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Ling H, Li Y, Peng C, Yang S, Seto E. HDAC10 inhibition represses melanoma cell growth and BRAF inhibitor resistance via upregulating SPARC expression. NAR Cancer 2024; 6:zcae018. [PMID: 38650694 PMCID: PMC11034028 DOI: 10.1093/narcan/zcae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/08/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Secreted protein acidic and rich in cysteine (SPARC), a conserved secreted glycoprotein, plays crucial roles in regulating various biological processes. SPARC is highly expressed and has profound implications in several cancer types, including melanoma. Understanding the mechanisms that govern SPARC expression in cancers has the potential to lead to improved cancer diagnosis, prognosis, treatment strategies, and patient outcomes. Here, we demonstrate that histone deacetylase 10 (HDAC10) is a key regulator of SPARC expression in melanoma cells. Depletion or inhibition of HDAC10 upregulates SPARC expression, whereas overexpression of HDAC10 downregulates it. Mechanistically, HDAC10 coordinates with histone acetyltransferase p300 to modulate the state of acetylation of histone H3 at lysine 27 (H3K27ac) at SPARC regulatory elements and the recruitment of bromodomain-containing protein 4 (BRD4) to these regions, thereby fine-tuning SPARC transcription. HDAC10 depletion and resultant SPARC upregulation repress melanoma cell growth primarily by activating AMPK signaling and inducing autophagy. Moreover, SPARC upregulation due to HDAC10 depletion partly accounts for the resensitization of resistant cells to a BRAF inhibitor. Our work reveals the role of HDAC10 in gene regulation through indirect histone modification and suggests a potential therapeutic strategy for melanoma or other cancers by targeting HDAC10 and SPARC.
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Affiliation(s)
- Hongbo Ling
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
| | - Yixuan Li
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
| | - Changmin Peng
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
| | - Shengyu Yang
- Department of Cellular and Molecular Physiology, Penn State Cancer Institute, The Penn State University, 400 University Drive, Hershey, PA 17033, USA
| | - Edward Seto
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
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2
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Breimann L, Bahry E, Zouinkhi M, Kolyvanov K, Street LA, Preibisch S, Ercan S. Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594414. [PMID: 38798598 PMCID: PMC11118362 DOI: 10.1101/2024.05.15.594414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Regulation of transcription during embryogenesis is key to development and differentiation. To study transcript expression throughout Caenorhabditis elegans embryogenesis at single-molecule resolution, we developed a high-throughput single-molecule fluorescence in situ hybridization (smFISH) method that relies on computational methods to developmentally stage embryos and quantify individual mRNA molecules in single embryos. We applied our system to sdc-2, a zygotically transcribed gene essential for hermaphrodite development and dosage compensation. We found that sdc-2 is rapidly activated during early embryogenesis by increasing both the number of mRNAs produced per transcription site and the frequency of sites engaged in transcription. Knockdown of sdc-2 and dpy-27, a subunit of the dosage compensation complex (DCC), increased the number of active transcription sites for the X chromosomal gene dpy-23 but not the autosomal gene mdh-1, suggesting that the DCC reduces the frequency of dpy-23 transcription. The temporal resolution from in silico staging of embryos showed that the deletion of a single DCC recruitment element near the dpy-23 gene causes higher dpy-23 mRNA expression after the start of dosage compensation, which could not be resolved using mRNAseq from mixed-stage embryos. In summary, we have established a computational approach to quantify temporal regulation of transcription throughout C. elegans embryogenesis and demonstrated its potential to provide new insights into developmental gene regulation.
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Affiliation(s)
- Laura Breimann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ella Bahry
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Helmholtz Imaging, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Marwan Zouinkhi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Klim Kolyvanov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Lena Annika Street
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Stephan Preibisch
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
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3
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Ayyamperumal P, Naik HC, Naskar AJ, Bammidi LS, Gayen S. Epigenomic states contribute to coordinated allelic transcriptional bursting in iPSC reprogramming. Life Sci Alliance 2024; 7:e202302337. [PMID: 38320809 PMCID: PMC10847334 DOI: 10.26508/lsa.202302337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Two alleles of a gene can be transcribed independently or coordinatedly, which can lead to temporal expression heterogeneity with potentially distinct impacts on cell fate. Here, we profiled genome-wide allelic transcriptional burst kinetics during the reprogramming of MEF to induced pluripotent stem cells. We show that the degree of coordination of allelic bursting differs among genes, and alleles of many reprogramming-related genes burst in a highly coordinated fashion. Notably, we show that the chromatin accessibility of the two alleles of highly coordinated genes is similar, unlike the semi-coordinated or independent genes, suggesting the degree of coordination of allelic bursting is linked to allelic chromatin accessibility. Consistently, we show that many transcription factors have differential binding affinity between alleles of semi-coordinated or independent genes. We show that highly coordinated genes are enriched with chromatin accessibility regulators such as H3K4me3, H3K4me1, H3K36me3, H3K27ac, histone variant H3.3, and BRD4. Finally, we demonstrate that enhancer elements are highly enriched in highly coordinated genes. Our study demonstrates that epigenomic states contribute to coordinated allelic bursting to fine-tune gene expression during induced pluripotent stem cell reprogramming.
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Affiliation(s)
- Parichitran Ayyamperumal
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Hemant Chandru Naik
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Amlan Jyoti Naskar
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Lakshmi Sowjanya Bammidi
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Srimonta Gayen
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
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4
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Mohamad Zamberi NN, Abuhamad AY, Low TY, Mohtar MA, Syafruddin SE. dCas9 Tells Tales: Probing Gene Function and Transcription Regulation in Cancer. CRISPR J 2024; 7:73-87. [PMID: 38635328 DOI: 10.1089/crispr.2023.0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing is evolving into an essential tool in the field of biological and medical research. Notably, the development of catalytically deactivated Cas9 (dCas9) enzyme has substantially broadened its traditional boundaries in gene editing or perturbation. The conjugation of dCas9 with various molecular effectors allows precise control over transcriptional processes, epigenetic modifications, visualization of chromosomal dynamics, and several other applications. This expanded repertoire of CRISPR-Cas9 applications has emerged as an invaluable molecular tool kit that empowers researchers to comprehensively interrogate and gain insights into health and diseases. This review delves into the advancements in Cas9 protein engineering, specifically on the generation of various dCas9 tools that have significantly enhanced the CRISPR-based technology capability and versatility. We subsequently discuss the multifaceted applications of dCas9, especially in interrogating the regulation and function of genes that involve in supporting cancer pathogenesis. In addition, we also delineate the designing and utilization of dCas9-based tools as well as highlighting its current constraints and transformative potentials in cancer research.
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Affiliation(s)
- Nurul Nadia Mohamad Zamberi
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Asmaa Y Abuhamad
- Bionanotechnology Research Group, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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5
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Tang G, Xia H, Huang Y, Guo Y, Chen Y, Ma Z, Liu W. Liquid-liquid phase separation of H3K27me3 reader BP1 regulates transcriptional repression. Genome Biol 2024; 25:67. [PMID: 38468348 PMCID: PMC10926671 DOI: 10.1186/s13059-024-03209-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Bromo-adjacent homology-plant homeodomain domain containing protein 1 (BP1) is a reader of histone post-translational modifications in fungi. BP1 recognizes trimethylation of lysine 27 in histone H3 (H3K27me3), an epigenetic hallmark of gene silencing. However, whether and how BP1 participates in transcriptional repression remains poorly understood. RESULTS We report that BP1 forms phase-separated liquid condensates to modulate its biological function in Fusarium graminearum. Deletion assays reveal that intrinsically disordered region 2 (IDR2) of BP1 mediates its liquid-liquid phase separation. The phase separation of BP1 is indispensable for its interaction with suppressor of Zeste 12, a component of polycomb repressive complex 2. Furthermore, IDR2 deletion abolishes BP1-H3K27me3 binding and alleviates the transcriptional repression of secondary metabolism-related genes, especially deoxynivalenol mycotoxin biosynthesis genes. CONCLUSIONS BP1 maintains transcriptional repression by forming liquid-liquid phase-separated condensates, expanding our understanding of the relationship between post-translational modifications and liquid-liquid phase separation.
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Affiliation(s)
- Guangfei Tang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haoxue Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yufei Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuanwen Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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6
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Chen Y, Luo X, Kang R, Cui K, Ou J, Zhang X, Liang P. Current therapies for osteoarthritis and prospects of CRISPR-based genome, epigenome, and RNA editing in osteoarthritis treatment. J Genet Genomics 2024; 51:159-183. [PMID: 37516348 DOI: 10.1016/j.jgg.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
Osteoarthritis (OA) is one of the most common degenerative joint diseases worldwide, causing pain, disability, and decreased quality of life. The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA. Currently, there is a lack of effective therapeutic strategies for OA treatment. With the development of CRISPR-based genome, epigenome, and RNA editing tools, OA treatment has been improved by targeting genetic risk factors, activating chondrogenic elements, and modulating inflammatory regulators. Supported by cell therapy and in vivo delivery vectors, genome, epigenome, and RNA editing tools may provide a promising approach for personalized OA therapy. This review summarizes CRISPR-based genome, epigenome, and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment. Moreover, in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.
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Affiliation(s)
- Yuxi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xiao Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Rui Kang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Kaixin Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jianping Ou
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Xiya Zhang
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China.
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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7
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Arzate-Mejia RG, Carullo NVN, Mansuy IM. The epigenome under pressure: On regulatory adaptation to chronic stress in the brain. Curr Opin Neurobiol 2024; 84:102832. [PMID: 38141414 DOI: 10.1016/j.conb.2023.102832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 12/25/2023]
Abstract
Chronic stress (CS) can have long-lasting consequences on behavior and cognition, that are associated with stable changes in gene expression in the brain. Recent work has examined the role of the epigenome in the effects of CS on the brain. This review summarizes experimental evidence in rodents showing that CS can alter the epigenome and the expression of epigenetic modifiers in brain cells, and critically assesses their functional effect on genome function. It discusses the influence of the developmental time of stress exposure on the type of epigenetic changes, and proposes new lines of research that can help clarify these changes and their causal involvement in the impact of CS.
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Affiliation(s)
- Rodrigo G Arzate-Mejia
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty of the University of Zurich and Institute of Neurosciences, Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Switzerland. https://twitter.com/RodrigoArzt
| | - Nancy V N Carullo
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty of the University of Zurich and Institute of Neurosciences, Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Switzerland. https://twitter.com/DrNancyCarullo
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty of the University of Zurich and Institute of Neurosciences, Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Switzerland.
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8
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Atsumi Y, Iwata R, Kimura H, Vanderhaeghen P, Yamamoto N, Sugo N. Repetitive CREB-DNA interactions at gene loci predetermined by CBP induce activity-dependent gene expression in human cortical neurons. Cell Rep 2024; 43:113576. [PMID: 38128530 DOI: 10.1016/j.celrep.2023.113576] [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: 05/23/2023] [Revised: 11/10/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Neuronal activity-dependent transcription plays a key role in plasticity and pathology in the brain. An intriguing question is how neuronal activity controls gene expression via interactions of transcription factors with DNA and chromatin modifiers in the nucleus. By utilizing single-molecule imaging in human embryonic stem cell (ESC)-derived cortical neurons, we demonstrate that neuronal activity increases repetitive emergence of cAMP response element-binding protein (CREB) at histone acetylation sites in the nucleus, where RNA polymerase II (RNAPII) accumulation and FOS expression occur rapidly. Neuronal activity also enhances co-localization of CREB and CREB-binding protein (CBP). Increased binding of a constitutively active CREB to CBP efficiently induces CREB repetitive emergence. On the other hand, the formation of histone acetylation sites is dependent on CBP histone modification via acetyltransferase (HAT) activity but is not affected by neuronal activity. Taken together, our results suggest that neuronal activity promotes repetitive CREB-CRE and CREB-CBP interactions at predetermined histone acetylation sites, leading to rapid gene expression.
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Affiliation(s)
- Yuri Atsumi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryohei Iwata
- VIB-KU Leuven, Center for Brain & Disease Research and KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Pierre Vanderhaeghen
- VIB-KU Leuven, Center for Brain & Disease Research and KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Nobuhiko Yamamoto
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan; Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China.
| | - Noriyuki Sugo
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
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Ling H, Li Y, Peng C, Yang S, Seto E. HDAC10 blockade upregulates SPARC expression thereby repressing melanoma cell growth and BRAF inhibitor resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570182. [PMID: 38106051 PMCID: PMC10723323 DOI: 10.1101/2023.12.05.570182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Secreted Protein Acidic and Rich in Cysteine (SPARC), a highly conserved secreted glycoprotein, is crucial for various bioprocesses. Here we demonstrate that histone deacetylase 10 (HDAC10) is a key regulator of SPARC expression. HDAC10 depletion or inhibition upregulates, while overexpression of HDAC10 downregulates, SPARC expression. Mechanistically, HDAC10 coordinates with histone acetyltransferase p300 to modulate the acetylation state of histone H3 lysine 27 (H3K27ac) at SPARC regulatory elements and the recruitment of bromodomain-containing protein 4 (BRD4) to these regions, thereby tuning SPARC transcription. HDAC10 depletion and resultant SPARC upregulation repress melanoma cell growth, primarily by induction of autophagy via activation of AMPK signaling. Moreover, SPARC upregulation due to HDAC10 depletion partly accounts for the resensitivity of resistant cells to a BRAF inhibitor. Our work reveals the role of HDAC10 in gene regulation through epigenetic modification and suggests a potential therapeutic strategy for melanoma or other cancers by targeting HDAC10 and SPARC. Highlights HDAC10 is the primary HDAC member that tightly controls SPARC expression. HDAC10 coordinates with p300 in modulating the H3K27ac state at SPARC regulatory elements and the recruitment of BRD4 to these regions. HDAC10 depletion and resultant SPARC upregulation inhibit melanoma cell growth by inducing autophagy via activation of AMPK signaling.SPARC upregulation as a result of HDAC10 depletion resensitizes resistant cells to BRAF inhibitors.
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10
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Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ. Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. eLife 2023; 12:RP89993. [PMID: 37938195 PMCID: PMC10631760 DOI: 10.7554/elife.89993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 hr) enriched for inducible transcription factors and later changes (4 hr) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 hr, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 hr after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.
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Affiliation(s)
- Robert A Phillips
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Jennifer J Tuscher
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - David Reid
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Olivia R Drake
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Lara Ianov
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
- Civitan International Research Center, University of Alabama at BirminghamBirminghamUnited States
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
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11
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Cai R, Lv R, Shi X, Yang G, Jin J. CRISPR/dCas9 Tools: Epigenetic Mechanism and Application in Gene Transcriptional Regulation. Int J Mol Sci 2023; 24:14865. [PMID: 37834313 PMCID: PMC10573330 DOI: 10.3390/ijms241914865] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
CRISPR/Cas9-mediated cleavage of DNA, which depends on the endonuclease activity of Cas9, has been widely used for gene editing due to its excellent programmability and specificity. However, the changes to the DNA sequence that are mediated by CRISPR/Cas9 affect the structures and stability of the genome, which may affect the accuracy of results. Mutations in the RuvC and HNH regions of the Cas9 protein lead to the inactivation of Cas9 into dCas9 with no endonuclease activity. Despite the loss of endonuclease activity, dCas9 can still bind the DNA strand using guide RNA. Recently, proteins with active/inhibitory effects have been linked to the end of the dCas9 protein to form fusion proteins with transcriptional active/inhibitory effects, named CRISPRa and CRISPRi, respectively. These CRISPR tools mediate the transcription activity of protein-coding and non-coding genes by regulating the chromosomal modification states of target gene promoters, enhancers, and other functional elements. Here, we highlight the epigenetic mechanisms and applications of the common CRISPR/dCas9 tools, by which we hope to provide a reference for future related gene regulation, gene function, high-throughput target gene screening, and disease treatment.
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Affiliation(s)
- Ruijie Cai
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Runyu Lv
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xin'e Shi
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Gongshe Yang
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jianjun Jin
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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12
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Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Wang Z, Tong L, Wang Q, Xu X, Levin JZ, Jin X. Massively parallel in vivo Perturb-seq reveals cell type-specific transcriptional networks in cortical development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558077. [PMID: 37790302 PMCID: PMC10542124 DOI: 10.1101/2023.09.18.558077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Systematic analysis of gene function across diverse cell types in vivo is hindered by two challenges: obtaining sufficient cells from live tissues and accurately identifying each cell's perturbation in high-throughput single-cell assays. Leveraging AAV's versatile cell type tropism and high labeling capacity, we expanded the resolution and scale of in vivo CRISPR screens: allowing phenotypic analysis at single-cell resolution across a multitude of cell types in the embryonic brain, adult brain, and peripheral nervous system. We undertook extensive tests of 86 AAV serotypes, combined with a transposon system, to substantially amplify labeling and accelerate in vivo gene delivery from weeks to days. Using this platform, we performed an in utero genetic screen as proof-of-principle and identified pleiotropic regulatory networks of Foxg1 in cortical development, including Layer 6 corticothalamic neurons where it tightly controls distinct networks essential for cell fate specification. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% (mediated by lentivirus), and achieve analysis of over 30,000 cells in one experiment, thus enabling massively parallel in vivo Perturb-seq. Compatible with various perturbation techniques (CRISPRa/i) and phenotypic measurements (single-cell or spatial multi-omics), our platform presents a flexible, modular approach to interrogate gene function across diverse cell types in vivo, connecting gene variants to their causal functions.
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Affiliation(s)
- Xinhe Zheng
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Boli Wu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Yuejia Liu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Sean K. Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kwanho Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace S. Clarke
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Abdullah Ashiq
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Joshua Park
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Zhilin Wang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Liqi Tong
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Qizhao Wang
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Xiangmin Xu
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Joshua Z. Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Jin
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
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13
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Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ. Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543489. [PMID: 37333110 PMCID: PMC10274686 DOI: 10.1101/2023.06.02.543489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 h) enriched for inducible transcription factors and later changes (4 h) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 h, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 h after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.
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Affiliation(s)
- Robert A Phillips
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jennifer J Tuscher
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David Reid
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Olivia R Drake
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lara Ianov
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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14
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Sardar D, Cheng YT, Woo J, Choi DJ, Lee ZF, Kwon W, Chen HC, Lozzi B, Cervantes A, Rajendran K, Huang TW, Jain A, Arenkiel B, Maze I, Deneen B. Induction of astrocytic Slc22a3 regulates sensory processing through histone serotonylation. Science 2023; 380:eade0027. [PMID: 37319217 PMCID: PMC10874521 DOI: 10.1126/science.ade0027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 06/17/2023]
Abstract
Neuronal activity drives alterations in gene expression within neurons, yet how it directs transcriptional and epigenomic changes in neighboring astrocytes in functioning circuits is unknown. We found that neuronal activity induces widespread transcriptional up-regulation and down-regulation in astrocytes, highlighted by the identification of Slc22a3 as an activity-inducible astrocyte gene that encodes neuromodulator transporter Slc22a3 and regulates sensory processing in the mouse olfactory bulb. Loss of astrocytic Slc22a3 reduced serotonin levels in astrocytes, leading to alterations in histone serotonylation. Inhibition of histone serotonylation in astrocytes reduced the expression of γ-aminobutyric acid (GABA) biosynthetic genes and GABA release, culminating in olfactory deficits. Our study reveals that neuronal activity orchestrates transcriptional and epigenomic responses in astrocytes while illustrating new mechanisms for how astrocytes process neuromodulatory input to gate neurotransmitter release for sensory processing.
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Affiliation(s)
- Debosmita Sardar
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
| | - Yi-Ting Cheng
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Program in Developmental Biology, Baylor College of Medicine, Houston TX
| | - Junsung Woo
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
| | - Dong-Joo Choi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
| | - Zhung-Fu Lee
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
- Program in Development, Disease Models, and Therapeutics, Baylor College of Medicine, Houston TX
| | - Wookbong Kwon
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
| | - Hsiao-Chi Chen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
- The Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston TX
| | - Brittney Lozzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston TX
| | - Alexis Cervantes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
| | - Kavitha Rajendran
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
| | - Teng-Wei Huang
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
| | - Antrix Jain
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston TX
| | - Benjamin Arenkiel
- Program in Developmental Biology, Baylor College of Medicine, Houston TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX
- Neurological Research Institute, Texas Children’s Hospital, Houston TX
| | - Ian Maze
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York NY
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York NY
- Howard Hughes Medical Institute, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston TX
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston TX
- Program in Developmental Biology, Baylor College of Medicine, Houston TX
- Program in Development, Disease Models, and Therapeutics, Baylor College of Medicine, Houston TX
- Department of Neurosurgery, Baylor College of Medicine, Houston TX 77030
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15
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Cabej NR. On the origin and nature of nongenetic information in eumetazoans. Ann N Y Acad Sci 2023. [PMID: 37154677 DOI: 10.1111/nyas.15001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nongenetic information implies all the forms of biological information not related to genes and DNA in general. Despite the deep scientific relevance of the concept, we currently lack reliable knowledge about its carriers and origins; hence, we still do not understand its true nature. Given that genes are the targets of nongenetic information, it appears that a parsimonious approach to find the ultimate source of that information is to trace back the sequential steps of the causal chain upstream of the target genes up to the ultimate link as the source of the nongenetic information. From this perspective, I examine seven nongenetically determined phenomena: placement of locus-specific epigenetic marks on DNA and histones, changes in snRNA expression patterns, neural induction of gene expression, site-specific alternative gene splicing, predator-induced morphological changes, and cultural inheritance. Based on the available evidence, I propose a general model of the common neural origin of all these forms of nongenetic information in eumetazoans.
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Affiliation(s)
- Nelson R Cabej
- Department of Biology, University of Tirana, Tirana, Albania
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16
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Porter RS, Iwase S. Modulation of chromatin architecture influences the neuronal nucleus through activity-regulated gene expression. Biochem Soc Trans 2023; 51:703-713. [PMID: 36929379 PMCID: PMC10959270 DOI: 10.1042/bst20220889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/02/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023]
Abstract
The disruption of chromatin-regulating genes is associated with many neurocognitive syndromes. While most of these genes are ubiquitously expressed across various cell-types, many chromatin regulators act upon activity regulated genes (ARGs) that play central roles in synaptic development and plasticity. Recent literature suggests a link between ARG expression disruption in neurons with the human phenotypes observed in various neurocognitive syndromes. Advances in chromatin biology have demonstrated how chromatin structure, from nucleosome occupancy to higher-order structures such as topologically associated domains, impacts the kinetics of transcription. This review discusses the dynamics of these various levels of chromatin structure and their influence on the expression of ARGs.
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Affiliation(s)
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
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17
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Arzate-Mejia RG, Mansuy IM. Remembering through the genome: the role of chromatin states in brain functions and diseases. Transl Psychiatry 2023; 13:122. [PMID: 37041131 PMCID: PMC10090084 DOI: 10.1038/s41398-023-02415-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
Chromatin is the physical substrate of the genome that carries the DNA sequence and ensures its proper functions and regulation in the cell nucleus. While a lot is known about the dynamics of chromatin during programmed cellular processes such as development, the role of chromatin in experience-dependent functions remains not well defined. Accumulating evidence suggests that in brain cells, environmental stimuli can trigger long-lasting changes in chromatin structure and tri-dimensional (3D) organization that can influence future transcriptional programs. This review describes recent findings suggesting that chromatin plays an important role in cellular memory, particularly in the maintenance of traces of prior activity in the brain. Inspired by findings in immune and epithelial cells, we discuss the underlying mechanisms and the implications for experience-dependent transcriptional regulation in health and disease. We conclude by presenting a holistic view of chromatin as potential molecular substrate for the integration and assimilation of environmental information that may constitute a conceptual basis for future research.
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Affiliation(s)
- Rodrigo G Arzate-Mejia
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty, University of Zurich, Zurich, Switzerland
- Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology Zürich (ETHZ), Zurich, Switzerland
- Center for Neuroscience Zürich, University Zürich and ETHZ, Zürich, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty, University of Zurich, Zurich, Switzerland.
- Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology Zürich (ETHZ), Zurich, Switzerland.
- Center for Neuroscience Zürich, University Zürich and ETHZ, Zürich, Switzerland.
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18
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Sardar D, Cheng YT, Woo J, Choi DJ, Lee ZF, Kwon W, Chen HC, Lozzi B, Cervantes A, Rajendran K, Huang TW, Jain A, Arenkiel B, Maze I, Deneen B. Activity-dependent induction of astrocytic Slc22a3 regulates sensory processing through histone serotonylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529904. [PMID: 36909526 PMCID: PMC10002681 DOI: 10.1101/2023.02.24.529904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Neuronal activity drives global alterations in gene expression within neurons, yet how it directs transcriptional and epigenomic changes in neighboring astrocytes in functioning circuits is unknown. Here we show that neuronal activity induces widespread transcriptional upregulation and downregulation in astrocytes, highlighted by the identification of a neuromodulator transporter Slc22a3 as an activity-inducible astrocyte gene regulating sensory processing in the olfactory bulb. Loss of astrocytic Slc22a3 reduces serotonin levels in astrocytes, leading to alterations in histone serotonylation. Inhibition of histone serotonylation in astrocytes reduces expression of GABA biosynthetic genes and GABA release, culminating in olfactory deficits. Our study reveals that neuronal activity orchestrates transcriptional and epigenomic responses in astrocytes, while illustrating new mechanisms for how astrocytes process neuromodulatory input to gate neurotransmitter release for sensory processing.
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19
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Elucidation of the Landscape of Alternatively Spliced Genes and Features in the Dorsal Striatum of Aggressive/Aggression-Deprived Mice in the Model of Chronic Social Conflicts. Genes (Basel) 2023; 14:genes14030599. [PMID: 36980872 PMCID: PMC10048575 DOI: 10.3390/genes14030599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Both aggressive and aggression-deprived (AD) individuals represent pathological cases extensively studied in psychiatry and substance abuse disciplines. We employed the animal model of chronic social conflicts curated in our laboratory for over 30 years. In the study, we pursued the task of evaluation of the key events in the dorsal striatum transcriptomes of aggression-experienced mice and AD species, as compared with the controls, using RNA-seq profiling. We evaluated the alternative splicing-mediated transcriptome dynamics based on the RNA-seq data. We confined our attention to the exon skipping (ES) events as the major AS type for animals. We report the concurrent posttranscriptional and posttranslational regulation of the ES events observed in the phosphorylation cycles (in phosphoproteins and their targets) in the neuron-specific genes of the striatum. Strikingly, we found that major neurospecific splicing factors (Nova1, Ptbp1, 2, Mbnl1, 2, and Sam68) related to the alternative splicing regulation of cAMP genes (Darpp-32, Grin1, Ptpn5, Ppp3ca, Pde10a, Prkaca, Psd95, and Adora1) are upregulated specifically in aggressive individuals as compared with the controls and specifically AD animals, assuming intense switching between isoforms in the cAMP-mediated (de)phosphorylation signaling cascade. We found that the coding alternative splicing events were mostly attributed to synaptic plasticity and neural development-related proteins, while the nonsense-mediated decay-associated splicing events are mostly attributed to the mRNA processing of genes, including the spliceosome and splicing factors. In addition, considering the gene families, the transporter (Slc) gene family manifested most of the ES events. We found out that the major molecular systems employing AS for their plasticity are the ‘spliceosome’, ‘chromatin rearrangement complex’, ‘synapse’, and ‘neural development/axonogenesis’ GO categories. Finally, we state that approximately 35% of the exon skipping variants in gene coding regions manifest the noncoding variants subject to nonsense-mediated decay, employed as a homeostasis-mediated expression regulation layer and often associated with the corresponding gene expression alteration.
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20
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Levy S, Ruohola-Baker H. AI-driven designed protein epigenomics. CLINICAL RESEARCH IN ONCOLOGY 2023; 1:1-3. [PMID: 38037660 PMCID: PMC10686789 DOI: 10.46439/oncology.1.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
The biological revolutions of computationally designed proteins, induced pluripotent stem cells (iPSCs), and the CRISPR-Cas9 system finally enables modifications that can spur deep understanding of spatial requirement of epigenetic information. This commentary describes the utility of a computationally designed protein, EED Binder (EB), when fused to dCas9 (EBdCas9) for identifying critical sites of PRC2 dependent histone H3K27me3 marks in the chromatin. By using EBdCas9 and gRNA, PRC2 function can be inhibited at specific loci, resulting in precise reduction of EZH2 and H3K27me3 marks, and in some (but not all) locations, activation of the gene and functional outcomes (such as regulation of cell cycle or trophoblast transdifferentiation). Interestingly, a functional TATA box located more than 500bp upstream of a TBX18 TSS was found to be repressed by PRC2, supporting the theory that epigenetic regulators control the repression of transcriptional elements on the promoter region. The EBdCas9 technology may provide a useful tool for controlling gene regulation through epigenomic control.
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Affiliation(s)
- Shiri Levy
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
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21
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Lambert É, Puwakdandawa K, Tao YF, Robert F. From structure to molecular condensates: emerging mechanisms for Mediator function. FEBS J 2023; 290:286-309. [PMID: 34698446 DOI: 10.1111/febs.16250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 02/05/2023]
Abstract
Mediator is a large modular protein assembly whose function as a coactivator of transcription is conserved in all eukaryotes. The Mediator complex can integrate and relay signals from gene-specific activators bound at enhancers to activate the general transcription machinery located at promoters. It has thus been described as a bridge between these elements during initiation of transcription. Here, we review recent studies on Mediator relating to its structure, gene specificity and general requirement, roles in chromatin architecture as well as novel concepts involving phase separation and transcriptional bursting. We revisit the mechanism of action of Mediator and ultimately put forward models for its mode of action in gene activation.
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Affiliation(s)
- Élie Lambert
- Institut de recherches cliniques de Montréal, Canada
| | | | - Yi Fei Tao
- Institut de recherches cliniques de Montréal, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Canada
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22
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Haynes KA, Priode JH. Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering. Methods Mol Biol 2023; 2599:191-214. [PMID: 36427151 DOI: 10.1007/978-1-0716-2847-8_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chromatin is the nucleoprotein complex that organizes genomic DNA in the nuclei of eukaryotic cells. Chromatin-modifying enzymes and chromatin-binding regulators generate chromatin states that affect DNA compaction, repair, gene expression, and ultimately cell phenotype. Many natural chromatin mediators contain subdomains that can be isolated and recombined to build synthetic regulators and probes. Engineered chromatin proteins make up a growing collection of new tools for cell engineering and can help deepen our understanding of the mechanism by which chromatin features, such as modifications of histones and DNA, contribute to the epigenetic states that govern DNA-templated processes. To support efficient exploration of the large combinatorial design space of synthetic chromatin proteins, we have developed a Golden Gate assembly method for one-step construction of protein-encoding recombinant DNA. A set of standard 2-amino acid linkers allows facile assembly of any combination of up to four protein modules, obviating the need to design different compatible overhangs to ligate different modules. Beginning with the identification of protein modules of interest, a synthetic chromatin protein can be built and expressed in vitro or in cells in under 2 weeks.
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Affiliation(s)
- Karmella A Haynes
- W. H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA.
| | - J Harrison Priode
- W. H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA
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23
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Dorman CJ. Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations. Mol Microbiol 2023; 119:19-28. [PMID: 36565252 PMCID: PMC10108321 DOI: 10.1111/mmi.15014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/25/2022]
Abstract
Transcription is a noisy and stochastic process that produces sibling-to-sibling variations in physiology across a population of genetically identical cells. This pattern of diversity reflects, in part, the burst-like nature of transcription. Transcription bursting has many causes and a failure to remove the supercoils that accumulate in DNA during transcription elongation is an important contributor. Positive supercoiling of the DNA ahead of the transcription elongation complex can result in RNA polymerase stalling if this DNA topological roadblock is not removed. The relaxation of these positive supercoils is performed by the ATP-dependent type II topoisomerases DNA gyrase and topoisomerase IV. Interference with the action of these topoisomerases involving, inter alia, topoisomerase poisons, fluctuations in the [ATP]/[ADP] ratio, and/or the intervention of nucleoid-associated proteins with GapR-like or YejK-like activities, may have consequences for the smooth operation of the transcriptional machinery. Antibiotic-tolerant (but not resistant) persister cells are among the phenotypic outliers that may emerge. However, interference with type II topoisomerase activity can have much broader consequences, making it an important epigenetic driver of physiological diversity in the bacterial population.
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Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
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24
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Balasooriya GI, Spector DL. Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage. Nat Commun 2022; 13:5984. [PMID: 36216821 PMCID: PMC9550772 DOI: 10.1038/s41467-022-33722-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/27/2022] [Indexed: 11/29/2022] Open
Abstract
Each mammalian autosomal gene is represented by two alleles in diploid cells. To our knowledge, no insights have been made in regard to allele-specific regulatory mechanisms of autosomes. Here we use allele-specific single cell transcriptomic analysis to elucidate the establishment of monoallelic gene expression in the cardiac lineage. We find that monoallelically expressed autosomal genes in mESCs and mouse blastocyst cells are differentially regulated based on the genetic background of the parental alleles. However, the genetic background of the allele does not affect the establishment of monoallelic genes in differentiated cardiomyocytes. Additionally, we observe epigenetic differences between deterministic and random autosomal monoallelic genes. Moreover, we also find a greater contribution of the maternal versus paternal allele to the development and homeostasis of cardiac tissue and in cardiac health, highlighting the importance of maternal influence in male cardiac tissue homeostasis. Our findings emphasize the significance of allele-specific insights into gene regulation in development, homeostasis and disease.
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25
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Li J, Pertsinidis A. Nanoscale nuclear environments, fine-scale 3D genome organization and transcription regulation. CURRENT OPINION IN SYSTEMS BIOLOGY 2022; 31:100436. [PMID: 37091742 PMCID: PMC10118054 DOI: 10.1016/j.coisb.2022.100436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Decades of in vitro biochemical reconstitution, genetics and structural biology studies have established a vast knowledge base on the molecular mechanisms of chromatin regulation and transcription. A remaining challenge is to understand how these intricate biochemical systems operate in the context of the 3D genome organization and in the crowded and compartmentalized nuclear milieu. Here we review recent progress in this area based on high-resolution imaging approaches.
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Affiliation(s)
- Jieru Li
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, NY 10065, USA
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26
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Alexander DC, Corman T, Mendoza M, Glass A, Belity T, Wu R, Campbell RR, Han J, Keiser AA, Winkler J, Wood MA, Kim T, Garcia BA, Cohen H, Mews P, Egervari G, Berger SL. Targeting acetyl-CoA metabolism attenuates the formation of fear memories through reduced activity-dependent histone acetylation. Proc Natl Acad Sci U S A 2022; 119:e2114758119. [PMID: 35921439 PMCID: PMC9371679 DOI: 10.1073/pnas.2114758119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Histone acetylation is a key component in the consolidation of long-term fear memories. Histone acetylation is fueled by acetyl-coenzyme A (acetyl-CoA), and recently, nuclear-localized metabolic enzymes that produce this metabolite have emerged as direct and local regulators of chromatin. In particular, acetyl-CoA synthetase 2 (ACSS2) mediates histone acetylation in the mouse hippocampus. However, whether ACSS2 regulates long-term fear memory remains to be determined. Here, we show that Acss2 knockout is well tolerated in mice, yet the Acss2-null mouse exhibits reduced acquisition of long-term fear memory. Loss of Acss2 leads to reductions in both histone acetylation and expression of critical learning and memory-related genes in the dorsal hippocampus, specifically following fear conditioning. Furthermore, systemic administration of blood-brain barrier-permeable Acss2 inhibitors during the consolidation window reduces fear-memory formation in mice and rats and reduces anxiety in a predator-scent stress paradigm. Our findings suggest that nuclear acetyl-CoA metabolism via ACSS2 plays a critical, previously unappreciated, role in the formation of fear memories.
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Affiliation(s)
- Desi C. Alexander
- aEpigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- bDepartment of Genetics, University of Pennsylvania, Philadelphia, PA 19104
| | - Tanya Corman
- aEpigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Mariel Mendoza
- aEpigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- cDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrew Glass
- dDepartment of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Tal Belity
- eDepartment of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Ranran Wu
- aEpigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- cDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Rianne R. Campbell
- fDepartment of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, CA 92697
| | - Joseph Han
- fDepartment of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, CA 92697
| | - Ashley A. Keiser
- fDepartment of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, CA 92697
| | - Jeffrey Winkler
- dDepartment of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Marcelo A. Wood
- fDepartment of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, CA 92697
| | | | - Benjamin A. Garcia
- aEpigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- cDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Hagit Cohen
- eDepartment of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- hBeer-Sheva Mental Health Center, Ministry of Health, Anxiety and Stress Research Unit, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Philipp Mews
- iFishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- 2To whom correspondence may be addressed. , , or
| | - Gabor Egervari
- aEpigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- jDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- 2To whom correspondence may be addressed. , , or
| | - Shelley L. Berger
- aEpigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- bDepartment of Genetics, University of Pennsylvania, Philadelphia, PA 19104
- jDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- kDepartment of Biology, University of Pennsylvania, Philadelphia, PA 19104
- 2To whom correspondence may be addressed. , , or
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27
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Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters. Nat Commun 2022; 13:4342. [PMID: 35896525 PMCID: PMC9329429 DOI: 10.1038/s41467-022-31192-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/06/2022] [Indexed: 01/25/2023] Open
Abstract
Innate immune responses rely on inducible gene expression programmes which, in contrast to steady-state transcription, are highly dependent on cohesin. Here we address transcriptional parameters underlying this cohesin-dependence by single-molecule RNA-FISH and single-cell RNA-sequencing. We show that inducible innate immune genes are regulated predominantly by an increase in the probability of active transcription, and that probabilities of enhancer and promoter transcription are coordinated. Cohesin has no major impact on the fraction of transcribed inducible enhancers, or the number of mature mRNAs produced per transcribing cell. Cohesin is, however, required for coupling the probabilities of enhancer and promoter transcription. Enhancer-promoter coupling may not be explained by spatial proximity alone, and at the model locus Il12b can be disrupted by selective inhibition of the cohesinopathy-associated BET bromodomain BD2. Our data identify discrete steps in enhancer-mediated inducible gene expression that differ in cohesin-dependence, and suggest that cohesin and BD2 may act on shared pathways.
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28
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Rienecker KDA, Poston RG, Segales JS, Finholm IW, Sono MH, Munteanu SJ, Ghaninejad-Esfahani M, Rejepova A, Tejeda-Garibay S, Wickman K, Marron Fernandez de Velasco E, Thayer SA, Saha RN. Mild membrane depolarization in neurons induces immediate early gene transcription and acutely subdues responses to successive stimulus. J Biol Chem 2022; 298:102278. [PMID: 35863435 PMCID: PMC9396413 DOI: 10.1016/j.jbc.2022.102278] [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: 05/21/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/22/2022] Open
Abstract
Immediate early genes (IEGs) are transcribed in response to neuronal activity from sensory stimulation during multiple adaptive processes in the brain. The transcriptional profile of IEGs is indicative of the duration of neuronal activity, but its sensitivity to the strength of depolarization remains unknown. Also unknown is whether activity history of graded potential changes influence future neuronal activity. In this work with dissociated rat cortical neurons, we found that mild depolarization—mediated by elevated extracellular potassium (K+)—induces a wide array of rapid IEGs and transiently depresses transcriptional and signaling responses to a successive stimulus. This latter effect was independent of de novo transcription, translation, and signaling via calcineurin or mitogen-activated protein kinase. Furthermore, as measured by multiple electrode arrays and calcium imaging, mild depolarization acutely subdues subsequent spontaneous and bicuculline-evoked activity via calcium- and N-methyl-d-aspartate receptor–dependent mechanisms. Collectively, this work suggests that a recent history of graded potential changes acutely depress neuronal intrinsic properties and subsequent responses. Such effects may have several potential downstream implications, including reducing signal-to-noise ratio during synaptic plasticity processes.
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Affiliation(s)
- Kira D A Rienecker
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California, USA, 95343
| | - Robert G Poston
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California, USA, 95343
| | - Joshua S Segales
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California, USA, 95343
| | - Isabelle W Finholm
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Morgan H Sono
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California, USA, 95343
| | - Sorina J Munteanu
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California, USA, 95343
| | - Mina Ghaninejad-Esfahani
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California, USA, 95343
| | - Ayna Rejepova
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California, USA, 95343
| | - Susana Tejeda-Garibay
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California, USA, 95343
| | - Kevin Wickman
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | | | - Stanley A Thayer
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Ramendra N Saha
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California, USA, 95343.
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29
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The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intracellular communication after learning. Proc Natl Acad Sci U S A 2022; 119:e2116797119. [PMID: 35613054 PMCID: PMC9295763 DOI: 10.1073/pnas.2116797119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Memory formation relies on a plethora of functions, including epigenetic modifications. Over recent years, multiple studies have indicated the potential of HDAC inhibitors (HDACis) as cognitive enhancers, but their mode of action is not fully understood. Here, we tested whether HDACi treatment improves memory formation via “cognitive epigenetic priming,” stipulating that HDACis—without inherent target specificity—specifically enhance naturally occurring plasticity processes. We found that combining HDACis with fear learning, but not either treatment alone, enhances synaptic plasticity as well as memory-promoting transcriptional signaling in the hippocampus, a brain area recruited by fear learning, but not in unrelated areas. These results lend experimental support to the theory of cognitive epigenetic priming. Long-term memory formation relies on synaptic plasticity, neuronal activity-dependent gene transcription, and epigenetic modifications. Multiple studies have shown that HDAC inhibitor (HDACi) treatments can enhance individual aspects of these processes and thereby act as putative cognitive enhancers. However, their mode of action is not fully understood. In particular, it is unclear how systemic application of HDACis, which are devoid of substrate specificity, can target pathways that promote memory formation. In this study, we explore the electrophysiological, transcriptional, and epigenetic responses that are induced by CI-994, a class I HDACi, combined with contextual fear conditioning (CFC) in mice. We show that CI-994–mediated improvement of memory formation is accompanied by enhanced long-term potentiation in the hippocampus, a brain region recruited by CFC, but not in the striatum, a brain region not primarily implicated in fear learning. Furthermore, using a combination of bulk and single-cell RNA-sequencing, we find that, when paired with CFC, HDACi treatment engages synaptic plasticity-promoting gene expression more strongly in the hippocampus, specifically in the dentate gyrus (DG). Finally, using chromatin immunoprecipitation-sequencing (ChIP-seq) of DG neurons, we show that the combined action of HDACi application and conditioning is required to elicit enhancer histone acetylation in pathways that underlie improved memory performance. Together, these results indicate that systemic HDACi administration amplifies brain region-specific processes that are naturally induced by learning.
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30
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Pumo GM, Kitazawa T, Rijli FM. Epigenetic and Transcriptional Regulation of Spontaneous and Sensory Activity Dependent Programs During Neuronal Circuit Development. Front Neural Circuits 2022; 16:911023. [PMID: 35664458 PMCID: PMC9158562 DOI: 10.3389/fncir.2022.911023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Spontaneous activity generated before the onset of sensory transduction has a key role in wiring developing sensory circuits. From axonal targeting, to synapse formation and elimination, to the balanced integration of neurons into developing circuits, this type of activity is implicated in a variety of cellular processes. However, little is known about its molecular mechanisms of action, especially at the level of genome regulation. Conversely, sensory experience-dependent activity implements well-characterized transcriptional and epigenetic chromatin programs that underlie heterogeneous but specific genomic responses that shape both postnatal circuit development and neuroplasticity in the adult. In this review, we focus on our knowledge of the developmental processes regulated by spontaneous activity and the underlying transcriptional mechanisms. We also review novel findings on how chromatin regulates the specificity and developmental induction of the experience-dependent program, and speculate their relevance for our understanding of how spontaneous activity may act at the genomic level to instruct circuit assembly and prepare developing neurons for sensory-dependent connectivity refinement and processing.
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Affiliation(s)
- Gabriele M. Pumo
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
| | - Taro Kitazawa
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Filippo M. Rijli
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
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31
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Kershanskaya OI, Yessenbaeva GL, Nelidova DS, Karabekova AN, Sadullaeva ZN. CRISPR/Cas genome editing perspectives for barley breeding. PHYSIOLOGIA PLANTARUM 2022; 174:e13686. [PMID: 35451132 DOI: 10.1111/ppl.13686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 02/01/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
The CRISPR/Cas9 technology shows potential to improve crop breeding efficiency and antiviral defense. The interest in DNA editing in crops has grown due to the possibility of increasing the resistance of different plants to many viruses. Our aim was to create an elite disease-resistant local barley cultivar using CRISPR/Cas9 biotechnology. For this purpose, we used CRISPR/Cas 9-eIF4E with the eukaryotic translation initiation factor 4E (eIF4E) barley gene to edit the genomes of five local Kazakhstan barley cultivars. After identifying the single guide RNA (sgRNA) target sequences, they were synthesized and cloned into the CRISPR-plant vector before being introduced into barley cells via our own patented Agrobacterium germ-line transformation technique. Barley plants eIF4E-modified were successfully obtained and were resistant to virus infection. Based on our research, the CRISPR/Cas9 system for plant genome editing could be a prospect for applying this breakthrough biotechnology in barley breeding.
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Affiliation(s)
- Olga I Kershanskaya
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Gulvira L Yessenbaeva
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Darya S Nelidova
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Aizhan N Karabekova
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Zarina N Sadullaeva
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
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32
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Wei W, Zhao Q, Wang Z, Liau WS, Basic D, Ren H, Marshall PR, Zajaczkowski EL, Leighton LJ, Madugalle SU, Musgrove M, Periyakaruppiah A, Shi J, Zhang J, Mattick JS, Mercer TR, Spitale RC, Li X, Bredy TW. ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3. Cell Rep 2022; 38:110546. [PMID: 35320727 PMCID: PMC9015815 DOI: 10.1016/j.celrep.2022.110546] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/03/2022] [Accepted: 02/28/2022] [Indexed: 11/25/2022] Open
Abstract
Here, we used RNA capture-seq to identify a large population of lncRNAs that are expressed in the infralimbic prefrontal cortex of adult male mice in response to fear-related learning. Combining these data with cell-type-specific ATAC-seq on neurons that had been selectively activated by fear extinction learning, we find inducible 434 lncRNAs that are derived from enhancer regions in the vicinity of protein-coding genes. In particular, we discover an experience-induced lncRNA we call ADRAM (activity-dependent lncRNA associated with memory) that acts as both a scaffold and a combinatorial guide to recruit the brain-enriched chaperone protein 14-3-3 to the promoter of the memory-associated immediate-early gene Nr4a2 and is required fear extinction memory. This study expands the lexicon of experience-dependent lncRNA activity in the brain and highlights enhancer-derived RNAs (eRNAs) as key players in the epigenomic regulation of gene expression associated with the formation of fear extinction memory. Wei et al. use targeted RNA capture sequencing to examine experience-dependent long noncoding RNA activity in the infralimbic prefrontal cortex of adult mice. They discover a gene, which they call ADRAM, that is directly involved in the epigenomic regulation of gene expression underlying memory formation.
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Affiliation(s)
- Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China; Medical Research Institute, Wuhan University, Wuhan, China.
| | - Qiongyi Zhao
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Ziqi Wang
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Dean Basic
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Esmi L Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Mason Musgrove
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Ambika Periyakaruppiah
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Jichun Shi
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianjian Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - Timothy R Mercer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, USA
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China; Medical Research Institute, Wuhan University, Wuhan, China
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
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Levy S, Somasundaram L, Raj IX, Ic-Mex D, Phal A, Schmidt S, Ng WI, Mar D, Decarreau J, Moss N, Alghadeer A, Honkanen H, Sarthy J, Vitanza N, Hawkins RD, Mathieu J, Wang Y, Baker D, Bomsztyk K, Ruohola-Baker H. dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region. Cell Rep 2022; 38:110457. [PMID: 35235780 PMCID: PMC8984963 DOI: 10.1016/j.celrep.2022.110457] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 11/23/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Bifurcation of cellular fates, a critical process in development, requires histone 3 lysine 27 methylation (H3K27me3) marks propagated by the polycomb repressive complex 2 (PRC2). However, precise chromatin loci of functional H3K27me3 marks are not yet known. Here, we identify critical PRC2 functional sites at high resolution. We fused a computationally designed protein, EED binder (EB), which competes with EZH2 and thereby inhibits PRC2 function, to dCas9 (EBdCas9) to allow for PRC2 inhibition at a precise locus using gRNA. Targeting EBdCas9 to four different genes (TBX18, p16, CDX2, and GATA3) results in precise H3K27me3 and EZH2 reduction, gene activation, and functional outcomes in the cell cycle (p16) or trophoblast transdifferentiation (CDX2 and GATA3). In the case of TBX18, we identify a PRC2-controlled, functional TATA box >500 bp upstream of the TBX18 transcription start site (TSS) using EBdCas9. Deletion of this TATA box eliminates EBdCas9-dependent TATA binding protein (TBP) recruitment and transcriptional activation. EBdCas9 technology may provide a broadly applicable tool for epigenomic control of gene regulation. Levy et al. fused a computationally designed protein, EED binder (EB), which competes with EZH2 and thereby inhibits PRC2 function, to dCas9 (EBdCas9). EBdCas9 represses PRC2 action in precise loci, remodels epigenomic marks, exposes transcriptional elements, and induces transdifferentiation.
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Affiliation(s)
- Shiri Levy
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Logeshwaran Somasundaram
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Infencia Xavier Raj
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Diego Ic-Mex
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Ashish Phal
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, School of Medicine, Seattle, WA 98105, USA
| | - Sven Schmidt
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Weng I Ng
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Daniel Mar
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA 98195, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Moss
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Division of Medical Genetics, Department of Medicine, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ammar Alghadeer
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98109, USA; Department of Biomedical Dental Sciences, Imam Abdulrahman Bin Faisal University, College of Dentistry, Dammam 31441, Saudi Arabia
| | - Henrik Honkanen
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Jay Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorder Center, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Nicholas Vitanza
- The Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - R David Hawkins
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Division of Medical Genetics, Department of Medicine, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Karol Bomsztyk
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA 98195, USA
| | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, School of Medicine, Seattle, WA 98105, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98109, USA.
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34
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Chen YJC, Koutelou E, Dent SY. Now open: Evolving insights to the roles of lysine acetylation in chromatin organization and function. Mol Cell 2022; 82:716-727. [PMID: 35016034 PMCID: PMC8857060 DOI: 10.1016/j.molcel.2021.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
Protein acetylation is conserved across phylogeny and has been recognized as one of the most prominent post-translational modifications since its discovery nearly 60 years ago. Histone acetylation is an active mark characteristic of open chromatin, but acetylation on specific lysine residues and histone variants occurs in different biological contexts and can confer various outcomes. The significance of acetylation events is indicated by the associations of lysine acetyltransferases, deacetylases, and acetyl-lysine readers with developmental disorders and pathologies. Recent advances have uncovered new roles of acetylation regulators in chromatin-centric events, which emphasize the complexity of these functional networks. In this review, we discuss mechanisms and dynamics of acetylation in chromatin organization and DNA-templated processes, including gene transcription and DNA repair and replication.
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Affiliation(s)
- Ying-Jiun C. Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sharon Y.R. Dent
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Correspondence:
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Kyzar EJ, Bohnsack JP, Pandey SC. Current and Future Perspectives of Noncoding RNAs in Brain Function and Neuropsychiatric Disease. Biol Psychiatry 2022; 91:183-193. [PMID: 34742545 PMCID: PMC8959010 DOI: 10.1016/j.biopsych.2021.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/05/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023]
Abstract
Noncoding RNAs (ncRNAs) represent the majority of the transcriptome and play important roles in regulating neuronal functions. ncRNAs are exceptionally diverse in both structure and function and include enhancer RNAs, long ncRNAs, and microRNAs, all of which demonstrate specific temporal and regional expression in the brain. Here, we review recent studies demonstrating that ncRNAs modulate chromatin structure, act as chaperone molecules, and contribute to synaptic remodeling and behavior. In addition, we discuss ncRNA function within the context of neuropsychiatric diseases, particularly focusing on addiction and schizophrenia, and the recent methodological developments that allow for better understanding of ncRNA function in the brain. Overall, ncRNAs represent an underrecognized molecular contributor to complex neuronal processes underlying neuropsychiatric disorders.
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Affiliation(s)
- Evan J Kyzar
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois; Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, New York
| | - John Peyton Bohnsack
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, University of Illinois at Chicago, Chicago, Illinois; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, Illinois.
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36
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Teague CD, Nestler EJ. Key transcription factors mediating cocaine-induced plasticity in the nucleus accumbens. Mol Psychiatry 2022; 27:687-709. [PMID: 34079067 PMCID: PMC8636523 DOI: 10.1038/s41380-021-01163-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 02/01/2023]
Abstract
Repeated cocaine use induces coordinated changes in gene expression that drive plasticity in the nucleus accumbens (NAc), an important component of the brain's reward circuitry, and promote the development of maladaptive, addiction-like behaviors. Studies on the molecular basis of cocaine action identify transcription factors, a class of proteins that bind to specific DNA sequences and regulate transcription, as critical mediators of this cocaine-induced plasticity. Early methods to identify and study transcription factors involved in addiction pathophysiology primarily relied on quantifying the expression of candidate genes in bulk brain tissue after chronic cocaine treatment, as well as conventional overexpression and knockdown techniques. More recently, advances in next generation sequencing, bioinformatics, cell-type-specific targeting, and locus-specific neuroepigenomic editing offer a more powerful, unbiased toolbox to identify the most important transcription factors that drive drug-induced plasticity and to causally define their downstream molecular mechanisms. Here, we synthesize the literature on transcription factors mediating cocaine action in the NAc, discuss the advancements and remaining limitations of current experimental approaches, and emphasize recent work leveraging bioinformatic tools and neuroepigenomic editing to study transcription factors involved in cocaine addiction.
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37
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Jones-Tabah J, Martin RD, Chen JJ, Tanny JC, Clarke PBS, Hébert TE. A role for BET proteins in regulating basal, dopamine-induced and cAMP/PKA-dependent transcription in rat striatal neurons. Cell Signal 2021; 91:110226. [PMID: 34974082 DOI: 10.1016/j.cellsig.2021.110226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023]
Abstract
The activity of striatal medium-spiny projection neurons is regulated by D1 and D2 dopamine receptors. The D1 receptor (D1R) is a Gαs/olf-coupled GPCR which activates a cAMP/PKA/DARPP-32 signalling cascade that increases excitability and facilitates plasticity, partly through the regulation of transcription. Upon activation via D1R, PKA can translocate to the nucleus to regulate transcription through the phosphorylation of various targets. One candidate effector of PKA-dependent transcriptional regulation is the BET protein Brd4. It is known that when Brd4 is activated by phosphorylation, it binds more readily to acetylated histones at promoters and enhancers; moreover, in non-neuronal cells, PKA signalling has been shown to increase recruitment of Brd4 to chromatin. However, it is unknown whether BET proteins, or Brd4 specifically, are involved in transcriptional activation by cAMP/PKA in neurons. Here, we demonstrate that in adult rats, inhibition of BET proteins with the bromodomain inhibitor JQ1 suppressed the expression of ~25% of D1R-upregulated genes, while also increasing the expression of a subset of immediate-early genes. We further found that cAMP/PKA signalling promotes Brd4 recruitment to dopamine-induced genes in striatal neurons, and that knockdown of Brd4 attenuates D1R-induced gene expression. Finally, we report that JQ1 treatment downregulated expression of many GPCRs and also impaired ERK1/2 signalling in striatal neurons. Our findings identify the BET protein family, and Brd4 in particular, as novel regulators of basal and D1R-dependent transcription in rat striatal neurons, and delineate complex bi-directional effects of bromodomain inhibitors on neuronal transcription.
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Affiliation(s)
- Jace Jones-Tabah
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Ryan D Martin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Jennifer J Chen
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Paul B S Clarke
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada.
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada.
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38
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Carrera S, O'Donnell A, Li Y, Nowicki-Osuch K, Yang SH, Baker SM, Spiller D, Sharrocks AD. Complexities in the role of acetylation dynamics in modifying inducible gene activation parameters. Nucleic Acids Res 2021; 49:12744-12756. [PMID: 34850951 PMCID: PMC8682737 DOI: 10.1093/nar/gkab1176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 11/22/2022] Open
Abstract
High levels of histone acetylation are associated with the regulatory elements of active genes, suggesting a link between acetylation and gene activation. We revisited this model, in the context of EGF-inducible gene expression and found that rather than a simple unifying model, there are two broad classes of genes; one in which high lysine acetylation activity is required for efficient gene activation, and a second group where the opposite occurs and high acetylation activity is inhibitory. We examined the latter class in more detail using EGR2 as a model gene and found that lysine acetylation levels are critical for several activation parameters, including the timing of expression onset, and overall amplitudes of the transcriptional response. In contrast, DUSP1 responds in the canonical manner and its transcriptional activity is promoted by acetylation. Single cell approaches demonstrate heterogenous activation kinetics of a given gene in response to EGF stimulation. Acetylation levels modify these heterogenous patterns and influence both allele activation frequencies and overall expression profile parameters. Our data therefore point to a complex interplay between acetylation equilibria and target gene induction where acetylation level thresholds are an important determinant of transcriptional induction dynamics that are sensed in a gene-specific manner.
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Affiliation(s)
- Samantha Carrera
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Amanda O'Donnell
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Yaoyong Li
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Karol Nowicki-Osuch
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Shen-Hsi Yang
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Syed Murtuza Baker
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - David Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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39
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Gowthaman U, Ivanov M, Schwarz I, Patel HP, Müller NA, García‐Pichardo D, Lenstra TL, Marquardt S. The Hda1 histone deacetylase limits divergent non-coding transcription and restricts transcription initiation frequency. EMBO J 2021; 40:e108903. [PMID: 34661296 PMCID: PMC8634119 DOI: 10.15252/embj.2021108903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/31/2021] [Accepted: 09/28/2021] [Indexed: 01/01/2023] Open
Abstract
Nucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA and a divergent non-coding (DNC) transcript of unclear purpose. Here, we characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast. Using high-throughput reverse genetic screens based on quantitative single-cell fluorescence measurements, we identified the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC transcription. Nascent transcription profiling showed a genome-wide role of Hda1C in repression of DNC transcription. Live-cell imaging of transcription revealed that mutations in the Hda3 subunit increased the frequency of DNC transcription. Hda1C contributed to decreased acetylation of histone H3 in DNC transcription regions, supporting DNC transcription repression by histone deacetylation. Our data support the interpretation that DNC transcription results as a consequence of the NDR-based architecture of eukaryotic promoters, but that it is governed by locus-specific repression to maintain genome fidelity.
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Affiliation(s)
- Uthra Gowthaman
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Maxim Ivanov
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Isabel Schwarz
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Heta P Patel
- Division of Gene RegulationThe Netherlands Cancer Institute (NKI)Oncode InstituteAmsterdamThe Netherlands
| | - Niels A Müller
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Present address:
Thünen Institute of Forest GeneticsGrosshansdorfGermany
| | - Desiré García‐Pichardo
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Tineke L Lenstra
- Division of Gene RegulationThe Netherlands Cancer Institute (NKI)Oncode InstituteAmsterdamThe Netherlands
| | - Sebastian Marquardt
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
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40
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Ma S, Lv J, Feng Z, Rong Z, Lin Y. Get ready for the CRISPR/Cas system: A beginner's guide to the engineering and design of guide RNAs. J Gene Med 2021; 23:e3377. [PMID: 34270141 DOI: 10.1002/jgm.3377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/18/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is a state-of-the-art tool for versatile genome editing that has advanced basic research dramatically, with great potential for clinic applications. The system consists of two key molecules: a CRISPR-associated (Cas) effector nuclease and a single guide RNA. The simplicity of the system has enabled the development of a wide spectrum of derivative methods. Almost any laboratory can utilize these methods, although new users may initially be confused when faced with the potentially overwhelming abundance of choices. Cas nucleases and their engineering have been systematically reviewed previously. In the present review, we discuss single guide RNA engineering and design strategies that facilitate more efficient, more specific and safer gene editing.
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Affiliation(s)
- Shufeng Ma
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Zinan Feng
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
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41
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McClarty B, Rodriguez G, Dong H. Dose Effects of Histone Deacetylase Inhibitor Tacedinaline (CI-994) on Antipsychotic Haloperidol-Induced Motor and Memory Side Effects in Aged Mice. Front Neurosci 2021; 15:674745. [PMID: 34690667 PMCID: PMC8526546 DOI: 10.3389/fnins.2021.674745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/07/2021] [Indexed: 01/02/2023] Open
Abstract
Background: Elderly patients treated with antipsychotic drugs often experience increased severity and frequency of side effects, yet the mechanisms are not well understood. Studies from our group indicate age-related histone modifications at drug targeted receptor gene promoters may contribute to the increased side effects, and histone deacetylase (HDAC) inhibitors entinostat (MS-275) and valproic acid (VPA) could reverse typical antipsychotic haloperidol (HAL) induced motor-side effects. However, whether such effects could be dose dependent and whether HDAC inhibitors could improve memory function in aged mice is unknown. Methods: We co-treated selective class 1 HDAC inhibitor tacedinaline (CI-994) at different doses (10, 20, and 30 mg/kg) with HAL (0.05 mg/kg) in young (3 months) and aged (21 months) mice for 14 consecutive days, then motor and memory behavioral tests were conducted, followed by biochemical measurements. Results: CI-994 at doses of 10 and 20 mg/kg could decrease HAL-induced cataleptic episodes but only 20 mg/kg was sufficient to improve motor coordination in aged mice. Additionally, CI-994 at 10 and 20 mg/kg mitigate HAL-induced memory impairment in aged mice. Biochemical analyses showed increased acetylation of histone marks H3K27ac and H3K18ac at the dopamine 2 receptor (D2R) gene (Drd2) promoter and increased expression of the Drd2 mRNA and D2R protein in the striatum of aged mice after administration of CI-994 at 20 mg/kg. Conclusions: Our results suggest CI-994 can reduce HAL-induced motor and memory side effects in aged mice. These effects may act through an increase of acetylation at the Drd2 promoter, thereby restoring D2R expression and improving antipsychotic drug action.
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Affiliation(s)
- Bryan McClarty
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Guadalupe Rodriguez
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Hongxin Dong
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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42
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Reduction in gene expression noise by targeted increase in accessibility at gene loci. Proc Natl Acad Sci U S A 2021; 118:2018640118. [PMID: 34625470 DOI: 10.1073/pnas.2018640118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 01/30/2023] Open
Abstract
Many eukaryotic genes are expressed in randomly initiated bursts that are punctuated by periods of quiescence. Here, we show that the intermittent access of the promoters to transcription factors through relatively impervious chromatin contributes to this "noisy" transcription. We tethered a nuclease-deficient Cas9 fused to a histone acetyl transferase at the promoters of two endogenous genes in HeLa cells. An assay for transposase-accessible chromatin using sequencing showed that the activity of the histone acetyl transferase altered the chromatin architecture locally without introducing global changes in the nucleus and rendered the targeted promoters constitutively accessible. We measured the gene expression variability from the gene loci by performing single-molecule fluorescence in situ hybridization against mature messenger RNAs (mRNAs) and by imaging nascent mRNA molecules present at active gene loci in single cells. Because of the increased accessibility of the promoter to transcription factors, the transcription from two genes became less noisy, even when the average levels of expression did not change. In addition to providing evidence for chromatin accessibility as a determinant of the noise in gene expression, our study offers a mechanism for controlling gene expression noise which is otherwise unavoidable.
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43
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Dobrinić P, Szczurek AT, Klose RJ. PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency. Nat Struct Mol Biol 2021; 28:811-824. [PMID: 34608337 PMCID: PMC7612713 DOI: 10.1038/s41594-021-00661-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 08/10/2021] [Indexed: 12/15/2022]
Abstract
The Polycomb repressive system plays a fundamental role in controlling gene expression during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) bind target genes and use histone modification-dependent feedback mechanisms to form Polycomb chromatin domains and repress transcription. The inter-relatedness of PRC1 and PRC2 activity at these sites has made it difficult to discover the specific components of Polycomb chromatin domains that drive gene repression and to understand mechanistically how this is achieved. Here, by exploiting rapid degron-based approaches and time-resolved genomics, we kinetically dissect Polycomb-mediated repression and discover that PRC1 functions independently of PRC2 to counteract RNA polymerase II binding and transcription initiation. Using single-cell gene expression analysis, we reveal that PRC1 acts uniformly within the cell population and that repression is achieved by controlling transcriptional burst frequency. These important new discoveries provide a mechanistic and conceptual framework for Polycomb-dependent transcriptional control.
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Affiliation(s)
- Paula Dobrinić
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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44
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Marco A. Activity-dependent remodeling of genome architecture in engram cells facilitates memory formation and recall. Neural Regen Res 2021; 17:991-993. [PMID: 34558515 PMCID: PMC8552845 DOI: 10.4103/1673-5374.324834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Asaf Marco
- Neuro-Epigenetics Laboratory, the Robert H. Smith Faculty of Food, Environment and Agriculture, the Hebrew University of Jerusalem, Rehovol Campus, Israel
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45
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Liu S, Striebel J, Pasquini G, Ng AHM, Khoshakhlagh P, Church GM, Busskamp V. Neuronal Cell-type Engineering by Transcriptional Activation. Front Genome Ed 2021; 3:715697. [PMID: 34713262 PMCID: PMC8525383 DOI: 10.3389/fgeed.2021.715697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/12/2021] [Indexed: 12/26/2022] Open
Abstract
Gene activation with the CRISPR-Cas system has great implications in studying gene function, controlling cellular behavior, and modulating disease progression. In this review, we survey recent studies on targeted gene activation and multiplexed screening for inducing neuronal differentiation using CRISPR-Cas transcriptional activation (CRISPRa) and open reading frame (ORF) expression. Critical technical parameters of CRISPRa and ORF-based strategies for neuronal programming are presented and discussed. In addition, recent progress on in vivo applications of CRISPRa to the nervous system are highlighted. Overall, CRISPRa represents a valuable addition to the experimental toolbox for neuronal cell-type programming.
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Affiliation(s)
- Songlei Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Johannes Striebel
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Giovanni Pasquini
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | | | | | - George M. Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
- GC Therapeutics, Inc, Cambridge, MA, United States
| | - Volker Busskamp
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
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46
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Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering. EPIGENOMES 2021; 5:epigenomes5030017. [PMID: 34968366 PMCID: PMC8594717 DOI: 10.3390/epigenomes5030017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 01/23/2023] Open
Abstract
CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss how recent progress in plants and animals provides new routes to investigate the function of chromatin regulators and address the complexity of associated regulations that are often interconnected. While efficient transcriptional engineering methodologies have been developed and can be used as tools to alter the chromatin state of a locus, examples of direct manipulation of chromatin regulators remain scarce in plants. These reports also reveal pitfalls and limitations of epigenome engineering approaches that are nevertheless informative as they are often associated with locus- and context-dependent features, which include DNA accessibility, initial chromatin and transcriptional state or cellular dynamics. Strategies implemented in different organisms to overcome and even take advantage of these limitations are highlighted, which will further improve our ability to establish the causality and hierarchy of chromatin dynamics on genome regulation.
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47
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Tong Y, Zhang S, Riddle S, Zhang L, Song R, Yue D. Intrauterine Hypoxia and Epigenetic Programming in Lung Development and Disease. Biomedicines 2021; 9:944. [PMID: 34440150 PMCID: PMC8394854 DOI: 10.3390/biomedicines9080944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Clinically, intrauterine hypoxia is the foremost cause of perinatal morbidity and developmental plasticity in the fetus and newborn infant. Under hypoxia, deviations occur in the lung cell epigenome. Epigenetic mechanisms (e.g., DNA methylation, histone modification, and miRNA expression) control phenotypic programming and are associated with physiological responses and the risk of developmental disorders, such as bronchopulmonary dysplasia. This developmental disorder is the most frequent chronic pulmonary complication in preterm labor. The pathogenesis of this disease involves many factors, including aberrant oxygen conditions and mechanical ventilation-mediated lung injury, infection/inflammation, and epigenetic/genetic risk factors. This review is focused on various aspects related to intrauterine hypoxia and epigenetic programming in lung development and disease, summarizes our current knowledge of hypoxia-induced epigenetic programming and discusses potential therapeutic interventions for lung disease.
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Affiliation(s)
- Yajie Tong
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China;
| | - Shuqing Zhang
- School of Pharmacy, China Medical University, Shenyang 110122, China;
| | - Suzette Riddle
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Lubo Zhang
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA;
| | - Rui Song
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA;
| | - Dongmei Yue
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China;
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48
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Gemberling MP, Siklenka K, Rodriguez E, Tonn-Eisinger KR, Barrera A, Liu F, Kantor A, Li L, Cigliola V, Hazlett MF, Williams CA, Bartelt LC, Madigan VJ, Bodle JC, Daniels H, Rouse DC, Hilton IB, Asokan A, Ciofani M, Poss KD, Reddy TE, West AE, Gersbach CA. Transgenic mice for in vivo epigenome editing with CRISPR-based systems. Nat Methods 2021; 18:965-974. [PMID: 34341582 PMCID: PMC8349887 DOI: 10.1038/s41592-021-01207-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 06/08/2021] [Indexed: 01/08/2023]
Abstract
CRISPR-Cas9 technologies have dramatically increased the ease of targeting DNA sequences in the genomes of living systems. The fusion of chromatin-modifying domains to nuclease-deactivated Cas9 (dCas9) has enabled targeted epigenome editing in both cultured cells and animal models. However, delivering large dCas9 fusion proteins to target cells and tissues is an obstacle to the widespread adoption of these tools for in vivo studies. Here, we describe the generation and characterization of two conditional transgenic mouse lines for epigenome editing, Rosa26:LSL-dCas9-p300 for gene activation and Rosa26:LSL-dCas9-KRAB for gene repression. By targeting the guide RNAs to transcriptional start sites or distal enhancer elements, we demonstrate regulation of target genes and corresponding changes to epigenetic states and downstream phenotypes in the brain and liver in vivo, and in T cells and fibroblasts ex vivo. These mouse lines are convenient and valuable tools for facile, temporally controlled, and tissue-restricted epigenome editing and manipulation of gene expression in vivo.
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Affiliation(s)
- Matthew P Gemberling
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Keith Siklenka
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Erica Rodriguez
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Fang Liu
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Ariel Kantor
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Liqing Li
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Valentina Cigliola
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Regeneration Next Initiative, Duke University, Durham, NC, USA
| | - Mariah F Hazlett
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Courtney A Williams
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Luke C Bartelt
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | | | - Josephine C Bodle
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Heather Daniels
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Douglas C Rouse
- Division of Laboratory Animal Resources, Duke University School of Medicine, Durham, NC, USA
| | - Isaac B Hilton
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Aravind Asokan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Regeneration Next Initiative, Duke University, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Maria Ciofani
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Kenneth D Poss
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Regeneration Next Initiative, Duke University, Durham, NC, USA
| | - Timothy E Reddy
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Anne E West
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
- Regeneration Next Initiative, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
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49
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Kim B, Luo Y, Zhan X, Zhang Z, Shi X, Yi J, Xuan Z, Wu J. Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation. Cell Rep 2021; 36:109357. [PMID: 34260936 PMCID: PMC8315893 DOI: 10.1016/j.celrep.2021.109357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/16/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
Neuronal activity-induced enhancers drive gene activation. We demonstrate that BRG1, the core subunit of SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes, regulates neuronal activity-induced enhancers. Upon stimulation, BRG1 is recruited to enhancers in an H3K27Ac-dependent manner. BRG1 regulates enhancer basal activities and inducibility by affecting cohesin binding, enhancer-promoter looping, RNA polymerase II recruitment, and enhancer RNA expression. We identify a serine phosphorylation site in BRG1 that is induced by neuronal stimulations and is sensitive to CaMKII inhibition. BRG1 phosphorylation affects its interaction with several transcription co-factors, including the NuRD repressor complex and cohesin, possibly modulating BRG1-mediated transcription outcomes. Using mice with knockin mutations, we show that non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, whereas phosphomimic BRG1 increases enhancer activity and inducibility. These mutant mice display anxiety-like phenotypes and altered responses to stress. Therefore, we reveal a mechanism connecting neuronal signaling to enhancer activities through BRG1 phosphorylation.
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Affiliation(s)
- BongWoo Kim
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Luo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zilai Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuanming Shi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiaqing Yi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jiang Wu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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50
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Bass VL, Wong VC, Bullock ME, Gaudet S, Miller‐Jensen K. TNF stimulation primarily modulates transcriptional burst size of NF-κB-regulated genes. Mol Syst Biol 2021; 17:e10127. [PMID: 34288498 PMCID: PMC8290835 DOI: 10.15252/msb.202010127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Cell-to-cell heterogeneity is a feature of the tumor necrosis factor (TNF)-stimulated inflammatory response mediated by the transcription factor NF-κB, motivating an exploration of the underlying sources of this noise. Here, we combined single-transcript measurements with computational models to study transcriptional noise at six NF-κB-regulated inflammatory genes. In the basal state, NF-κB-target genes displayed an inverse correlation between mean and noise characteristic of transcriptional bursting. By analyzing transcript distributions with a bursting model, we found that TNF primarily activated transcription by increasing burst size while maintaining burst frequency for gene promoters with relatively high basal histone 3 acetylation (AcH3) that marks open chromatin environments. For promoters with lower basal AcH3 or when AcH3 was decreased with a small molecule drug, the contribution of burst frequency to TNF activation increased. Finally, we used a mathematical model to show that TNF positive feedback amplified gene expression noise resulting from burst size-mediated transcription, leading to a subset of cells with high TNF protein expression. Our results reveal potential sources of noise underlying intercellular heterogeneity in the TNF-mediated inflammatory response.
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Affiliation(s)
- Victor L Bass
- Department of Molecular, Cellular, and Developmental BiologyYale UniversityNew HavenCTUSA
- Present address:
Neuro‐Immune Regulome UnitNational Eye InstituteNational Institutes of HealthBethesdaMDUSA
| | - Victor C Wong
- Department of Molecular, Cellular, and Developmental BiologyYale UniversityNew HavenCTUSA
- Present address:
Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
| | - M Elise Bullock
- Department of Biomedical EngineeringYale UniversityNew HavenCTUSA
| | - Suzanne Gaudet
- Department of Cancer Biology and Center for Cancer Systems BiologyDana‐Farber Cancer InstituteBostonMAUSA
- Department of GeneticsHarvard Medical SchoolBostonMAUSA
- Present address:
Novartis Institute for BioMedical ResearchCambridgeMAUSA
| | - Kathryn Miller‐Jensen
- Department of Molecular, Cellular, and Developmental BiologyYale UniversityNew HavenCTUSA
- Department of Biomedical EngineeringYale UniversityNew HavenCTUSA
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