collapse
|
40
|
Nishibuchi G, Machida S, Nakagawa R, Yoshimura Y, Hiragami-Hamada K, Abe Y, Kurumizaka H, Tagami H, Nakayama JI. Mitotic phosphorylation of HP1α regulates its cell cycle-dependent chromatin binding. J Biochem 2018; 165:433-446. [DOI: 10.1093/jb/mvy117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/14/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Gohei Nishibuchi
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Reiko Nakagawa
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
| | - Yuriko Yoshimura
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Japan
| | - Kyoko Hiragami-Hamada
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Nishigonaka 38, Myodaiji, Okazaki, Japan
| | - Yusuke Abe
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hideaki Tagami
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Jun-ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Japan
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Nishigonaka 38, Myodaiji, Okazaki, Japan
| |
Collapse
|
41
|
The binding of Chp2's chromodomain to methylated H3K9 is essential for Chp2's role in heterochromatin assembly in fission yeast. PLoS One 2018; 13:e0201101. [PMID: 30110338 PMCID: PMC6093649 DOI: 10.1371/journal.pone.0201101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 07/09/2018] [Indexed: 12/19/2022] Open
Abstract
The binding of heterochromatin protein 1 (HP1) to lysine 9–methylated histone H3 (H3K9me) is an essential step in heterochromatin assembly. Chp2, an HP1-family protein in the fission yeast Schizosaccharomyces pombe, is required for heterochromatic silencing. Chp2 recruits SHREC, a multifunctional protein complex containing the nucleosome remodeler Mit1 and the histone deacetylase Clr3. Although the targeting of SHREC to chromatin is thought to occur via two distinct modules regulated by the SHREC components Chp2 and Clr2, it is not clear how Chp2’s chromatin binding regulates SHREC function. Here, we show that H3K9me binding by Chp2’s chromodomain (CD) is essential for Chp2’s silencing function and for SHREC’s targeting to chromatin. Cells expressing a Chp2 mutant with defective H3K9me binding (Chp2-W199A) have a silencing defect, with a phenotype similar to that of chp2-null cells. Genetic analysis using a synthetic silencing system revealed that a Chp2 mutant and SHREC-component mutants had similar phenotypes, suggesting that Chp2’s function also affects SHREC’s chromatin binding. Size-exclusion chromatography of native protein complexes showed that Chp2-CD’s binding of H3K9me3 ensures Clr3’s chromatin binding, and suggested that SHREC’s chromatin binding is mediated by separable functional modules. Interestingly, we found that the stability of the Chp2 protein depended on the Clr3 protein’s histone deacetylase activity. Our findings demonstrate that Chp2’s H3K9me binding is critical for SHREC function and that the two modules within the SHREC complex are interdependent.
Collapse
|
42
|
Gil RS, Vagnarelli P. Protein phosphatases in chromatin structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:90-101. [PMID: 30036566 PMCID: PMC6227384 DOI: 10.1016/j.bbamcr.2018.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/29/2018] [Accepted: 07/18/2018] [Indexed: 12/19/2022]
Abstract
Chromatin structure and dynamics are highly controlled and regulated processes that play an essential role in many aspects of cell biology. The chromatin transition stages and the factors that control this process are regulated by post-translation modifications, including phosphorylation. While the role of protein kinases in chromatin dynamics has been quite well studied, the nature and regulation of the counteracting phosphatases represent an emerging field but are still at their infancy. In this review we summarize the current literature on phosphatases involved in the regulation of chromatin structure and dynamics, with emphases on the major knowledge gaps that should require attention and more investigation.
Collapse
Affiliation(s)
- Raquel Sales Gil
- Colleges of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Paola Vagnarelli
- Colleges of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK.
| |
Collapse
|
43
|
Yu B, Lin YA, Parhad SS, Jin Z, Ma J, Theurkauf WE, Zhang ZZ, Huang Y. Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification. EMBO Rep 2018; 19:embr.201745418. [PMID: 29858487 DOI: 10.15252/embr.201745418] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/28/2018] [Accepted: 05/14/2018] [Indexed: 11/09/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) silence transposons in germ cells to maintain genome stability and animal fertility. Rhino, a rapidly evolving heterochromatin protein 1 (HP1) family protein, binds Deadlock in a species-specific manner and so defines the piRNA-producing loci in the Drosophila genome. Here, we determine the crystal structures of Rhino-Deadlock complex in Drosophila melanogaster and simulans In both species, one Rhino binds the N-terminal helix-hairpin-helix motif of one Deadlock protein through a novel interface formed by the beta-sheet in the Rhino chromoshadow domain. Disrupting the interface leads to infertility and transposon hyperactivation in flies. Our structural and functional experiments indicate that electrostatic repulsion at the interaction interface causes cross-species incompatibility between the sibling species. By determining the molecular architecture of this piRNA-producing machinery, we discover a novel HP1-partner interacting mode that is crucial to piRNA biogenesis and transposon silencing. We thus explain the cross-species incompatibility of two sibling species at the molecular level.
Collapse
Affiliation(s)
- Bowen Yu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu An Lin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhaohui Jin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zz Zhao Zhang
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Ying Huang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
44
|
Watanabe S, Mishima Y, Shimizu M, Suetake I, Takada S. Interactions of HP1 Bound to H3K9me3 Dinucleosome by Molecular Simulations and Biochemical Assays. Biophys J 2018; 114:2336-2351. [PMID: 29685391 PMCID: PMC6129468 DOI: 10.1016/j.bpj.2018.03.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/27/2018] [Accepted: 03/26/2018] [Indexed: 01/01/2023] Open
Abstract
Heterochromatin protein 1 (HP1), associated with heterochromatin formation, recognizes an epigenetically repressive marker, trimethylated lysine 9 in histone H3 (H3K9me3), and generally contributes to long-term silencing. How HP1 induces heterochromatin is not fully understood. Recent experiments suggested that not one, but two nucleosomes provide a platform for this recognition. Integrating previous and new biochemical assays with computational modeling, we provide near-atomic structural models for HP1 binding to the dinucleosomes. We found that the dimeric HP1α tends to bind two H3K9me3s that are in adjacent nucleosomes, thus bridging two nucleosomes. We identified, to our knowledge, a novel DNA binding motif in the hinge region that is specific to HP1α and is essential for recognizing the H3K9me3 sites of two nucleosomes. An HP1 isoform, HP1γ, does not easily bridge two nucleosomes in extended conformations because of the absence of the above binding motif and its shorter hinge region. We propose a molecular mechanism for chromatin structural changes caused by HP1.
Collapse
Affiliation(s)
- Shuhei Watanabe
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Japan
| | - Yuichi Mishima
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masahiro Shimizu
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Japan
| | - Isao Suetake
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan; College of Nutrition, Koshien University, Takarazuka, Japan.
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Japan.
| |
Collapse
|
45
|
Larson AG, Narlikar GJ. The Role of Phase Separation in Heterochromatin Formation, Function, and Regulation. Biochemistry 2018; 57:2540-2548. [DOI: 10.1021/acs.biochem.8b00401] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
46
|
Kilic S, Felekyan S, Doroshenko O, Boichenko I, Dimura M, Vardanyan H, Bryan LC, Arya G, Seidel CAM, Fierz B. Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α. Nat Commun 2018; 9:235. [PMID: 29339721 PMCID: PMC5770380 DOI: 10.1038/s41467-017-02619-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/11/2017] [Indexed: 01/17/2023] Open
Abstract
The dynamic architecture of chromatin fibers, a key determinant of genome regulation, is poorly understood. Here, we employ multimodal single-molecule Förster resonance energy transfer studies to reveal structural states and their interconversion kinetics in chromatin fibers. We show that nucleosomes engage in short-lived (micro- to milliseconds) stacking interactions with one of their neighbors. This results in discrete tetranucleosome units with distinct interaction registers that interconvert within hundreds of milliseconds. Additionally, we find that dynamic chromatin architecture is modulated by the multivalent architectural protein heterochromatin protein 1α (HP1α), which engages methylated histone tails and thereby transiently stabilizes stacked nucleosomes. This compacted state nevertheless remains dynamic, exhibiting fluctuations on the timescale of HP1α residence times. Overall, this study reveals that exposure of internal DNA sites and nucleosome surfaces in chromatin fibers is governed by an intrinsic dynamic hierarchy from micro- to milliseconds, allowing the gene regulation machinery to access compact chromatin. Chromatin fibers undergo continuous structural rearrangements but their dynamic architecture is poorly understood. Here, the authors use single-molecule FRET to determine the structural states and interconversion kinetics of chromatin fibers, monitoring their effector protein-dependent dynamic motions.
Collapse
Affiliation(s)
- Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zurich, 8057, Zurich, Switzerland
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Olga Doroshenko
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Iuliia Boichenko
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Mykola Dimura
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hayk Vardanyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Louise C Bryan
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Gaurav Arya
- Pratt School of Engineering, Duke University, 144 Hudson Hall, Box 90300, Durham, NC, 27708, USA
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| |
Collapse
|
47
|
Structural Basis of Heterochromatin Formation by Human HP1. Mol Cell 2018; 69:385-397.e8. [PMID: 29336876 DOI: 10.1016/j.molcel.2017.12.011] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/01/2017] [Accepted: 12/13/2017] [Indexed: 12/17/2022]
Abstract
Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1β, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin.
Collapse
|
48
|
Kawaguchi T, Machida S, Kurumizaka H, Tagami H, Nakayama JI. Phosphorylation of CBX2 controls its nucleosome-binding specificity. J Biochem 2017; 162:343-355. [PMID: 28992316 DOI: 10.1093/jb/mvx040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 05/22/2017] [Indexed: 01/08/2023] Open
Abstract
Chromobox 2 (CBX2), a component of polycomb repressive complex 1 (PRC1), binds lysine 27-methylated histone H3 (H3K27me3) via its chromodomain (CD) and plays a critical role in repressing developmentally regulated genes. The phosphorylation of CBX2 has been described in several studies, but the biological implications of this modification remain largely elusive. Here, we show that CBX2's phosphorylation plays an important role in its nucleosome binding. CBX2 is stably phosphorylated in vivo, and domain analysis showed that residues in CBX2's serine-rich (SR) region are the predominant phosphorylation sites. The serine residues in an SR region followed by an acidic-residue (AR) cluster coincide with the consensus target of casein kinase II (CK2), and CK2 efficiently phosphorylated the SR region in vitro. A nucleosome pull-down assay revealed that CK2-phosphorylated CBX2 had a high specificity for H3K27me3-modified nucleosomes. An electrophoretic mobility-shift assay showed that CK2-mediated phosphorylation diminished CBX2's AT-hook-associated DNA-binding activity. Mutant CBX2 lacking the SR region or its neighboring AR cluster failed to repress the transcription of p21, a gene targeted by PRC1. These results suggest that CBX2's phosphorylation is critical for its transcriptional repression of target genes.
Collapse
Affiliation(s)
- Takayuki Kawaguchi
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hideaki Tagami
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| |
Collapse
|
49
|
Bryan LC, Weilandt DR, Bachmann AL, Kilic S, Lechner CC, Odermatt PD, Fantner GE, Georgeon S, Hantschel O, Hatzimanikatis V, Fierz B. Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions. Nucleic Acids Res 2017; 45:10504-10517. [PMID: 28985346 PMCID: PMC5737501 DOI: 10.1093/nar/gkx697] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/27/2017] [Indexed: 12/20/2022] Open
Abstract
Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is currently not understood how effectors dynamically sample the chromatin landscape. Here, we dissect the dynamic chromatin interactions of a family of multivalent effectors, heterochromatin protein 1 (HP1) proteins, using single-molecule fluorescence imaging and computational modeling. We show that the three human HP1 isoforms are recruited and retained on chromatin by a dynamic exchange between histone PTM and DNA bound states. These interactions depend on local chromatin structure, the HP1 isoforms as well as on PTMs on HP1 itself. Of the HP1 isoforms, HP1α exhibits the longest residence times and fastest binding rates due to DNA interactions in addition to PTM binding. HP1α phosphorylation further increases chromatin retention through strengthening of multivalency while reducing DNA binding. As DNA binding in combination with specific PTM recognition is found in many chromatin effectors, we propose a general dynamic capture mechanism for effector recruitment. Multiple weak protein and DNA interactions result in a multivalent interaction network that targets effectors to a specific chromatin modification state, where their activity is required.
Collapse
Affiliation(s)
- Louise C Bryan
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Daniel R Weilandt
- Laboratory of Computational Systems Biotechnology, ISIC, EPFL, 1015 Lausanne, Switzerland
| | - Andreas L Bachmann
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Carolin C Lechner
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Pascal D Odermatt
- Laboratory for Bio- and Nano instrumentation, Institute of Bioengineering, EPFL, 1015 Lausanne, Switzerland
| | - Georg E Fantner
- Laboratory for Bio- and Nano instrumentation, Institute of Bioengineering, EPFL, 1015 Lausanne, Switzerland
| | - Sandrine Georgeon
- ISREC foundation chair in translational oncology, School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Oliver Hantschel
- ISREC foundation chair in translational oncology, School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, ISIC, EPFL, 1015 Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| |
Collapse
|
50
|
Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 2017; 547:236-240. [PMID: 28636604 PMCID: PMC5606208 DOI: 10.1038/nature22822] [Citation(s) in RCA: 1109] [Impact Index Per Article: 158.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 05/16/2017] [Indexed: 01/15/2023]
Abstract
Gene silencing by heterochromatin is proposed to occur in part as a result of the ability of heterochromatin protein 1 (HP1) proteins to spread across large regions of the genome, compact the underlying chromatin and recruit diverse ligands. Here we identify a new property of the human HP1α protein: the ability to form phase-separated droplets. While unmodified HP1α is soluble, either phosphorylation of its N-terminal extension or DNA binding promotes the formation of phase-separated droplets. Phosphorylation-driven phase separation can be promoted or reversed by specific HP1α ligands. Known components of heterochromatin such as nucleosomes and DNA preferentially partition into the HP1α droplets, but molecules such as the transcription factor TFIIB show no preference. Using a single-molecule DNA curtain assay, we find that both unmodified and phosphorylated HP1α induce rapid compaction of DNA strands into puncta, although with different characteristics. We show by direct protein delivery into mammalian cells that an HP1α mutant incapable of phase separation in vitro forms smaller and fewer nuclear puncta than phosphorylated HP1α. These findings suggest that heterochromatin-mediated gene silencing may occur in part through sequestration of compacted chromatin in phase-separated HP1 droplets, which are dissolved or formed by specific ligands on the basis of nuclear context.
Collapse
Affiliation(s)
- Adam G. Larson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel Elnatan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Madeline M. Keenen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael J. Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan B. Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|