1
|
Kaimala S, Lootah SS, Mehra N, Kumar CA, Marzooqi SA, Sampath P, Ansari SA, Emerald BS. The Long Non-Coding RNA Obesity-Related (Obr) Contributes To Lipid Metabolism Through Epigenetic Regulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401939. [PMID: 38704700 PMCID: PMC11234455 DOI: 10.1002/advs.202401939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Indexed: 05/07/2024]
Abstract
Obesity is a multifactorial disease that is part of today's epidemic and also increases the risk of other metabolic diseases. Long noncoding RNAs (lncRNAs) provide one tier of regulatory mechanisms to maintain metabolic homeostasis. Although lncRNAs are a significant constituent of the mammalian genome, studies aimed at their metabolic significance, including obesity, are only beginning to be addressed. Here, a developmentally regulated lncRNA, termed as obesity related (Obr), whose expression in metabolically relevant tissues such as skeletal muscle, liver, and pancreas is altered in diet-induced obesity, is identified. The Clone 9 cell line and high-fat diet-induced obese Wistar rats are used as a model system to verify the function of Obr. By using stable expression and antisense oligonucleotide-mediated downregulation of the expression of Obr followed by different molecular biology experiments, its role in lipid metabolism is verified. It is shown that Obr associates with the cAMP response element-binding protein (Creb) and activates different transcription factors involved in lipid metabolism. Its association with the Creb histone acetyltransferase complex, which includes the cAMP response element-binding protein (CBP) and p300, positively regulates the transcription of genes involved in lipid metabolism. In addition, Obr is regulated by Pparγ in response to lipid accumulation.
Collapse
Affiliation(s)
- Suneesh Kaimala
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Shareena Saeed Lootah
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Neha Mehra
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Challagandla Anil Kumar
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Saeeda Al Marzooqi
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
| | - Prabha Sampath
- A*STAR Skin Research Laboratory, Agency for Science Technology & Research (A*STAR), Singapore, 138648, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Genome Institute of Singapore, Agency for Science Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Suraiya Anjum Ansari
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
- ASPIRE Precision Medicine, Research Institute Abu Dhabi, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
- ASPIRE Precision Medicine, Research Institute Abu Dhabi, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
| |
Collapse
|
2
|
Sato Y, Takenoshita M, Ueoka M, Ueda J, Yamagata K, Kimura H. Visualizing histone H4K20me1 in knock-in mice expressing the mCherry-tagged modification-specific intracellular antibody. Histochem Cell Biol 2024; 162:41-52. [PMID: 38762823 PMCID: PMC11227479 DOI: 10.1007/s00418-024-02296-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2024] [Indexed: 05/20/2024]
Abstract
During development and differentiation, histone modifications dynamically change locally and globally, associated with transcriptional regulation, DNA replication and repair, and chromosome condensation. The level of histone H4 Lys20 monomethylation (H4K20me1) increases during the G2 to M phases of the cell cycle and is enriched in facultative heterochromatin, such as inactive X chromosomes in cycling cells. To track the dynamic changes of H4K20me1 in living cells, we have developed a genetically encoded modification-specific intracellular antibody (mintbody) probe that specifically binds to the modification. Here, we report the generation of knock-in mice in which the coding sequence of the mCherry-tagged version of the H4K20me1-mintbody is inserted into the Rosa26 locus. The knock-in mice, which ubiquitously expressed the H4K20me1-mintbody, developed normally and were fertile, indicating that the expression of the probe does not disturb the cell growth, development, or differentiation. Various tissues isolated from the knock-in mice exhibited nuclear fluorescence without the need for fixation. The H4K20me1-mintbody was enriched in inactive X chromosomes in developing embryos and in XY bodies during spermatogenesis. The knock-in mice will be useful for the histochemical analysis of H4K20me1 in any cell types.
Collapse
Affiliation(s)
- Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8501, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8501, Japan
| | - Maoko Takenoshita
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8501, Japan
| | - Miku Ueoka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8501, Japan
| | - Jun Ueda
- Center for Genetic Analysis of Biological Responses, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Advanced Medical Science, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Kazuo Yamagata
- Center for Genetic Analysis of Biological Responses, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, 649-6493, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8501, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8501, Japan.
| |
Collapse
|
3
|
Hoboth P, Sztacho M, Hozák P. Nuclear patterns of phosphatidylinositol 4,5- and 3,4-bisphosphate revealed by super-resolution microscopy differ between the consecutive stages of RNA polymerase II transcription. FEBS J 2024. [PMID: 38734927 DOI: 10.1111/febs.17136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/12/2023] [Accepted: 04/05/2024] [Indexed: 05/13/2024]
Abstract
Phosphatidylinositol phosphates are powerful signaling molecules that orchestrate signaling and direct membrane trafficking in the cytosol. Interestingly, phosphatidylinositol phosphates also localize within the membrane-less compartments of the cell nucleus, where they participate in the regulation of gene expression. Nevertheless, current models of gene expression, which include condensates of proteins and nucleic acids, do not include nuclear phosphatidylinositol phosphates. This gap is partly a result of the missing detailed analysis of the subnuclear distribution of phosphatidylinositol phosphates and their relationships with gene expression. Here, we used quantitative dual-color direct stochastic optical reconstruction microscopy to analyze the nanoscale co-patterning between RNA polymerase II transcription initiation and elongation markers with respect to phosphatidylinositol 4,5- or 3,4-bisphosphate in the nucleoplasm and nuclear speckles and compared it with randomized data and cells with inhibited transcription. We found specific co-patterning of the transcription initiation marker P-S5 with phosphatidylinositol 4,5-bisphosphate in the nucleoplasm and with phosphatidylinositol 3,4-bisphosphate at the periphery of nuclear speckles. We showed the specific accumulation of the transcription elongation marker PS-2 and of nascent RNA in the proximity of phosphatidylinositol 3,4-bisphosphate associated with nuclear speckles. Taken together, this shows that the distinct spatial associations between the consecutive stages of RNA polymerase II transcription and nuclear phosphatidylinositol phosphates exhibit specificity within the gene expression compartments. Thus, in analogy to the cellular membranes, where phospholipid composition orchestrates signaling pathways and directs membrane trafficking, we propose a model in which the phospholipid identity of gene expression compartments orchestrates RNA polymerase II transcription.
Collapse
Affiliation(s)
- Peter Hoboth
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Viničná Microscopy Core Facility, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Sztacho
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Cancer Cell Architecture, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pavel Hozák
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
4
|
Tomimatsu K, Fujii T, Bise R, Hosoda K, Taniguchi Y, Ochiai H, Ohishi H, Ando K, Minami R, Tanaka K, Tachibana T, Mori S, Harada A, Maehara K, Nagasaki M, Uchida S, Kimura H, Narita M, Ohkawa Y. Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states. Nat Commun 2024; 15:3657. [PMID: 38719795 PMCID: PMC11078938 DOI: 10.1038/s41467-024-47989-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
Cell states are regulated by the response of signaling pathways to receptor ligand-binding and intercellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we develop Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes.
Collapse
Affiliation(s)
- Kosuke Tomimatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Takeru Fujii
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Ryoma Bise
- Department of Advanced Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | | | - Yosuke Taniguchi
- Department of Medicinal Sciences, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Hiroshi Ochiai
- Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Hiroaki Ohishi
- Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Kanta Ando
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Ryoma Minami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Taro Tachibana
- Department of Chemistry and Bioengineering, Osaka Metropolitan University, Osaka, 558-8585, Japan
| | - Seiichi Mori
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Masao Nagasaki
- Division of Biomedical Information Analysis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Seiichi Uchida
- Department of Advanced Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Center, University of Cambridge, Cambridge, CB2 0RE, UK
- World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan.
| |
Collapse
|
5
|
Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin binding dynamics of RNA Polymerase II general transcription machinery components. EMBO J 2024; 43:1799-1821. [PMID: 38565951 PMCID: PMC11066129 DOI: 10.1038/s44318-024-00089-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
A great deal of work has revealed, in structural detail, the components of the preinitiation complex (PIC) machinery required for initiation of mRNA gene transcription by RNA polymerase II (Pol II). However, less-well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining how rates of in vivo RNA synthesis are established. We used competition ChIP in budding yeast to obtain genome-scale estimates of the residence times for five general transcription factors (GTFs): TBP, TFIIA, TFIIB, TFIIE and TFIIF. While many GTF-chromatin interactions were short-lived ( < 1 min), there were numerous interactions with residence times in the range of several minutes. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism, offering a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription.
Collapse
Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Savera J Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Elizabeth A Hoffman
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA.
| |
Collapse
|
6
|
Li J, Gu W, Yang Z, Chen J, Yi F, Li T, Li J, Zhou Y, Guo Y, Song W, Lai J, Zhao H. ZmELP1, an Elongator complex subunit, is required for the maintenance of histone acetylation and RNA Pol II phosphorylation in maize kernels. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1251-1268. [PMID: 38098341 PMCID: PMC11022810 DOI: 10.1111/pbi.14262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 01/26/2024]
Abstract
The Elongator complex was originally identified as an interactor of hyperphosphorylated RNA polymerase II (RNAPII) in yeast and has histone acetyltransferase (HAT) activity. However, the genome-wide regulatory roles of Elongator on transcriptional elongation and histone acetylation remain unclear. We characterized a maize miniature seed mutant, mn7 and map-based cloning revealed that Mn7 encodes one of the subunits of the Elongator complex, ZmELP1. ZmELP1 deficiency causes marked reductions in the kernel size and weight. Molecular analyses showed that ZmELP1 interacts with ZmELP3, which is required for H3K14 acetylation (H3K14ac), and Elongator complex subunits interact with RNA polymerase II (RNAPII) C-terminal domain (CTD). Genome-wide analyses indicated that loss of ZmELP1 leads to a significant decrease in the deposition of H3K14ac and the CTD of phosphorylated RNAPII on Ser2 (Ser2P). These chromatin changes positively correlate with global transcriptomic changes. ZmELP1 mutation alters the expression of genes involved in transcriptional regulation and kernel development. We also showed that the decrease of Ser2P depends on the deposition of Elongator complex-mediated H3K14ac. Taken together, our results reveal an important role of ZmELP1 in the H3K14ac-dependent transcriptional elongation, which is critical for kernel development.
Collapse
Affiliation(s)
- Jianrui Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Wei Gu
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Crop Breeding, Cultivation Research Institution/CIMMYT‐China Specialty Maize Research Center, Shanghai Engineering Research Center of Specialty Maize, Shanghai Key Laboratory of Agricultural Genetics and BreedingShanghai Academy of Agricultural SciencesShanghaiChina
| | - Zhijia Yang
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jian Chen
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Fei Yi
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Tong Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jingrui Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Weibin Song
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Haiming Zhao
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| |
Collapse
|
7
|
Hwang DW, Maekiniemi A, Singer RH, Sato H. Real-time single-molecule imaging of transcriptional regulatory networks in living cells. Nat Rev Genet 2024; 25:272-285. [PMID: 38195868 DOI: 10.1038/s41576-023-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
Gene regulatory networks drive the specific transcriptional programmes responsible for the diversification of cell types during the development of multicellular organisms. Although our knowledge of the genes involved in these dynamic networks has expanded rapidly, our understanding of how transcription is spatiotemporally regulated at the molecular level over a wide range of timescales in the small volume of the nucleus remains limited. Over the past few decades, advances in the field of single-molecule fluorescence imaging have enabled real-time behaviours of individual transcriptional components to be measured in living cells and organisms. These efforts are now shedding light on the dynamic mechanisms of transcription, revealing not only the temporal rules but also the spatial coordination of underlying molecular interactions during various biological events.
Collapse
Affiliation(s)
- Dong-Woo Hwang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anna Maekiniemi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Robert H Singer
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Hanae Sato
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
- Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan.
| |
Collapse
|
8
|
Woodworth MA, Lakadamyali M. Toward a comprehensive view of gene architecture during transcription. Curr Opin Genet Dev 2024; 85:102154. [PMID: 38309073 PMCID: PMC10989512 DOI: 10.1016/j.gde.2024.102154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
The activation of genes within the nucleus of eukaryotic cells is a tightly regulated process, orchestrated by a complex interplay of various physical properties and interacting factors. Studying the multitude of components and features that collectively contribute to gene activation has proven challenging due to the complexities of simultaneously visualizing the dynamic and transiently interacting elements that coalesce within the small space occupied by each individual gene. However, various labeling and imaging advances are now starting to overcome this challenge, enabling visualization of gene activation at different lengths and timescales. In this review, we aim to highlight these microscopy-based advances and suggest how they can be combined to provide a comprehensive view of the mechanisms regulating gene activation.
Collapse
Affiliation(s)
- Marcus A Woodworth
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
9
|
Ugolini M, Kerlin MA, Kuznetsova K, Oda H, Kimura H, Vastenhouw NL. Transcription bodies regulate gene expression by sequestering CDK9. Nat Cell Biol 2024; 26:604-612. [PMID: 38589534 PMCID: PMC11021188 DOI: 10.1038/s41556-024-01389-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells. It remains unclear, however, if and how transcription bodies affect gene expression. Here we disrupted the formation of two prominent endogenous transcription bodies that mark the onset of zygotic transcription in zebrafish embryos and analysed the effect on gene expression using enriched SLAM-seq and live-cell imaging. We find that the disruption of transcription bodies results in the misregulation of hundreds of genes. Here we focus on genes that are upregulated. These genes have accessible chromatin and are poised to be transcribed in the presence of the two transcription bodies, but they do not go into elongation. Live-cell imaging shows that disruption of the two large transcription bodies enables these poised genes to be transcribed in ectopic transcription bodies, suggesting that the large transcription bodies sequester a pause release factor. Supporting this hypothesis, we find that CDK9-the kinase that releases paused polymerase II-is highly enriched in the two large transcription bodies. Overexpression of CDK9 in wild-type embryos results in the formation of ectopic transcription bodies and thus phenocopies the removal of the two large transcription bodies. Taken together, our results show that transcription bodies regulate transcription by sequestering machinery, thereby preventing genes elsewhere in the nucleus from being transcribed.
Collapse
Affiliation(s)
- Martino Ugolini
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Maciej A Kerlin
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ksenia Kuznetsova
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Institute of Human Genetics, CNRS, Montpellier, France
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Nadine L Vastenhouw
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland.
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
| |
Collapse
|
10
|
Archuleta SR, Goodrich JA, Kugel JF. Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle. Biomolecules 2024; 14:176. [PMID: 38397413 PMCID: PMC10886972 DOI: 10.3390/biom14020176] [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] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Central to the development and survival of all organisms is the regulation of gene expression, which begins with the process of transcription catalyzed by RNA polymerases. During transcription of protein-coding genes, the general transcription factors (GTFs) work alongside RNA polymerase II (Pol II) to assemble the preinitiation complex at the transcription start site, open the promoter DNA, initiate synthesis of the nascent messenger RNA, transition to productive elongation, and ultimately terminate transcription. Through these different stages of transcription, Pol II is dynamically phosphorylated at the C-terminal tail of its largest subunit, serving as a control mechanism for Pol II elongation and a signaling/binding platform for co-transcriptional factors. The large number of core protein factors participating in the fundamental steps of transcription add dense layers of regulation that contribute to the complexity of temporal and spatial control of gene expression within any given cell type. The Pol II transcription system is highly conserved across different levels of eukaryotes; however, most of the information here will focus on the human Pol II system. This review walks through various stages of transcription, from preinitiation complex assembly to termination, highlighting the functions and mechanisms of the core machinery that participates in each stage.
Collapse
Affiliation(s)
| | - James A. Goodrich
- Department of Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309, USA;
| | - Jennifer F. Kugel
- Department of Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309, USA;
| |
Collapse
|
11
|
Meeussen JVW, Lenstra TL. Time will tell: comparing timescales to gain insight into transcriptional bursting. Trends Genet 2024; 40:160-174. [PMID: 38216391 PMCID: PMC10860890 DOI: 10.1016/j.tig.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
Recent imaging studies have captured the dynamics of regulatory events of transcription inside living cells. These events include transcription factor (TF) DNA binding, chromatin remodeling and modification, enhancer-promoter (E-P) proximity, cluster formation, and preinitiation complex (PIC) assembly. Together, these molecular events culminate in stochastic bursts of RNA synthesis, but their kinetic relationship remains largely unclear. In this review, we compare the timescales of upstream regulatory steps (input) with the kinetics of transcriptional bursting (output) to generate mechanistic models of transcription dynamics in single cells. We highlight open questions and potential technical advances to guide future endeavors toward a quantitative and kinetic understanding of transcription regulation.
Collapse
Affiliation(s)
- Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands.
| |
Collapse
|
12
|
Yamamoto T, Yamazaki T, Ninomiya K, Hirose T. Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus. Commun Biol 2023; 6:1129. [PMID: 37935838 PMCID: PMC10630424 DOI: 10.1038/s42003-023-05519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has been thought to be the biophysical principle governing the assembly of the multiphase structures of nucleoli, the site of ribosomal biogenesis. Condensates assembled through LLPS increase their sizes to minimize the surface energy as far as their components are available. However, multiple microphases, fibrillar centers (FCs), dispersed in a nucleolus are stable and their sizes do not grow unless the transcription of pre-ribosomal RNA (pre-rRNA) is inhibited. To understand the mechanism of the suppression of the FC growth, we here construct a minimal theoretical model by taking into account nascent pre-rRNAs tethered to FC surfaces by RNA polymerase I. The prediction of this theory was supported by our experiments that quantitatively measure the dependence of the size of FCs on the transcription level. This work sheds light on the role of nascent RNAs in controlling the size of nuclear bodies.
Collapse
Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, 001-0021, Japan.
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan.
| | - Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan
| |
Collapse
|
13
|
Jiao D, Sun R, Ren X, Wang Y, Tian P, Wang Y, Yuan D, Yue X, Wu Z, Li C, Gao L, Ma C, Liang X. Lipid accumulation-mediated histone hypoacetylation drives persistent NK cell dysfunction in anti-tumor immunity. Cell Rep 2023; 42:113211. [PMID: 37792534 DOI: 10.1016/j.celrep.2023.113211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/04/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
Hyperlipidemia impairs anti-tumor immune responses and is closely associated with increased human cancer incidence and mortality. However, the underlying mechanisms are not well understood. In the present study, we show that natural killer (NK) cells isolated from high-fat-diet mice or treated with oleic acid (OA) in vitro exhibit sustainable functional defects even after removal from hyperlipidemic milieu. This is accompanied by reduced chromatin accessibility in the promoter region of NK cell effector molecules. Mechanistically, OA exposure blunts P300-mediated c-Myc acetylation and shortens its protein half-life in NK cells, which in turn reduces P300 accumulation and H3K27 acetylation and leads to persistent NK cell dysfunction. NK cells engineered with hyperacetylated c-Myc mutants surmount the suppressive effect of hyperlipidemia and display superior anti-tumor activity. Our findings reveal the persistent dysfunction of NK cells in dyslipidemia milieu and extend engineered NK cells as a promising strategy for tumor immunotherapy.
Collapse
Affiliation(s)
- Deyan Jiao
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Renhui Sun
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Xiaolei Ren
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Yingchun Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Panpan Tian
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Yuzhen Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Detian Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Xuetian Yue
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhuanchang Wu
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China; Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China
| | - Chunyang Li
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Histology and Embryology, School of Basic Medical Science, Shandong University, Jinan, China
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China; Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China; Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China.
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China; Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China.
| |
Collapse
|
14
|
Crawford MC, Tripu DR, Barritt SA, Jing Y, Gallimore D, Kales SC, Bhanu NV, Xiong Y, Fang Y, Butler KAT, LeClair CA, Coussens NP, Simeonov A, Garcia BA, Dibble CC, Meier JL. Comparative Analysis of Drug-like EP300/CREBBP Acetyltransferase Inhibitors. ACS Chem Biol 2023; 18:2249-2258. [PMID: 37737090 PMCID: PMC11059198 DOI: 10.1021/acschembio.3c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
The human acetyltransferase paralogues EP300 and CREBBP are master regulators of lysine acetylation whose activity has been implicated in various cancers. In the half-decade since the first drug-like inhibitors of these proteins were reported, three unique molecular scaffolds have taken precedent: an indane spiro-oxazolidinedione (A-485), a spiro-hydantoin (iP300w), and an aminopyridine (CPI-1612). Despite increasing use of these molecules to study lysine acetylation, the dearth of data regarding their relative biochemical and biological potencies makes their application as chemical probes a challenge. To address this gap, here we present a comparative study of drug-like EP300/CREBBP acetyltransferase inhibitors. First, we determine the biochemical and biological potencies of A-485, iP300w, and CPI-1612, highlighting the increased potencies of the latter two compounds at physiological acetyl-CoA concentrations. Cellular evaluation shows that inhibition of histone acetylation and cell growth closely aligns with the biochemical potencies of these molecules, consistent with an on-target mechanism. Finally, we demonstrate the utility of comparative pharmacology by using it to investigate the hypothesis that increased CoA synthesis caused by knockout of PANK4 can competitively antagonize the binding of EP300/CREBBP inhibitors and demonstrate proof-of-concept photorelease of a potent inhibitor molecule. Overall, our study demonstrates how knowledge of the relative inhibitor potency can guide the study of EP300/CREBBP-dependent mechanisms and suggests new approaches to target delivery, thus broadening the therapeutic window of these preclinical epigenetic drug candidates.
Collapse
Affiliation(s)
- McKenna C Crawford
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Deepika R Tripu
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Samuel A Barritt
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yihang Jing
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Diamond Gallimore
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Natarajan V Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Ying Xiong
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Kamaria A T Butler
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Nathan P Coussens
- Molecular Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Christian C Dibble
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jordan L Meier
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| |
Collapse
|
15
|
Saxton MN, Morisaki T, Krapf D, Kimura H, Stasevich TJ. Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility. SCIENCE ADVANCES 2023; 9:eadh4819. [PMID: 37792937 PMCID: PMC10550241 DOI: 10.1126/sciadv.adh4819] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Histone acetylation and RNA polymerase II phosphorylation are associated with transcriptionally active chromatin, but their spatiotemporal relationship in live cells remains poorly understood. To address this problem, we combine Fab-based labeling of endogenous protein modifications with single-molecule tracking to quantify the dynamics of chromatin enriched with histone H3 lysine-27 acetylation (H3K27ac) and RNA polymerase II serine-5 phosphorylation (RNAP2-Ser5ph). Our analysis reveals that chromatin enriched with these two modifications is generally separate. In these separated sites, we show that the two modifications are inversely correlated with one another on the minutes time scale and that single nucleosomes within each region display distinct and opposing dynamics on the subsecond time scale. While nucleosomes diffuse ~15% faster in chromatin enriched with H3K27ac, they diffuse ~15% slower in chromatin enriched with RNAP2-Ser5ph. These results argue that high levels of H3K27ac and RNAP2-Ser5ph are not often present together at the same place and time, but rather each marks distinct transcriptionally poised or active sites, respectively.
Collapse
Affiliation(s)
- Matthew N. Saxton
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Diego Krapf
- Department of Electrical and Computer Engineering, and School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Hiroshi Kimura
- Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
- Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
16
|
Nakato R, Sakata T, Wang J, Nagai LAE, Nagaoka Y, Oba GM, Bando M, Shirahige K. Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors. Nat Commun 2023; 14:5647. [PMID: 37726281 PMCID: PMC10509244 DOI: 10.1038/s41467-023-41316-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer-promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. We developed a computational workflow to explore how three-dimensional (3D) structure and gene expression are regulated collectively or individually by cohesin and related factors. The main component is CustardPy, by which multi-omics datasets are compared systematically. To validate our methodology, we generated 3D genome, transcriptome, and epigenome data before and after depletion of cohesin and related factors and compared the effects of depletion. We observed diverse effects on the 3D genome and transcriptome, and gene expression changes were correlated with the splitting of TADs caused by cohesin loss. We also observed variations in long-range interactions across TADs, which correlated with their epigenomic states. These computational tools and datasets will be valuable for 3D genome and epigenome studies.
Collapse
Affiliation(s)
- Ryuichiro Nakato
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan.
| | - Toyonori Sakata
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
- Karolinska Institutet, Department of Biosciences and Nutrition, Biomedicum, Quarter A6, 171 77, Stockholm, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Quarter A6, 171 77, Stockholm, Sweden
| | - Jiankang Wang
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Luis Augusto Eijy Nagai
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
| | - Yuya Nagaoka
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
| | - Gina Miku Oba
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
| | - Masashige Bando
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan.
- Karolinska Institutet, Department of Biosciences and Nutrition, Biomedicum, Quarter A6, 171 77, Stockholm, Sweden.
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Quarter A6, 171 77, Stockholm, Sweden.
| |
Collapse
|
17
|
Zhou S, Zhao F, Zhu D, Zhang Q, Dai Z, Wu Z. Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis. Genome Biol 2023; 24:206. [PMID: 37697420 PMCID: PMC10496290 DOI: 10.1186/s13059-023-03050-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulated remains largely elusive. RESULT Here, we analyze Pol II dynamics at 3' ends by combining comprehensive experiments with mathematical modelling. We generate high-resolution serine 2 phosphorylated (Ser2P) Pol II positioning data specifically enriched at 3' ends and define a 3' end pause index (3'PI). The position but not the extent of the 3' end pause correlates with the termination window size. The 3'PI is not decreased but even mildly increased in the termination deficient mutant xrn3, indicating 3' end pause is a regulatory step early during the termination and before XRN3-mediated RNA decay that releases Pol II. Unexpectedly, 3'PI is closely associated with gene exon numbers and co-transcriptional splicing efficiency. Multiple exons genes often display stronger 3' end pauses and more efficient on-chromatin splicing than genes with fewer exons. Chemical inhibition of splicing strongly reduces the 3'PI and disrupts its correlation with exon numbers but does not globally impact 3' end readthrough levels. These results are further confirmed by fitting Pol II positioning data with a mathematical model, which enables the estimation of parameters that define Pol II dynamics. CONCLUSION Our work highlights that the number of exons via co-transcriptional splicing is a major determinant of Pol II pausing levels at the 3' end of genes in plants.
Collapse
Affiliation(s)
- Sixian Zhou
- Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fengli Zhao
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Danling Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiqi Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ziwei Dai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| |
Collapse
|
18
|
Yamamoto T, Asanuma T, Murakami Y. Polymeric nature of tandemly repeated genes enhances assembly of constitutive heterochromatin in fission yeast. Commun Biol 2023; 6:796. [PMID: 37542144 PMCID: PMC10403545 DOI: 10.1038/s42003-023-05154-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023] Open
Abstract
Motivated by our recent experiments that demonstrate that the tandemly repeated genes become heterochromatin, here we show a theory of heterochromatin assembly by taking into account the connectivity of these genes along the chromatin in the kinetic equations of small RNA production and histone methylation, which are the key biochemical reactions involved in the heterochromatin assembly. Our theory predicts that the polymeric nature of the tandemly repeated genes ensures the steady production of small RNAs because of the stable binding of nascent RNAs produced from the genes to RDRC/Dicers at the surface of nuclear membrane. This theory also predicts that the compaction of the tandemly repeated genes suppresses the production of small RNAs, consistent with our recent experiments. This theory can be extended to the small RNA-dependent gene silencing in higher organisms.
Collapse
Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, 001-0021, Hokkaido, Japan.
| | - Takahiro Asanuma
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan
| | - Yota Murakami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Hokkaido, Japan
| |
Collapse
|
19
|
Mumby S, Perros F, Grynblat J, Manaud G, Papi A, Casolari P, Caramori G, Humbert M, John Wort S, Adcock IM. Differential responses of pulmonary vascular cells from PAH patients and controls to TNFα and the effect of the BET inhibitor JQ1. Respir Res 2023; 24:193. [PMID: 37516840 PMCID: PMC10386603 DOI: 10.1186/s12931-023-02499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) encompasses a group of diseases characterized by raised pulmonary vascular resistance, resulting from vascular remodelling and inflammation. Bromodomain and extra-terminal (BET) proteins are required for the expression of a subset of NF-κB-induced inflammatory genes which can be inhibited by the BET mimic JQ1+. We hypothesised that JQ+ would supress TNFα-driven inflammatory responses in human pulmonary vascular cells from PAH patients. METHODS Immunohistochemical staining of human peripheral lung tissue (N = 14 PAH and N = 12 non-PAH) was performed for the BET proteins BRD2 and 4. Human pulmonary microvascular endothelial cells (HPMEC) and pulmonary artery smooth muscle cells (HPASMC) from PAH patients (N = 4) and non-PAH controls (N = 4) were stimulated with TNFα in presence or absence of JQ1+ or its inactive isomer JQ1-. IL-6 and -8 mRNA was measured by RT-qPCR and protein levels by ELISA. Chromatin immunoprecipitation analysis was performed using EZ-ChIP™ and NF-κB p65 activation determined using a TransAm kit. MTT assay was used to measure cell viability. RESULTS Nuclear staining of BRD2 and BRD4 was significantly (p < 0.0001) increased in the lung vascular endothelial and smooth muscle cells from PAH patients compared to controls with normal lung function. TNFα-driven IL-6 release from both HPMECs and HPASMCs was greater in PAH cells than control cells. Levels of CXCL8/IL-8 protein release was higher in PAH HPASMCs than in control cells with similar release observed in HPMECs. TNFα-induced recruitment of activated NF-κB p65 to the IL-6 and CXCL8/IL-8 promoters were similar in both cell types and between subject groups. JQ1+ suppressed TNFα-induced IL-6 and CXCL8/IL-8 release and mRNA expression to a comparable extent in control and PAH HPMECs and HPASMCs. JQ1 had a greater efficacy on IL-6 release in HPMEC and on CXCL8/IL-8 release in HPASMC. CONCLUSION BET inhibition decreases TNFα driven inflammation in primary pulmonary vascular cells. The anti-inflammatory actions of JQ1 suggests distinct cell-specific regulatory control of these genes. BET proteins could be a target for future therapies for PAH.
Collapse
Affiliation(s)
- Sharon Mumby
- Respiratory Science, NHLI, Imperial College London, London, UK.
| | - Frederic Perros
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon1, Pierre-Bénite, France
| | - Julien Grynblat
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
| | - Gregoire Manaud
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
| | - Alberto Papi
- Interdepartmental Study Center for Inflammatory and Smoke-Related Airway Diseases, Cardiorespiratory and Internal Medicine Section, University of Ferrara, Ferrara, Italy
| | - Paolo Casolari
- Interdepartmental Study Center for Inflammatory and Smoke-Related Airway Diseases, Cardiorespiratory and Internal Medicine Section, University of Ferrara, Ferrara, Italy
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e Delle Immagini Morfologiche e Funzionali (BIOMORF), Università Degli Studi di Messina, Messina, Italy
| | - Marc Humbert
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
- Department of Respiratory and Intensive Care Medicine, AP-HP, Hôpital Bicêtre, Pulmonary Hypertension National Referral Center, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - S John Wort
- Respiratory Science, NHLI, Imperial College London, London, UK
- National Pulmonary Hypertension Service, Royal Brompton Hospital, London, UK
| | - Ian M Adcock
- Respiratory Science, NHLI, Imperial College London, London, UK
| |
Collapse
|
20
|
Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550532. [PMID: 37546819 PMCID: PMC10402067 DOI: 10.1101/2023.07.25.550532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background A great deal of work has revealed in structural detail the components of the machinery responsible for mRNA gene transcription initiation. These include the general transcription factors (GTFs), which assemble at promoters along with RNA Polymerase II (Pol II) to form a preinitiation complex (PIC) aided by the activities of cofactors and site-specific transcription factors (TFs). However, less well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining on a mechanistic level how rates of in vivo RNA synthesis are established and how cofactors and TFs impact them. Results We used competition ChIP to obtain genome-scale estimates of the residence times for five GTFs: TBP, TFIIA, TFIIB, TFIIE and TFIIF in budding yeast. While many GTF-chromatin interactions were short-lived (< 1 min), there were numerous interactions with residence times in the several minutes range. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. Conclusions The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism and therefore offer a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription. The relationships between gene function and GTF dynamics suggest that shared sets of TFs tune PIC assembly kinetics to ensure appropriate levels of expression.
Collapse
Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA 22908
| | - Savera J. Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - Elizabeth A. Hoffman
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| |
Collapse
|
21
|
Chary S, Hayashi R. The absence of core piRNA biogenesis factors does not impact efficient transposon silencing in Drosophila. PLoS Biol 2023; 21:e3002099. [PMID: 37279192 DOI: 10.1371/journal.pbio.3002099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/30/2023] [Indexed: 06/08/2023] Open
Abstract
Organisms require mechanisms to distinguish self and non-self-RNA. This distinction is crucial to initiate the biogenesis of Piwi-interacting RNAs (piRNAs). In Drosophila ovaries, PIWI-guided slicing and the recognition of piRNA precursor transcripts by the DEAD-box RNA helicase Yb are the 2 known mechanisms to licence an RNA for piRNA biogenesis in the germline and the soma, respectively. Both the PIWI proteins and Yb are highly conserved across most Drosophila species and are thought to be essential to the piRNA pathway and for silencing transposons. However, we find that species closely related to Drosophila melanogaster have lost the yb gene, as well as the PIWI gene Ago3. We show that the precursor RNA is still selected in the absence of Yb to abundantly generate transposon antisense piRNAs in the soma. We further demonstrate that Drosophila eugracilis, which lacks Ago3, is completely devoid of ping-pong piRNAs and exclusively produces phased piRNAs in the absence of slicing. Thus, core piRNA pathway genes can be lost in evolution while still maintaining efficient transposon silencing.
Collapse
Affiliation(s)
- Shashank Chary
- John Curtin School of Medical Research, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Rippei Hayashi
- John Curtin School of Medical Research, The Australian National University, Acton, Australian Capital Territory, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Acton, Australian Capital Territory, Australia
| |
Collapse
|
22
|
Crawford MC, Tripu DR, Barritt SA, Jing Y, Gallimore D, Kales SC, Bhanu NV, Xiong Y, Fang Y, Butler KAT, LeClair CA, Coussens NP, Simeonov A, Garcia BA, Dibble CC, Meier JL. Comparative analysis of drug-like EP300/CREBBP acetyltransferase inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540887. [PMID: 37292747 PMCID: PMC10245587 DOI: 10.1101/2023.05.15.540887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The human acetyltransferase paralogs EP300 and CREBBP are master regulators of lysine acetylation whose activity has been implicated in various cancers. In the half-decade since the first drug-like inhibitors of these proteins were reported, three unique molecular scaffolds have taken precedent: an indane spiro-oxazolidinedione (A-485), a spiro-hydantoin (iP300w), and an aminopyridine (CPI-1612). Despite increasing use of these molecules to study lysine acetylation, the dearth of data regarding their relative biochemical and biological potencies makes their application as chemical probes a challenge. To address this gap, here we present a comparative study of drug-like EP300/CREBBP acetyltransferase inhibitors. First, we determine the biochemical and biological potencies of A-485, iP300w, and CPI-1612, highlighting the increased potency of the latter two compounds at physiological acetyl-CoA concentrations. Cellular evaluation shows that inhibition of histone acetylation and cell growth closely aligns with the biochemical potencies of these molecules, consistent with an on-target mechanism. Finally, we demonstrate the utility of comparative pharmacology by using it to investigate the hypothesis that increased CoA synthesis caused by knockout of PANK4 can competitively antagonize binding of EP300/CREBBP inhibitors and demonstrate proof-of-concept photorelease of a potent inhibitor molecule. Overall, our study demonstrates how knowledge of relative inhibitor potency can guide the study of EP300/CREBBP-dependent mechanisms and suggests new approaches to target delivery, thus broadening the therapeutic window of these preclinical epigenetic drug candidates.
Collapse
Affiliation(s)
- McKenna C Crawford
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Deepika R Tripu
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Samuel A Barritt
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yihang Jing
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Diamond Gallimore
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Natarajan V Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ying Xiong
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Kamaria A T Butler
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Nathan P Coussens
- Molecular Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Christian C Dibble
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jordan L Meier
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
23
|
Schade AE, Kuzmickas R, Rodriguez CL, Mattioli K, Enos M, Gardner A, Cichowski K. Combating castration-resistant prostate cancer by co-targeting the epigenetic regulators EZH2 and HDAC. PLoS Biol 2023; 21:e3002038. [PMID: 37104245 PMCID: PMC10138213 DOI: 10.1371/journal.pbio.3002038] [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: 09/10/2021] [Accepted: 02/16/2023] [Indexed: 04/28/2023] Open
Abstract
While screening and early detection have reduced mortality from prostate cancer, castration-resistant disease (CRPC) is still incurable. Here, we report that combined EZH2/HDAC inhibitors potently kill CRPCs and cause dramatic tumor regression in aggressive human and mouse CRPC models. Notably, EZH2 and HDAC both transmit transcriptional repressive signals: regulating histone H3 methylation and histone deacetylation, respectively. Accordingly, we show that suppression of both EZH2 and HDAC are required to derepress/induce a subset of EZH2 targets, by promoting the sequential demethylation and acetylation of histone H3. Moreover, we find that the induction of one of these targets, ATF3, which is a broad stress response gene, is critical for the therapeutic response. Importantly, in human tumors, low ATF3 levels are associated with decreased survival. Moreover, EZH2- and ATF3-mediated transcriptional programs inversely correlate and are most highly/lowly expressed in advanced disease. Together, these studies identify a promising therapeutic strategy for CRPC and suggest that these two major epigenetic regulators buffer prostate cancers from a lethal response to cellular stresses, thereby conferring a tractable therapeutic vulnerability.
Collapse
Affiliation(s)
- Amy E. Schade
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ryan Kuzmickas
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Carrie L. Rodriguez
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kaia Mattioli
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Miriam Enos
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alycia Gardner
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Karen Cichowski
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
24
|
Tanaka M, Harada H, Kimura H. The role of H3K9me3 in oral squamous cell carcinoma. Biochem Biophys Res Commun 2023; 640:56-63. [PMID: 36502632 DOI: 10.1016/j.bbrc.2022.11.102] [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: 11/20/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Carcinogenesis is often associated with alteration of epigenetic marks, including histone modifications. The global level and local distribution of specific histone modifications have been revealed to be prognostic factors in many cancers. However, the functional roles of histone modifications in oral squamous cell carcinoma (OSCC) remain unclear. This study investigates the levels of various histone modifications in 6 types of OSCC cell lines. We found that the level of H3K9me3 was significantly high in metastatic cell lines. In addition, the loss of H3K9me3 by SUV39H1 and SUV39H2 knockdown suppressed cell proliferation and cell migration. Our results indicate that a high level of H3K9me3 could be a marker of metastasis and possibly a therapeutic target for OSCC treatment.
Collapse
Affiliation(s)
- Misako Tanaka
- Department of Oral and Maxillofacial Surgical Oncology, Division of Oral Health Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8510, Japan; School of Life Science and Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroyuki Harada
- Department of Oral and Maxillofacial Surgical Oncology, Division of Oral Health Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8510, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| |
Collapse
|
25
|
Kuznetsova K, Chabot NM, Ugolini M, Wu E, Lalit M, Oda H, Sato Y, Kimura H, Jug F, Vastenhouw NL. Nanog organizes transcription bodies. Curr Biol 2023; 33:164-173.e5. [PMID: 36476751 DOI: 10.1016/j.cub.2022.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/21/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells.1-3 How proteins of the transcriptional machinery come together to form such bodies, however, is unclear. Here, we take advantage of two large, isolated, and long-lived transcription bodies that reproducibly form during early zebrafish embryogenesis to characterize the dynamics of transcription body formation. Once formed, these transcription bodies are enriched for initiating and elongating RNA polymerase II, as well as the transcription factors Nanog and Sox19b. Analyzing the events leading up to transcription, we find that Nanog and Sox19b cluster prior to transcription. The clustering of transcription factors is sequential; Nanog clusters first, and this is required for the clustering of Sox19b and the initiation of transcription. Mutant analysis revealed that both the DNA-binding domain as well as one of the two intrinsically disordered regions of Nanog are required to organize the two bodies of transcriptional activity. Taken together, our data suggest that the clustering of transcription factors dictates the formation of transcription bodies.
Collapse
Affiliation(s)
- Ksenia Kuznetsova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Noémie M Chabot
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Martino Ugolini
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Edlyn Wu
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Manan Lalit
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Florian Jug
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Fondazione Human Technopole, Viale Rita Levi-Montalcini 1, Area MIND, 20157 Milano, Italy
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland.
| |
Collapse
|
26
|
Ohishi H, Shimada S, Uchino S, Li J, Sato Y, Shintani M, Owada H, Ohkawa Y, Pertsinidis A, Yamamoto T, Kimura H, Ochiai H. STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity. Nat Commun 2022; 13:7672. [PMID: 36539402 PMCID: PMC9768169 DOI: 10.1038/s41467-022-35286-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Transcription is a dynamic process. To detect the dynamic relationship among protein clusters of RNA polymerase II and coactivators, gene loci, and transcriptional activity, we insert an MS2 repeat, a TetO repeat, and inteins with a selection marker just downstream of the transcription start site. By optimizing the individual elements, we develop the Spliced TetO REpeAt, MS2 repeat, and INtein sandwiched reporter Gene tag (STREAMING-tag) system. Clusters of RNA polymerase II and BRD4 are observed proximal to the transcription start site of Nanog when the gene is transcribed in mouse embryonic stem cells. In contrast, clusters of MED19 and MED22 tend to be located near the transcription start site, even without transcription activity. Thus, the STREAMING-tag system reveals the spatiotemporal relationships between transcriptional activity and protein clusters near the gene. This powerful tool is useful for quantitatively understanding transcriptional regulation in living cells.
Collapse
Affiliation(s)
- Hiroaki Ohishi
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Seiru Shimada
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Satoshi Uchino
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Jieru Li
- grid.51462.340000 0001 2171 9952Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Yuko Sato
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan ,grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Manabu Shintani
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Hitoshi Owada
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Yasuyuki Ohkawa
- grid.177174.30000 0001 2242 4849Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan
| | - Alexandros Pertsinidis
- grid.51462.340000 0001 2171 9952Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Takashi Yamamoto
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Hiroshi Kimura
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan ,grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Hiroshi Ochiai
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| |
Collapse
|
27
|
Tsirkas I, Zur T, Dovrat D, Cohen A, Ravkaie L, Aharoni A. Protein fluorescent labeling in live yeast cells using scFv-based probes. CELL REPORTS METHODS 2022; 2:100357. [PMID: 36590693 PMCID: PMC9795370 DOI: 10.1016/j.crmeth.2022.100357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/19/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022]
Abstract
The fusion of fluorescent proteins (FPs) to endogenous proteins is a widespread approach for microscopic examination of protein function, expression, and localization in the cell. However, proteins that are sensitive to FP fusion or expressed at low levels are difficult to monitor using this approach. Here, we develop a single-chain fragment variable (scFv)-FP approach to efficiently label Saccharomyces cerevisiae proteins that are tagged with repeats of hemagglutinin (HA)-tag sequences. We demonstrate the successful labeling of DNA-binding proteins and proteins localized to different cellular organelles including the nuclear membrane, peroxisome, Golgi apparatus, and mitochondria. This approach can lead to a significant increase in fluorescence intensity of the labeled protein, allows C'-terminal labeling of difficult-to-tag proteins and increased detection sensitivity of DNA-damage foci. Overall, the development of a scFv-FP labeling approach in yeast provides a general and simple tool for the function and localization analysis of the yeast proteome.
Collapse
Affiliation(s)
- Ioannis Tsirkas
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Tomer Zur
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Amit Cohen
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Lior Ravkaie
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| |
Collapse
|
28
|
Takeuchi C, Yokoshi M, Kondo S, Shibuya A, Saito K, Fukaya T, Siomi H, Iwasaki Y. Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers. Nucleic Acids Res 2022; 50:11580-11599. [PMID: 36373634 PMCID: PMC9723646 DOI: 10.1093/nar/gkac1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/17/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
Telomeres in Drosophila are composed of sequential non-LTR retrotransposons HeT-A, TART and TAHRE. Although they are repressed by the PIWI-piRNA pathway or heterochromatin in the germline, the regulation of these retrotransposons in somatic cells is poorly understood. In this study, we demonstrated that specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells. Among the variants, we found that the Mod(mdg4)-N variant represses HeT-A expression the most efficiently. Subtelomeric sequences bound by Mod(mdg4)-N block enhancer activity within subtelomeric TAS-R repeats. This enhancer-blocking activity is increased by the tandem association of Mod(mdg4)-N to repetitive subtelomeric sequences. In addition, the association of Mod(mdg4)-N couples with the recruitment of RNA polymerase II to the subtelomeres, which reinforces its enhancer-blocking function. Our findings provide novel insights into how telomeric retrotransposons are regulated by the specific variants of insulator proteins associated with subtelomeric sequences.
Collapse
Affiliation(s)
- Chikara Takeuchi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Moe Yokoshi
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Shu Kondo
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka 411-8540, Japan
| | - Aoi Shibuya
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kuniaki Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka 411-8540, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | | | - Yuka W Iwasaki
- To whom correspondence should be addressed. Tel: +81 3 5363 3529; Fax: +81 3 5363 3266;
| |
Collapse
|
29
|
Stepanov AI, Besedovskaia ZV, Moshareva MA, Lukyanov KA, Putlyaeva LV. Studying Chromatin Epigenetics with Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms23168988. [PMID: 36012253 PMCID: PMC9409072 DOI: 10.3390/ijms23168988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Epigenetic modifications of histones (methylation, acetylation, phosphorylation, etc.) are of great importance in determining the functional state of chromatin. Changes in epigenome underlay all basic biological processes, such as cell division, differentiation, aging, and cancerous transformation. Post-translational histone modifications are mainly studied by immunoprecipitation with high-throughput sequencing (ChIP-Seq). It enables an accurate profiling of target modifications along the genome, but suffers from the high cost of analysis and the inability to work with living cells. Fluorescence microscopy represents an attractive complementary approach to characterize epigenetics. It can be applied to both live and fixed cells, easily compatible with high-throughput screening, and provide access to rich spatial information down to the single cell level. In this review, we discuss various fluorescent probes for histone modification detection. Various types of live-cell imaging epigenetic sensors suitable for conventional as well as super-resolution fluorescence microscopy are described. We also focus on problems and future perspectives in the development of fluorescent probes for epigenetics.
Collapse
Affiliation(s)
- Afanasii I. Stepanov
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
| | - Zlata V. Besedovskaia
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
| | - Maria A. Moshareva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklay St. 16/10, 117997 Moscow, Russia
| | - Konstantin A. Lukyanov
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
- Correspondence: (K.A.L.); (L.V.P.)
| | - Lidia V. Putlyaeva
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
- Correspondence: (K.A.L.); (L.V.P.)
| |
Collapse
|
30
|
Wichmann J, Pitt C, Eccles S, Garnham AL, Li-Wai-Suen CSN, May R, Allan E, Wilcox S, Herold MJ, Smyth GK, Monahan BJ, Thomas T, Voss AK. Loss of TIP60 (KAT5) abolishes H2AZ lysine 7 acetylation and causes p53, INK4A, and ARF-independent cell cycle arrest. Cell Death Dis 2022; 13:627. [PMID: 35853868 PMCID: PMC9296491 DOI: 10.1038/s41419-022-05055-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/24/2022] [Accepted: 06/30/2022] [Indexed: 01/21/2023]
Abstract
Histone acetylation is essential for initiating and maintaining a permissive chromatin conformation and gene transcription. Dysregulation of histone acetylation can contribute to tumorigenesis and metastasis. Using inducible cre-recombinase and CRISPR/Cas9-mediated deletion, we investigated the roles of the histone lysine acetyltransferase TIP60 (KAT5/HTATIP) in human cells, mouse cells, and mouse embryos. We found that loss of TIP60 caused complete cell growth arrest. In the absence of TIP60, chromosomes failed to align in a metaphase plate during mitosis. In some TIP60 deleted cells, endoreplication occurred instead. In contrast, cell survival was not affected. Remarkably, the cell growth arrest caused by loss of TIP60 was independent of the tumor suppressors p53, INK4A and ARF. TIP60 was found to be essential for the acetylation of H2AZ, specifically at lysine 7. The mRNA levels of 6236 human and 8238 mouse genes, including many metabolism genes, were dependent on TIP60. Among the top 50 differentially expressed genes, over 90% were downregulated in cells lacking TIP60, supporting a role for TIP60 as a key co-activator of transcription. We propose a primary role of TIP60 in H2AZ lysine 7 acetylation and transcriptional activation, and that this fundamental role is essential for cell proliferation. Growth arrest independent of major tumor suppressors suggests TIP60 as a potential anti-cancer drug target.
Collapse
Affiliation(s)
- Johannes Wichmann
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Catherine Pitt
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Samantha Eccles
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia
| | - Alexandra L. Garnham
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Connie S. N. Li-Wai-Suen
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Rose May
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia
| | - Elizabeth Allan
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,Cancer Therapeutics CRC, Parkville, VIC Australia
| | - Stephen Wilcox
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia
| | - Marco J. Herold
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Gordon K. Smyth
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSchool of Mathematics and Statistics, University of Melbourne, Parkville, VIC Australia
| | - Brendon J. Monahan
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia ,Cancer Therapeutics CRC, Parkville, VIC Australia
| | - Tim Thomas
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Anne K. Voss
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| |
Collapse
|
31
|
Wang J, Bando M, Shirahige K, Nakato R. Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation. Nat Commun 2022; 13:3218. [PMID: 35680859 PMCID: PMC9184728 DOI: 10.1038/s41467-022-30792-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 05/14/2022] [Indexed: 12/19/2022] Open
Abstract
Cohesin, an essential protein complex for chromosome segregation, regulates transcription through a variety of mechanisms. It is not a trivial task to assign diverse cohesin functions. Moreover, the context-specific roles of cohesin-mediated interactions, especially on intragenic regions, have not been thoroughly investigated. Here we perform a comprehensive characterization of cohesin binding sites in several human cell types. We integrate epigenomic, transcriptomic and chromatin interaction data to explore the context-specific functions of intragenic cohesin related to gene activation. We identify a specific subset of cohesin binding sites, decreased intragenic cohesin sites (DICs), which are negatively correlated with transcriptional regulation. A subgroup of DICs is enriched with enhancer markers and RNA polymerase II, while the others are more correlated to chromatin architecture. DICs are observed in various cell types, including cells from patients with cohesinopathy. We also implement machine learning to our data and identified genomic features for isolating DICs from all cohesin sites. These results suggest a previously unidentified function of cohesin on intragenic regions for transcriptional regulation.
Collapse
Affiliation(s)
- Jiankang Wang
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashige Bando
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
32
|
Hajiabadi H, Mamontova I, Prizak R, Pancholi A, Koziolek A, Hilbert L. Deep-learning microscopy image reconstruction with quality control reveals second-scale rearrangements in RNA polymerase II clusters. PNAS NEXUS 2022; 1:pgac065. [PMID: 36741438 PMCID: PMC9896941 DOI: 10.1093/pnasnexus/pgac065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023]
Abstract
Fluorescence microscopy, a central tool of biological research, is subject to inherent trade-offs in experiment design. For instance, image acquisition speed can only be increased in exchange for a lowered signal quality, or for an increased rate of photo-damage to the specimen. Computational denoising can recover some loss of signal, extending the trade-off margin for high-speed imaging. Recently proposed denoising on the basis of neural networks shows exceptional performance but raises concerns of errors typical of neural networks. Here, we present a work-flow that supports an empirically optimized reduction of exposure times, as well as per-image quality control to exclude images with reconstruction errors. We implement this work-flow on the basis of the denoising tool Noise2Void and assess the molecular state and 3D shape of RNA polymerase II (Pol II) clusters in live zebrafish embryos. Image acquisition speed could be tripled, achieving 2-s time resolution and 350-nm lateral image resolution. The obtained data reveal stereotyped events of approximately 10 s duration: initially, the molecular mark for recruited Pol II increases, then the mark for active Pol II increases, and finally Pol II clusters take on a stretched and unfolded shape. An independent analysis based on fixed sample images reproduces this sequence of events, and suggests that they are related to the transient association of genes with Pol II clusters. Our work-flow consists of procedures that can be implemented on commercial fluorescence microscopes without any hardware or software modification, and should, therefore, be transferable to many other applications.
Collapse
Affiliation(s)
| | | | - Roshan Prizak
- Institute of Biological and Chemical Systems, Department of Biological Information Processing, Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Agnieszka Pancholi
- Institute of Biological and Chemical Systems, Department of Biological Information Processing, Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | | | | |
Collapse
|
33
|
Kuehner F, Stubenrauch F. Functions of Papillomavirus E8^E2 Proteins in Tissue Culture and In Vivo. Viruses 2022; 14:v14050953. [PMID: 35632695 PMCID: PMC9143700 DOI: 10.3390/v14050953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 12/04/2022] Open
Abstract
Papillomaviruses (PV) replicate in undifferentiated keratinocytes at low levels and to high levels in differentiated cells. The restricted replication in undifferentiated cells is mainly due to the expression of the conserved viral E8^E2 repressor protein, a fusion protein consisting of E8 and the hinge, DNA-binding, and dimerization domain of E2. E8^E2 binds to viral genomes and represses viral transcription and genome replication by recruiting cellular NCoR/SMRT-HDAC3 corepressor complexes. Tissue culture experiments have revealed that E8^E2 modulates long-term maintenance of extrachromosomal genomes, productive replication, and immortalization properties in a virus type-dependent manner. Furthermore, in vivo experiments have indicated that Mus musculus PV1 E8^E2 is required for tumor formation in immune-deficient mice. In summary, E8^E2 is a crucial inhibitor whose levels might determine the outcome of PV infections.
Collapse
|
34
|
Nissani N, Ulitsky I. Unique features of transcription termination and initiation at closely spaced tandem human genes. Mol Syst Biol 2022; 18:e10682. [PMID: 35362230 PMCID: PMC8972054 DOI: 10.15252/msb.202110682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/09/2022] Open
Abstract
The synthesis of RNA polymerase II (Pol2) products, which include messenger RNAs or long noncoding RNAs, culminates in transcription termination. How the transcriptional termination of a gene impacts the activity of promoters found immediately downstream of it, and which can be subject to potential transcriptional interference, remains largely unknown. We examined in an unbiased manner the features of the intergenic regions between pairs of 'tandem genes'-closely spaced (< 2 kb) human genes found on the same strand. Intergenic regions separating tandem genes are enriched with guanines and are characterized by binding of several proteins, including AGO1 and AGO2 of the RNA interference pathway. Additionally, we found that Pol2 is particularly enriched in this region, and it is lost upon perturbations affecting splicing or transcriptional elongation. Perturbations of genes involved in Pol2 pausing and R loop biology preferentially affect expression of downstream genes in tandem gene pairs. Overall, we find that features associated with Pol2 pausing and accumulation rather than those associated with avoidance of transcriptional interference are the predominant driving force shaping short tandem intergenic regions.
Collapse
Affiliation(s)
- Noa Nissani
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
35
|
Mori L, Valente ST. Cure and Long-Term Remission Strategies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2407:391-428. [PMID: 34985678 DOI: 10.1007/978-1-0716-1871-4_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The majority of virally suppressed individuals will experience rapid viral rebound upon antiretroviral therapy (ART) interruption, providing a strong rationale for the development of cure strategies. Moreover, despite ART virological control, HIV infection is still associated with chronic immune activation, inflammation, comorbidities, and accelerated aging. These effects are believed to be due, in part, to low-grade persistent transcription and trickling production of viral proteins from the pool of latent proviruses constituting the viral reservoir. In recent years there has been an increasing interest in developing what has been termed a functional cure for HIV. This approach entails the long-term, durable control of viral expression in the absence of therapy, preventing disease progression and transmission, despite the presence of detectable integrated proviruses. One such strategy, the block-and-lock approach for a functional cure, proposes the epigenetic silencing of proviral expression, locking the virus in a profound latent state, from which reactivation is very unlikely. The proof-of-concept for this approach was demonstrated with the use of a specific small molecule targeting HIV transcription. Here we review the principles behind the block-and-lock approach and some of the additional strategies proposed to silence HIV expression.
Collapse
Affiliation(s)
- Luisa Mori
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
| |
Collapse
|
36
|
Mann G, Sadhu P, Brik A. Multiplexed Delivery of Synthetic (Un)Conjugatable Ubiquitin and SUMO2 Enables Simultaneous Monitoring of their Localization and Function in Live Cells. Chembiochem 2022; 23:e202200122. [PMID: 35235714 PMCID: PMC9401080 DOI: 10.1002/cbic.202200122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Indexed: 11/17/2022]
Abstract
Ubiquitin (Ub) and its related small Ub like modifier (SUMO) are among the most influential protein post‐translational modifications in eukaryotes. Unfortunately, visualizing these modifications in live cells is a challenging task. Chemical protein synthesis offers great opportunities in studying and further understanding Ub and SUMO biology. Nevertheless, the low cell permeability of proteins limits these studies mainly for in vitro applications. Here, we introduce a multiplexed protein cell delivery approach, termed MBL (multiplexed bead loading), for simultaneous loading of up to four differentially labeled proteins with organic fluorophores. We applied MBL to visualize ubiquitination and SUMOylation events in live and untransfected cells without fluorescent protein tags or perturbation to their endogenous levels. Our study reveals unprecedented involvements of Ub and SUMO2 in lysosomes depending on conjugation states. We envision that this approach will improve our understanding of dynamic cellular processes such as formation and disassembly of membraneless organelles.
Collapse
Affiliation(s)
- Guy Mann
- Technion Israel Institute of Technology, Schulich faculty of chemistry, ISRAEL
| | - Pradeep Sadhu
- Technion Israel Institute of Technology, Schulich faculty of chemistry, ISRAEL
| | - Ashraf Brik
- Technion-Israel Institue of Technology, Schulich Faculty of chemistry, Technion City, 32000, Haifa, ISRAEL
| |
Collapse
|
37
|
Suraritdechachai S, Lakkanasirorat B, Uttamapinant C. Molecular probes for cellular imaging of post-translational proteoforms. RSC Chem Biol 2022; 3:201-219. [PMID: 35360891 PMCID: PMC8826509 DOI: 10.1039/d1cb00190f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However, it is not trivial to visualize post-translational modifications in a protein- and site-specific manner, especially in a living-cell context. Herein, we review recent advances in the development of molecular imaging tools to detect diverse classes of post-translational proteoforms in individual cells, and their applications in studying precise roles of PTMs in regulating the function of cellular proteins.
Collapse
Affiliation(s)
- Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Benya Lakkanasirorat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| |
Collapse
|
38
|
Uchino S, Ito Y, Sato Y, Handa T, Ohkawa Y, Tokunaga M, Kimura H. Live imaging of transcription sites using an elongating RNA polymerase II-specific probe. J Cell Biol 2022; 221:212888. [PMID: 34854870 PMCID: PMC8647360 DOI: 10.1083/jcb.202104134] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/12/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In eukaryotic nuclei, most genes are transcribed by RNA polymerase II (RNAP2), whose regulation is a key to understanding the genome and cell function. RNAP2 has a long heptapeptide repeat (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), and Ser2 is phosphorylated on an elongation form. To detect RNAP2 Ser2 phosphorylation (RNAP2 Ser2ph) in living cells, we developed a genetically encoded modification-specific intracellular antibody (mintbody) probe. The RNAP2 Ser2ph-mintbody exhibited numerous foci, possibly representing transcription “factories,” and foci were diminished during mitosis and in a Ser2 kinase inhibitor. An in vitro binding assay using phosphopeptides confirmed the mintbody’s specificity. RNAP2 Ser2ph-mintbody foci were colocalized with proteins associated with elongating RNAP2 compared with factors involved in the initiation. These results support the view that mintbody localization represents the sites of RNAP2 Ser2ph in living cells. RNAP2 Ser2ph-mintbody foci showed constrained diffusional motion like chromatin, but they were more mobile than DNA replication domains and p300-enriched foci, suggesting that the elongating RNAP2 complexes are separated from more confined chromatin domains.
Collapse
Affiliation(s)
- Satoshi Uchino
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
39
|
Kimura H, Sato Y. Imaging transcription elongation dynamics by new technologies unveils the organization of initiation and elongation in transcription factories. Curr Opin Cell Biol 2022; 74:71-79. [DOI: 10.1016/j.ceb.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 11/27/2022]
|
40
|
Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 256] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
Collapse
Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
| |
Collapse
|
41
|
Li M, Qiu C, Bian Y, Shi D, Wang B, Ma Q, Wang X, Shi J, Zhang L, Ma Y, Zhu P, Cheng T, Chu Y, Yuan W. SETD5 modulates homeostasis of hematopoietic stem cells by mediating RNA Polymerase II pausing in cooperation with HCF-1. Leukemia 2022; 36:1111-1122. [PMID: 34853439 PMCID: PMC8979820 DOI: 10.1038/s41375-021-01481-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 12/23/2022]
Abstract
SETD5 mutations were identified as the genetic causes of neurodevelopmental disorders. While the whole-body knockout of Setd5 in mice leads to embryonic lethality, the role of SETD5 in adult stem cell remains unexplored. Here, a critical role of Setd5 in hematopoietic stem cells (HSCs) is identified. Specific deletion of Setd5 in hematopoietic system significantly increased the number of immunophenotypic HSCs by promoting HSC proliferation. Setd5-deficient HSCs exhibited impaired long-term self-renewal capacity and multiple-lineage differentiation potentials under transplantation pressure. Transcriptome analysis of Setd5-deficient HSCs revealed a disruption of quiescence state of long-term HSCs, a cause of the exhaustion of functional HSCs. Mechanistically, SETD5 was shown to regulate HSC quiescence by mediating the release of promoter-proximal paused RNA polymerase II (Pol II) on E2F targets in cooperation with HCF-1 and PAF1 complex. Taken together, these findings reveal an essential role of SETD5 in regulating Pol II pausing-mediated maintenance of adult stem cells.
Collapse
Affiliation(s)
- Mengke Li
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Chen Qiu
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yujie Bian
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Deyang Shi
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Bichen Wang
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Qiuyi Ma
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiaomin Wang
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jun Shi
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Lianfeng Zhang
- grid.506261.60000 0001 0706 7839Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Yuanwu Ma
- grid.506261.60000 0001 0706 7839Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Ping Zhu
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Tao Cheng
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yajing Chu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| |
Collapse
|
42
|
DeLuca KF, Mick JE, Ide AH, Lima WC, Sherman L, Schaller KL, Anderson SM, Zhao N, Stasevich TJ, Varma D, Nilsson J, DeLuca JG. Generation and diversification of recombinant monoclonal antibodies. eLife 2021; 10:72093. [PMID: 34970967 PMCID: PMC8763395 DOI: 10.7554/elife.72093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Antibodies are indispensable tools used for a large number of applications in both foundational and translational bioscience research; however, there are drawbacks to using traditional antibodies generated in animals. These include a lack of standardization leading to problems with reproducibility, high costs of antibodies purchased from commercial sources, and ethical concerns regarding the large number of animals used to generate antibodies. To address these issues, we have developed practical methodologies and tools for generating low-cost, high-yield preparations of recombinant monoclonal antibodies and antibody fragments directed to protein epitopes from primary sequences. We describe these methods here, as well as approaches to diversify monoclonal antibodies, including customization of antibody species specificity, generation of genetically encoded small antibody fragments, and conversion of single chain antibody fragments (e.g. scFv) into full-length, bivalent antibodies. This study focuses on antibodies directed to epitopes important for mitosis and kinetochore function; however, the methods and reagents described here are applicable to antibodies and antibody fragments for use in any field.
Collapse
Affiliation(s)
- Keith F DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Jeanne E Mick
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Amy Hodges Ide
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Wanessa C Lima
- Geneva Antibody Facility, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Lori Sherman
- CU Cancer Center Cell Technologies Shared Resource, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Kristin L Schaller
- Department of Pediatric Hematology, Oncology and Bone Marrow Transplant, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Steven M Anderson
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Dileep Varma
- Department of Cell and Developmental Biology, Northwestern University, Chicago, United States
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Germany
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| |
Collapse
|
43
|
Changes in chromatin accessibility landscape and histone H3 core acetylation during valproic acid-induced differentiation of embryonic stem cells. Epigenetics Chromatin 2021; 14:58. [PMID: 34955095 PMCID: PMC8711205 DOI: 10.1186/s13072-021-00432-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/17/2021] [Indexed: 11/27/2022] Open
Abstract
Directed differentiation of mouse embryonic stem cells (mESCs) or induced pluripotent stem cells (iPSCs) provides powerful models to dissect the molecular mechanisms leading to the formation of specific cell lineages. Treatment with histone deacetylase inhibitors can significantly enhance the efficiency of directed differentiation. However, the mechanisms are not well understood. Here, we use CUT&RUN in combination with ATAC-seq to determine changes in both histone modifications and genome-wide chromatin accessibility following valproic acid (VPA) exposure. VPA induced a significant increase in global histone H3 acetylation (H3K56ac), a core histone modification affecting nucleosome stability, as well as enrichment at loci associated with cytoskeletal organization and cellular morphogenesis. In addition, VPA altered the levels of linker histone H1 subtypes and the total histone H1/nucleosome ratio indicative of initial differentiation events. Notably, ATAC-seq analysis revealed changes in chromatin accessibility of genes involved in regulation of CDK serine/threonine kinase activity and DNA duplex unwinding. Importantly, changes in chromatin accessibility were evident at several key genomic loci, such as the pluripotency factor Lefty, cardiac muscle troponin Tnnt2, and the homeodomain factor Hopx, which play critical roles in cardiomyocyte differentiation. Massive parallel transcription factor (TF) footprinting also indicates an increased occupancy of TFs involved in differentiation toward mesoderm and endoderm lineages and a loss of footprints of POU5F1/SOX2 pluripotency factors following VPA treatment. Our results provide the first genome-wide analysis of the chromatin landscape following VPA-induced differentiation in mESCs and provide new mechanistic insight into the intricate molecular processes that govern departure from pluripotency and early lineage commitment.
Collapse
|
44
|
Biswas J, Li W, Singer RH, Coleman RA. Imaging Organization of RNA Processing within the Nucleus. Cold Spring Harb Perspect Biol 2021; 13:a039453. [PMID: 34127450 PMCID: PMC8635003 DOI: 10.1101/cshperspect.a039453] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Within the nucleus, messenger RNA is generated and processed in a highly organized and regulated manner. Messenger RNA processing begins during transcription initiation and continues until the RNA is translated and degraded. Processes such as 5' capping, alternative splicing, and 3' end processing have been studied extensively with biochemical methods and more recently with single-molecule imaging approaches. In this review, we highlight how imaging has helped understand the highly dynamic process of RNA processing. We conclude with open questions and new technological developments that may further our understanding of RNA processing.
Collapse
Affiliation(s)
- Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Weihan Li
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Robert A Coleman
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| |
Collapse
|
45
|
Maehara K, Tomimatsu K, Harada A, Tanaka K, Sato S, Fukuoka M, Okada S, Handa T, Kurumizaka H, Saitoh N, Kimura H, Ohkawa Y. Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections. Mol Syst Biol 2021; 17:e10323. [PMID: 34730297 PMCID: PMC8564819 DOI: 10.15252/msb.202110323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 11/25/2022] Open
Abstract
Recent advances in genome‐wide technologies have enabled analyses using small cell numbers of even single cells. However, obtaining tissue epigenomes with cell‐type resolution from large organs and tissues still remains challenging, especially when the available material is limited. Here, we present a ChIL‐based approach for analyzing the diverse cellular dynamics at the tissue level using high‐depth epigenomic data. “ChIL for tissues” allows the analysis of a single tissue section and can reproducibly generate epigenomic profiles from several tissue types, based on the distribution of target epigenomic states, tissue morphology, and number of cells. The proposed method enabled the independent evaluation of changes in cell populations and gene activation in cells from regenerating skeletal muscle tissues, using a statistical model of RNA polymerase II distribution on gene loci. Thus, the integrative analyses performed using ChIL can elucidate in vivo cell‐type dynamics of tissues.
Collapse
Affiliation(s)
- Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kosuke Tomimatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Shoko Sato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Megumi Fukuoka
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiji Okada
- Division of Pathophysiology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| |
Collapse
|
46
|
Abstract
To predict transcription, one needs a mechanistic understanding of how the numerous required transcription factors (TFs) explore the nuclear space to find their target genes, assemble, cooperate, and compete with one another. Advances in fluorescence microscopy have made it possible to visualize real-time TF dynamics in living cells, leading to two intriguing observations: first, most TFs contact chromatin only transiently; and second, TFs can assemble into clusters through their intrinsically disordered regions. These findings suggest that highly dynamic events and spatially structured nuclear microenvironments might play key roles in transcription regulation that are not yet fully understood. The emerging model is that while some promoters directly convert TF-binding events into on/off cycles of transcription, many others apply complex regulatory layers that ultimately lead to diverse phenotypic outputs. Cracking this kinetic code is an ongoing and challenging task that is made possible by combining innovative imaging approaches with biophysical models.
Collapse
Affiliation(s)
- Feiyue Lu
- Institute for Systems Genetics and Cell Biology Department, NYU School of Medicine, New York, New York 10016, USA
| | - Timothée Lionnet
- Institute for Systems Genetics and Cell Biology Department, NYU School of Medicine, New York, New York 10016, USA
| |
Collapse
|
47
|
Zhang J, Cavallaro M, Hebenstreit D. Timing RNA polymerase pausing with TV-PRO-seq. CELL REPORTS METHODS 2021; 1:None. [PMID: 34723238 PMCID: PMC8547241 DOI: 10.1016/j.crmeth.2021.100083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/03/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022]
Abstract
Transcription of many genes in metazoans is subject to polymerase pausing, which is the transient stop of transcriptionally engaged polymerases. This is known to mainly occur in promoter-proximal regions but it is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking. We present here the time-variant precision nuclear run-on and sequencing (TV-PRO-seq) assay, an extension of the standard PRO-seq that allows us to estimate genome-wide pausing times at single-base resolution. Its application to human cells demonstrates that, proximal to promoters, polymerases pause more frequently but for shorter times than in other genomic regions. Comparison with single-cell gene expression data reveals that the polymerase pausing times are longer in highly expressed genes, while transcriptionally noisier genes have higher pausing frequencies and slightly longer pausing times. Analyses of histone modifications suggest that the marker H3K36me3 is related to the polymerase pausing.
Collapse
Affiliation(s)
- Jie Zhang
- School of Life Sciences, Gibbet Hill Campus, the University of Warwick, CV4 7AL Coventry, UK
| | - Massimo Cavallaro
- School of Life Sciences, Gibbet Hill Campus, the University of Warwick, CV4 7AL Coventry, UK
- Mathematics Institute and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, the University of Warwick, CV4 7AL Coventry, UK
| | - Daniel Hebenstreit
- School of Life Sciences, Gibbet Hill Campus, the University of Warwick, CV4 7AL Coventry, UK
| |
Collapse
|
48
|
Pancholi A, Klingberg T, Zhang W, Prizak R, Mamontova I, Noa A, Sobucki M, Kobitski AY, Nienhaus GU, Zaburdaev V, Hilbert L. RNA polymerase II clusters form in line with surface condensation on regulatory chromatin. Mol Syst Biol 2021; 17:e10272. [PMID: 34569155 PMCID: PMC8474054 DOI: 10.15252/msb.202110272] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/26/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state, and subsequent pause release toward transcription. Pol II recruitment and pause release occur in association with macromolecular clusters, which were proposed to be formed by a liquid-liquid phase separation mechanism. How such a phase separation mechanism relates to the interaction of Pol II with DNA during recruitment and transcription, however, remains poorly understood. Here, we use live and super-resolution microscopy in zebrafish embryos to reveal Pol II clusters with a large variety of shapes, which can be explained by a theoretical model in which regulatory chromatin regions provide surfaces for liquid-phase condensation at concentrations that are too low for canonical liquid-liquid phase separation. Model simulations and chemical perturbation experiments indicate that recruited Pol II contributes to the formation of these surface-associated condensates, whereas elongating Pol II is excluded from these condensates and thereby drives their unfolding.
Collapse
Affiliation(s)
- Agnieszka Pancholi
- Zoological InstituteDepartment of Systems Biology and BioinformaticsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Tim Klingberg
- Department of BiologyFriedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
| | - Weichun Zhang
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Roshan Prizak
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Irina Mamontova
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Amra Noa
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Marcel Sobucki
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Andrei Yu Kobitski
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Gerd Ulrich Nienhaus
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
- Department of PhysicsUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Vasily Zaburdaev
- Department of BiologyFriedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
| | - Lennart Hilbert
- Zoological InstituteDepartment of Systems Biology and BioinformaticsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| |
Collapse
|
49
|
Yue L, Li C, Xu M, Wu M, Ding J, Liu J, Zhang X, Yuan Z. Probing the spatiotemporal patterns of HBV multiplication reveals novel features of its subcellular processes. PLoS Pathog 2021; 17:e1009838. [PMID: 34370796 PMCID: PMC8376071 DOI: 10.1371/journal.ppat.1009838] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/19/2021] [Accepted: 07/25/2021] [Indexed: 02/06/2023] Open
Abstract
Through evolution, Hepatitis B Virus (HBV) developed highly intricate mechanisms exploiting host resources for its multiplication within a constrained genetic coding capacity. Yet a clear picture of viral hitchhiking of cellular processes with spatial resolution is still largely unsolved. Here, by leveraging bDNA-based fluorescence in situ hybridization (FISH) combined with immunofluorescence, we developed a microscopic approach for multiplex detection of viral nucleic acids and proteins, which enabled us to probe some of the key aspects of HBV life cycle. We confirmed the slow kinetics and revealed the high variability of viral replication at single-cell level. We directly visualized HBV minichromosome in contact with acetylated histone 3 and RNA polymerase II and observed HBV-induced degradation of Smc5/6 complex only in primary hepatocytes. We quantified the frequency of HBV pregenomic RNAs occupied by translating ribosome or capsids. Statistics at molecular level suggested a rapid translation phase followed by a slow encapsidation and maturation phase. Finally, the roles of microtubules (MTs) on nucleocapsid assembly and virion morphogenesis were analyzed. Disruption of MTs resulted in the perinuclear retention of nucleocapsid. Meanwhile, large multivesicular body (MVB) formation was significantly disturbed as evidenced by the increase in number and decrease in volume of CD63+ vesicles, thus inhibiting mature virion secretion. In conclusion, these data provided spatially resolved molecular snapshots in the context of specific subcellular activities. The heterogeneity observed at single-cell level afforded valuable molecular insights which are otherwise unavailable from bulk measurements. HBV is a hepatotropic, enveloped virus with a partially double-stranded relaxed circular DNA genome. Studies on the molecular biology of HBV mainly rely on biochemical extraction and bulk quantification methods. Detailed spatiotemporal information on virus components in subcellular context is still lacking. Here, we re-evaluated the reproduction schemes of HBV by fluorescence in situ hybridization (FISH). We visualized cccDNA minichromosome formation in an epigenetic context, identified pgRNA associated with actively translating ribosomes and capsids. Moreover, the active participation of microtubules in nucleocapsid transport and MVB-mediated virion secretion was identified. These observations have broad implications for understanding the HBV replication cycle and may facilitate the identification of novel antiviral targets.
Collapse
Affiliation(s)
- Lei Yue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chang Li
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Mingzhu Xu
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Min Wu
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jiahui Ding
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiangxia Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaonan Zhang
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, ACT, Australia
- * E-mail: (XZ); (ZY)
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- * E-mail: (XZ); (ZY)
| |
Collapse
|
50
|
Sato Y, Nakao M, Kimura H. Live-Cell Imaging Probes to Track Chromatin Modification Dynamics. Microscopy (Oxf) 2021; 70:415-422. [PMID: 34329472 PMCID: PMC8491620 DOI: 10.1093/jmicro/dfab030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
The spatiotemporal organization of chromatin is regulated at different levels in the nucleus. Epigenetic modifications such as DNA methylation and histone modifications are involved in chromatin regulation and play fundamental roles in genome function. While the one-dimensional epigenomic landscape in many cell types has been revealed by chromatin immunoprecipitation and sequencing, the dynamic changes of chromatin modifications and their relevance to chromatin organization and genome function remain elusive. Live-cell probes to visualize chromatin and its modifications have become powerful tools to monitor dynamic chromatin regulation. Bulk chromatin can be visualized by both small fluorescent dyes and fluorescent proteins, and specific endogenous genomic loci have been detected by adapting genome-editing tools. To track chromatin modifications in living cells, various types of probes have been developed. Protein domains that bind weakly to specific modifications, such as chromodomains for histone methylation, can be repeated to create a tighter binding probe that can then be tagged with a fluorescent protein. It has also been demonstrated that antigen-binding fragments and single-chain variable fragments from modification-specific antibodies can serve as binding probes without disturbing cell division, development and differentiation. These modification-binding modules are used in modification sensors based on fluorescence/Förster resonance energy transfer to measure the intramolecular conformational changes triggered by modifications. Other probes can be created using a bivalent binding system, such as fluorescence complementation or luciferase chemiluminescence. Live-cell chromatin modification imaging using these probes will address dynamic chromatin regulation and will be useful for assaying and screening effective epigenome drugs in cells and organisms.
Collapse
Affiliation(s)
- Yuko Sato
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Masaru Nakao
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| |
Collapse
|