1
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Fadul SM, Arshad A, Mehmood R. CRISPR-based epigenome editing: mechanisms and applications. Epigenomics 2023; 15:1137-1155. [PMID: 37990877 DOI: 10.2217/epi-2023-0281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Epigenomic anomalies contribute significantly to the development of numerous human disorders. The development of epigenetic research tools is essential for understanding how epigenetic marks contribute to gene expression. A gene-editing technique known as CRISPR (clustered regularly interspaced short palindromic repeats) typically targets a particular DNA sequence using a guide RNA (gRNA). CRISPR/Cas9 technology has been remodeled for epigenome editing by generating a 'dead' Cas9 protein (dCas9) that lacks nuclease activity and juxtaposing it with an epigenetic effector domain. Based on fusion partners of dCas9, a specific epigenetic state can be achieved. CRISPR-based epigenome editing has widespread application in drug screening, cancer treatment and regenerative medicine. This paper discusses the tools developed for CRISPR-based epigenome editing and their applications.
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Affiliation(s)
- Shaima M Fadul
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
| | - Aleeza Arshad
- Medical Teaching Insitute, Ayub Teaching Hospital, Abbottabad, 22020, Pakistan
| | - Rashid Mehmood
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
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2
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Crawford MC, Tripu DR, Barritt SA, Jing Y, Gallimore D, Kales SC, Bhanu NV, Xiong Y, Fang Y, Butler KAT, LeClair CA, Coussens NP, Simeonov A, Garcia BA, Dibble CC, Meier JL. Comparative Analysis of Drug-like EP300/CREBBP Acetyltransferase Inhibitors. ACS Chem Biol 2023; 18:2249-2258. [PMID: 37737090 PMCID: PMC11059198 DOI: 10.1021/acschembio.3c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
The human acetyltransferase paralogues EP300 and CREBBP are master regulators of lysine acetylation whose activity has been implicated in various cancers. In the half-decade since the first drug-like inhibitors of these proteins were reported, three unique molecular scaffolds have taken precedent: an indane spiro-oxazolidinedione (A-485), a spiro-hydantoin (iP300w), and an aminopyridine (CPI-1612). Despite increasing use of these molecules to study lysine acetylation, the dearth of data regarding their relative biochemical and biological potencies makes their application as chemical probes a challenge. To address this gap, here we present a comparative study of drug-like EP300/CREBBP acetyltransferase inhibitors. First, we determine the biochemical and biological potencies of A-485, iP300w, and CPI-1612, highlighting the increased potencies of the latter two compounds at physiological acetyl-CoA concentrations. Cellular evaluation shows that inhibition of histone acetylation and cell growth closely aligns with the biochemical potencies of these molecules, consistent with an on-target mechanism. Finally, we demonstrate the utility of comparative pharmacology by using it to investigate the hypothesis that increased CoA synthesis caused by knockout of PANK4 can competitively antagonize the binding of EP300/CREBBP inhibitors and demonstrate proof-of-concept photorelease of a potent inhibitor molecule. Overall, our study demonstrates how knowledge of the relative inhibitor potency can guide the study of EP300/CREBBP-dependent mechanisms and suggests new approaches to target delivery, thus broadening the therapeutic window of these preclinical epigenetic drug candidates.
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Affiliation(s)
- McKenna C Crawford
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Deepika R Tripu
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Samuel A Barritt
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yihang Jing
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Diamond Gallimore
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Natarajan V Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Ying Xiong
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Kamaria A T Butler
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Nathan P Coussens
- Molecular Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Christian C Dibble
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jordan L Meier
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
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3
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Crawford MC, Tripu DR, Barritt SA, Jing Y, Gallimore D, Kales SC, Bhanu NV, Xiong Y, Fang Y, Butler KAT, LeClair CA, Coussens NP, Simeonov A, Garcia BA, Dibble CC, Meier JL. Comparative analysis of drug-like EP300/CREBBP acetyltransferase inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540887. [PMID: 37292747 PMCID: PMC10245587 DOI: 10.1101/2023.05.15.540887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The human acetyltransferase paralogs EP300 and CREBBP are master regulators of lysine acetylation whose activity has been implicated in various cancers. In the half-decade since the first drug-like inhibitors of these proteins were reported, three unique molecular scaffolds have taken precedent: an indane spiro-oxazolidinedione (A-485), a spiro-hydantoin (iP300w), and an aminopyridine (CPI-1612). Despite increasing use of these molecules to study lysine acetylation, the dearth of data regarding their relative biochemical and biological potencies makes their application as chemical probes a challenge. To address this gap, here we present a comparative study of drug-like EP300/CREBBP acetyltransferase inhibitors. First, we determine the biochemical and biological potencies of A-485, iP300w, and CPI-1612, highlighting the increased potency of the latter two compounds at physiological acetyl-CoA concentrations. Cellular evaluation shows that inhibition of histone acetylation and cell growth closely aligns with the biochemical potencies of these molecules, consistent with an on-target mechanism. Finally, we demonstrate the utility of comparative pharmacology by using it to investigate the hypothesis that increased CoA synthesis caused by knockout of PANK4 can competitively antagonize binding of EP300/CREBBP inhibitors and demonstrate proof-of-concept photorelease of a potent inhibitor molecule. Overall, our study demonstrates how knowledge of relative inhibitor potency can guide the study of EP300/CREBBP-dependent mechanisms and suggests new approaches to target delivery, thus broadening the therapeutic window of these preclinical epigenetic drug candidates.
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Affiliation(s)
- McKenna C Crawford
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Deepika R Tripu
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Samuel A Barritt
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yihang Jing
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Diamond Gallimore
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Natarajan V Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ying Xiong
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Kamaria A T Butler
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Nathan P Coussens
- Molecular Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Christian C Dibble
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jordan L Meier
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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4
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Toward the Development of Epigenome Editing-Based Therapeutics: Potentials and Challenges. Int J Mol Sci 2023; 24:ijms24054778. [PMID: 36902207 PMCID: PMC10003136 DOI: 10.3390/ijms24054778] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The advancement in epigenetics research over the past several decades has led to the potential application of epigenome-editing technologies for the treatment of various diseases. In particular, epigenome editing is potentially useful in the treatment of genetic and other related diseases, including rare imprinted diseases, as it can regulate the expression of the epigenome of the target region, and thereby the causative gene, with minimal or no modification of the genomic DNA. Various efforts are underway to successfully apply epigenome editing in vivo, such as improving target specificity, enzymatic activity, and drug delivery for the development of reliable therapeutics. In this review, we introduce the latest findings, summarize the current limitations and future challenges in the practical application of epigenome editing for disease therapy, and introduce important factors to consider, such as chromatin plasticity, for a more effective epigenome editing-based therapy.
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5
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Kabir F, Atkinson R, Cook AL, Phipps AJ, King AE. The role of altered protein acetylation in neurodegenerative disease. Front Aging Neurosci 2023; 14:1025473. [PMID: 36688174 PMCID: PMC9845957 DOI: 10.3389/fnagi.2022.1025473] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
Acetylation is a key post-translational modification (PTM) involved in the regulation of both histone and non-histone proteins. It controls cellular processes such as DNA transcription, RNA modifications, proteostasis, aging, autophagy, regulation of cytoskeletal structures, and metabolism. Acetylation is essential to maintain neuronal plasticity and therefore essential for memory and learning. Homeostasis of acetylation is maintained through the activities of histone acetyltransferases (HAT) and histone deacetylase (HDAC) enzymes, with alterations to these tightly regulated processes reported in several neurodegenerative diseases including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). Both hyperacetylation and hypoacetylation can impair neuronal physiological homeostasis and increase the accumulation of pathophysiological proteins such as tau, α-synuclein, and Huntingtin protein implicated in AD, PD, and HD, respectively. Additionally, dysregulation of acetylation is linked to impaired axonal transport, a key pathological mechanism in ALS. This review article will discuss the physiological roles of protein acetylation and examine the current literature that describes altered protein acetylation in neurodegenerative disorders.
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6
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CRISPR-dCas9 system for epigenetic editing towards therapeutic applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:15-24. [DOI: 10.1016/bs.pmbts.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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7
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He M, Zhou X, Li Z, Yin X, Han W, Zhou J, Sun X, Liu X, Yao D, Liang H. Programmable Transcriptional Modulation with a Structured RNA-Mediated CRISPR-dCas9 Complex. J Am Chem Soc 2022; 144:12690-12697. [DOI: 10.1021/jacs.2c02271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miao He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiang Zhou
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhigang Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xue Yin
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wenjie Han
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Junxiang Zhou
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaoyun Sun
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaoyu Liu
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dongbao Yao
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Haojun Liang
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
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8
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Transcription activation is enhanced by multivalent interactions independent of phase separation. Mol Cell 2022; 82:1878-1893.e10. [DOI: 10.1016/j.molcel.2022.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/28/2022] [Accepted: 04/11/2022] [Indexed: 12/23/2022]
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9
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Truong VA, Lin YH, Nguyen NTK, Hsu MN, Pham NN, Chang YH, Chang CW, Shen CC, Lee HS, Lai PL, Parfyonova YV, Menshikov M, Wu JC, Chang YH, Hu YC. Bi-directional gene activation and repression promote ASC differentiation and enhance bone healing in osteoporotic rats. Mol Ther 2022; 30:92-104. [PMID: 34450254 PMCID: PMC8753367 DOI: 10.1016/j.ymthe.2021.08.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/16/2021] [Accepted: 08/08/2021] [Indexed: 01/07/2023] Open
Abstract
Calvarial bone healing is challenging, especially for individuals with osteoporosis because stem cells from osteoporotic patients are highly prone to adipogenic differentiation. Based on previous findings that chondrogenic induction of adipose-derived stem cells (ASCs) can augment calvarial bone healing, we hypothesized that activating chondroinductive Sox Trio genes (Sox5, Sox6, Sox9) and repressing adipoinductive genes (C/ebp-α, Ppar-γ) in osteoporotic ASCs can reprogram cell differentiation and improve calvarial bone healing after implantation. However, simultaneous gene activation and repression in ASCs is difficult. To tackle this problem, we built a CRISPR-BiD system for bi-directional gene regulation. Specifically, we built a CRISPR-AceTran system that exploited both histone acetylation and transcription activation for synergistic Sox Trio activation. We also developed a CRISPR interference (CRISPRi) system that exploited DNA methylation for repression of adipoinductive genes. We combined CRISPR-AceTran and CRISPRi to form the CRISPR-BiD system, which harnessed three mechanisms (transcription activation, histone acetylation, and DNA methylation). After delivery into osteoporotic rat ASCs, CRISPR-BiD significantly enhanced chondrogenesis and in vitro cartilage formation. Implantation of the engineered osteoporotic ASCs into critical-sized calvarial bone defects significantly improved bone healing in osteoporotic rats. These results implicated the potential of the CRISPR-BiD system for bi-directional regulation of cell fate and regenerative medicine.
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Affiliation(s)
- Vu Anh Truong
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Ya-Hui Lin
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Mu-Nung Hsu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Nam Ngoc Pham
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Hao Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Che Shen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsiang-Sheng Lee
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Po-Liang Lai
- Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan,Bone and Joint Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yelena V. Parfyonova
- National Medical Research Center of Cardiology, Russian Ministry of Health, Moscow, Russia,Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail Menshikov
- Institute of Experimental Cardiology, National Cardiology Research Center, Moscow, Russia
| | - Jaw-Ching Wu
- Medical Research Department, Taipei Veterans General Hospital, Taipei, Taiwan,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Han Chang
- Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan,College of Medicine, Chang Gung University, Taoyuan, Taiwan,Corresponding author: Yu-Chen Hu, Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan,Corresponding author: Yu-Han Chang, Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan.
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10
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Martella A, Fisher DI. Regulation of Gene Expression and the Elucidative Role of CRISPR-Based Epigenetic Modifiers and CRISPR-Induced Chromosome Conformational Changes. CRISPR J 2021; 4:43-57. [PMID: 33616442 DOI: 10.1089/crispr.2020.0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In complex multicellular systems, gene expression is regulated at multiple stages through interconnected complex molecular pathways and regulatory networks. Transcription is the first step in gene expression and is subject to multiple layers of regulation in which epigenetic mechanisms such as DNA methylation, histone tail modifications, and chromosomal conformation play an essential role. In recent years, CRISPR-Cas9 systems have been employed to unearth this complexity and provide new insights on the contribution of chromatin dysregulation in the development of genetic diseases, as well as new tools to prevent or reverse this dysregulation. In this review, we outline the recent development of a variety of CRISPR-based epigenetic editors for targeted DNA methylation/demethylation, histone modification, and three-dimensional DNA conformational change, highlighting their relative performance and impact on gene regulation. Finally, we provide insights on the future developments aimed to accelerate our understanding of the causal relationship between epigenetic marks, genome organization, and gene regulation.
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Affiliation(s)
- Andrea Martella
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - David I Fisher
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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11
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Nakamura M, Gao Y, Dominguez AA, Qi LS. CRISPR technologies for precise epigenome editing. Nat Cell Biol 2021; 23:11-22. [PMID: 33420494 DOI: 10.1038/s41556-020-00620-7] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023]
Abstract
The epigenome involves a complex set of cellular processes governing genomic activity. Dissecting this complexity necessitates the development of tools capable of specifically manipulating these processes. The repurposing of prokaryotic CRISPR systems has allowed for the development of diverse technologies for epigenome engineering. Here, we review the state of currently achievable epigenetic manipulations along with corresponding applications. With future optimization, CRISPR-based epigenomic editing stands as a set of powerful tools for understanding and controlling biological function.
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Affiliation(s)
- Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Yuchen Gao
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Cancer Biology Program, Stanford University, Stanford, CA, USA.,Mammoth Biosciences, South San Francisco, CA, USA
| | - Antonia A Dominguez
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Sana Biotechnology, South San Francisco, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA. .,Stanford ChEM-H Institute, Stanford University, Stanford, CA, USA.
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12
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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13
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Garlick JM, Mapp AK. Selective Modulation of Dynamic Protein Complexes. Cell Chem Biol 2020; 27:986-997. [PMID: 32783965 PMCID: PMC7469457 DOI: 10.1016/j.chembiol.2020.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022]
Abstract
Dynamic proteins perform critical roles in cellular machines, including those that control proteostasis, transcription, translation, and signaling. Thus, dynamic proteins are prime candidates for chemical probe and drug discovery but difficult targets because they do not conform to classical rules of design and screening. Selectivity is pivotal for candidate probe molecules due to the extensive interaction network of these dynamic hubs. Recognition that the traditional rules of probe discovery are not necessarily applicable to dynamic proteins and their complexes, as well as technological advances in screening, have produced remarkable results in the last 2-4 years. Particularly notable are the improvements in target selectivity for small-molecule modulators of dynamic proteins, especially with techniques that increase the discovery likelihood of allosteric regulatory mechanisms. We focus on approaches to small-molecule screening that appear to be more suitable for highly dynamic targets and have the potential to streamline identification of selective modulators.
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Affiliation(s)
- Julie M Garlick
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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14
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Shakirova KM, Ovchinnikova VY, Dashinimaev EB. Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems. Front Bioeng Biotechnol 2020; 8:882. [PMID: 32850737 PMCID: PMC7399070 DOI: 10.3389/fbioe.2020.00882] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
The speed of reprogramming technologies evolution is rising dramatically in modern science. Both the scientific community and health workers depend on such developments due to the lack of safe autogenic cells and tissues for regenerative medicine, genome editing tools and reliable screening techniques. To perform experiments efficiently and to propel the fundamental science it is important to keep up with novel modifications and techniques that are being discovered almost weekly. One of them is CRISPR/Cas9 based genome and transcriptome editing. The aim of this article is to summarize currently existing CRISPR/Cas9 applications for cell reprogramming, mainly, to compare them with other non-CRISPR approaches and to highlight future perspectives and opportunities.
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Affiliation(s)
- Ksenia M Shakirova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Viktoriia Y Ovchinnikova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Erdem B Dashinimaev
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
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15
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Lau CH, Tin C. The Synergy between CRISPR and Chemical Engineering. Curr Gene Ther 2020; 19:147-171. [PMID: 31267870 DOI: 10.2174/1566523219666190701100556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 02/06/2023]
Abstract
Gene therapy and transgenic research have advanced quickly in recent years due to the development of CRISPR technology. The rapid development of CRISPR technology has been largely benefited by chemical engineering. Firstly, chemical or synthetic substance enables spatiotemporal and conditional control of Cas9 or dCas9 activities. It prevents the leaky expression of CRISPR components, as well as minimizes toxicity and off-target effects. Multi-input logic operations and complex genetic circuits can also be implemented via multiplexed and orthogonal regulation of target genes. Secondly, rational chemical modifications to the sgRNA enhance gene editing efficiency and specificity by improving sgRNA stability and binding affinity to on-target genomic loci, and hence reducing off-target mismatches and systemic immunogenicity. Chemically-modified Cas9 mRNA is also more active and less immunogenic than the native mRNA. Thirdly, nonviral vehicles can circumvent the challenges associated with viral packaging and production through the delivery of Cas9-sgRNA ribonucleoprotein complex or large Cas9 expression plasmids. Multi-functional nanovectors enhance genome editing in vivo by overcoming multiple physiological barriers, enabling ligand-targeted cellular uptake, and blood-brain barrier crossing. Chemical engineering can also facilitate viral-based delivery by improving vector internalization, allowing tissue-specific transgene expression, and preventing inactivation of the viral vectors in vivo. This review aims to discuss how chemical engineering has helped improve existing CRISPR applications and enable new technologies for biomedical research. The usefulness, advantages, and molecular action for each chemical engineering approach are also highlighted.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong
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16
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Breunig CT, Köferle A, Neuner AM, Wiesbeck MF, Baumann V, Stricker SH. CRISPR Tools for Physiology and Cell State Changes: Potential of Transcriptional Engineering and Epigenome Editing. Physiol Rev 2020; 101:177-211. [PMID: 32525760 DOI: 10.1152/physrev.00034.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Given the large amount of genome-wide data that have been collected during the last decades, a good understanding of how and why cells change during development, homeostasis, and disease might be expected. Unfortunately, the opposite is true; triggers that cause cellular state changes remain elusive, and the underlying molecular mechanisms are poorly understood. Although genes with the potential to influence cell states are known, the historic dependency on methods that manipulate gene expression outside the endogenous chromatin context has prevented us from understanding how cells organize, interpret, and protect cellular programs. Fortunately, recent methodological innovations are now providing options to answer these outstanding questions, by allowing to target and manipulate individual genomic and epigenomic loci. In particular, three experimental approaches are now feasible due to DNA targeting tools, namely, activation and/or repression of master transcription factors in their endogenous chromatin context; targeting transcription factors to endogenous, alternative, or inaccessible sites; and finally, functional manipulation of the chromatin context. In this article, we discuss the molecular basis of DNA targeting tools and review the potential of these new technologies before we summarize how these have already been used for the manipulation of cellular states and hypothesize about future applications.
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Affiliation(s)
- Christopher T Breunig
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Anna Köferle
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Andrea M Neuner
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Maximilian F Wiesbeck
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Valentin Baumann
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
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17
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Zhao W, Wang Y, Liang FS. Chemical and Light Inducible Epigenome Editing. Int J Mol Sci 2020; 21:ijms21030998. [PMID: 32028669 PMCID: PMC7037166 DOI: 10.3390/ijms21030998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
The epigenome defines the unique gene expression patterns and resulting cellular behaviors in different cell types. Epigenome dysregulation has been directly linked to various human diseases. Epigenome editing enabling genome locus-specific targeting of epigenome modifiers to directly alter specific local epigenome modifications offers a revolutionary tool for mechanistic studies in epigenome regulation as well as the development of novel epigenome therapies. Inducible and reversible epigenome editing provides unique temporal control critical for understanding the dynamics and kinetics of epigenome regulation. This review summarizes the progress in the development of spatiotemporal-specific tools using small molecules or light as inducers to achieve the conditional control of epigenome editing and their applications in epigenetic research.
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18
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Abstract
The dynamic nature of histone post-translational modifications such as methylation or acetylation makes possible the alteration of disease associated epigenetic states through the manipulation of the associated epigenetic machinery. One approach is through small molecule perturbation. Chemical probes of epigenetic reader domains have been critical in improving our understanding of the biological consequences of modulating their targets, while also enabling the development of novel probe-based reagents. By appending a functional handle to a reader domain probe, a chemical toolbox of reagents can be created to facilitate chemiprecipitation of epigenetic complexes, evaluate probe selectivity, develop in vitro screening assays, visualize cellular target localization, enable target degradation and recruit epigenetic machinery to a site within the genome in a highly controlled fashion.
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19
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Chiarella AM, Butler KV, Gryder BE, Lu D, Wang TA, Yu X, Pomella S, Khan J, Jin J, Hathaway NA. Dose-dependent activation of gene expression is achieved using CRISPR and small molecules that recruit endogenous chromatin machinery. Nat Biotechnol 2020; 38:50-55. [PMID: 31712774 PMCID: PMC6954327 DOI: 10.1038/s41587-019-0296-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/24/2019] [Indexed: 01/10/2023]
Abstract
Gene expression can be activated or suppressed using CRISPR--Cas9 systems. However, tools that enable dose-dependent activation of gene expression without the use of exogenous transcription regulatory proteins are lacking. Here we describe chemical epigenetic modifiers (CEMs) designed to activate the expression of target genes by recruiting components of the endogenous chromatin-activating machinery, eliminating the need for exogenous transcriptional activators. The system has two parts: catalytically inactive Cas9 (dCas9) in complex with FK506-binding protein (FKBP) and a CEM consisting of FK506 linked to a molecule that interacts with cellular epigenetic machinery. We show that CEMs upregulate gene expression at target endogenous loci up to 20-fold or more depending on the gene. We also demonstrate dose-dependent control of transcriptional activation, function across multiple diverse genes, reversibility of CEM activity and specificity of our best-in-class CEM across the genome.
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Affiliation(s)
- Anna M Chiarella
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Kyle V Butler
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Berkley E Gryder
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Dongbo Lu
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Tiffany A Wang
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silvia Pomella
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Pediatric Hematology and Oncology, Bambino Gesu' Children's Hospital, Rome, Italy
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA.
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20
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Sajwan S, Mannervik M. Gene activation by dCas9-CBP and the SAM system differ in target preference. Sci Rep 2019; 9:18104. [PMID: 31792240 PMCID: PMC6888908 DOI: 10.1038/s41598-019-54179-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/08/2019] [Indexed: 12/21/2022] Open
Abstract
Gene overexpression through the targeting of transcription activation domains to regulatory DNA via catalytically defective Cas9 (dCas9) represents a powerful approach to investigate gene function as well as the mechanisms of gene control. To date, the most efficient dCas9-based activator is the Synergistic Activation Mediator (SAM) system whereby transcription activation domains are directly fused to dCas9 as well as tethered through MS2 loops engineered into the gRNA. Here, we show that dCas9 fused to the catalytic domain of the histone acetyltransferase CBP is a more potent activator than the SAM system at some loci, but less efficient at other locations in Drosophila cells. Our results suggest that different rate-limiting steps in the transcription cycle are affected by dCas9-CBP and the SAM system, and that comparing these activators may be useful for mechanistic studies of transcription as well as for increasing the number of hits in genome-wide overexpression screens.
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Affiliation(s)
- Suresh Sajwan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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21
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Cunningham-Bryant D, Sun J, Fernandez B, Zalatan JG. CRISPR-Cas-Mediated Chemical Control of Transcriptional Dynamics in Yeast. Chembiochem 2019; 20:1519-1523. [PMID: 30710419 PMCID: PMC6570556 DOI: 10.1002/cbic.201800823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Indexed: 11/07/2022]
Abstract
Synthetic CRISPR-Cas transcription factors enable the construction of complex gene-expression programs, and chemically inducible systems allow precise control over the expression dynamics. To provide additional modes of regulatory control, we have constructed a chemically inducible CRISPR activation (CRISPRa) system in yeast that is mediated by recruitment to MS2-functionalized guide RNAs. We use reporter gene assays to systematically map the dose dependence, time dependence, and reversibility of the system. Because the recruitment function is encoded at the level of the guide RNA, it is straightforward to target multiple genes and independently regulate expression dynamics at individual targets. This approach provides a new method to engineer sophisticated, multigene programs with precise control over the dynamics of gene expression.
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Affiliation(s)
| | - Jingwen Sun
- Department of Chemistry, University of Washington, 36 Bagley Hall, Seattle, WA, 98195, USA
| | - Brianna Fernandez
- Department of Chemistry, University of Washington, 36 Bagley Hall, Seattle, WA, 98195, USA
| | - Jesse G Zalatan
- Department of Chemistry, University of Washington, 36 Bagley Hall, Seattle, WA, 98195, USA
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22
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Lampreht Tratar U, Horvat S, Cemazar M. Transgenic Mouse Models in Cancer Research. Front Oncol 2018; 8:268. [PMID: 30079312 PMCID: PMC6062593 DOI: 10.3389/fonc.2018.00268] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/29/2018] [Indexed: 12/26/2022] Open
Abstract
The use of existing mouse models in cancer research is of utmost importance as they aim to explore the casual link between candidate cancer genes and carcinogenesis as well as to provide models to develop and test new therapies. However, faster progress in translating mouse cancer model research into the clinic has been hampered due to the limitations of these models to better reflect the complexities of human tumors. Traditionally, immunocompetent and immunodeficient mice with syngeneic and xenografted tumors transplanted subcutaneously or orthotopically have been used. These models are still being widely employed for many different types of studies, in part due to their widespread availability and low cost. Other types of mouse models used in cancer research comprise transgenic mice in which oncogenes can be constitutively or conditionally expressed and tumor-suppressor genes silenced using conventional methods, such as retroviral infection, microinjection of DNA constructs, and the so-called "gene-targeted transgene" approach. These traditional transgenic models have been very important in studies of carcinogenesis and tumor pathogenesis, as well as in studies evaluating the development of resistance to therapy. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing approach has revolutionized the field of mouse cancer models and has had a profound and rapid impact on the development of more effective systems to study human cancers. The CRISPR/Cas9-based transgenic models have the capacity to engineer a wide spectrum of mutations found in human cancers and provide solutions to problems that were previously unsolvable. Recently, humanized mouse xenograft models that accept patient-derived xenografts and CD34+ cells were developed to better mimic tumor heterogeneity, the tumor microenvironment, and cross-talk between the tumor and stromal/immune cells. These features make them extremely valuable models for the evaluation of investigational cancer therapies, specifically new immunotherapies. Taken together, improvements in both the CRISPR/Cas9 system producing more valid mouse models and in the humanized mouse xenograft models resembling complex interactions between the tumor and its environment might represent one of the successful pathways to precise individualized cancer therapy, leading to improved cancer patient survival and quality of life.
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Affiliation(s)
- Ursa Lampreht Tratar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Simon Horvat
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Cemazar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia.,Faculty of Health Sciences, University of Primorska, Isola, Slovenia
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23
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Breen ME, Mapp AK. Modulating the masters: chemical tools to dissect CBP and p300 function. Curr Opin Chem Biol 2018; 45:195-203. [PMID: 30025258 DOI: 10.1016/j.cbpa.2018.06.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/25/2018] [Accepted: 06/02/2018] [Indexed: 01/07/2023]
Abstract
Dysregulation of transcription is found in nearly every human disease, and as a result there has been intense interest in developing new therapeutics that target regulators of transcription. CREB binding protein (CBP) and its paralogue p300 are attractive targets due to their function as `master coactivators'. Although inhibitors of several CBP/p300 domains have been identified, the selectivity of many of these compounds has remained underexplored. Here, we review recent successes in the development of chemical tools targeting several CBP/p300 domains with selectivity acceptable for use as chemical probes. Additionally, we highlight recent studies which have used these probes to expand our understanding of interdomain interactions and differential coactivator usage.
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Affiliation(s)
- Meghan E Breen
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA
| | - Anna K Mapp
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA.
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24
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Abstract
The eukaryotic epigenome has an instrumental role in determining and maintaining cell identity and function. Epigenetic components such as DNA methylation, histone tail modifications, chromatin accessibility, and DNA architecture are tightly correlated with central cellular processes, while their dysregulation manifests in aberrant gene expression and disease. The ability to specifically edit the epigenome holds the promise of enhancing understanding of how epigenetic modifications function and enabling manipulation of cell phenotype for research or therapeutic purposes. Genome engineering technologies use highly specific DNA-targeting tools to precisely deposit epigenetic changes in a locus-specific manner, creating diverse epigenome editing platforms. This review summarizes these technologies and insights from recent studies, describes the complex relationship between epigenetic components and gene regulation, and highlights caveats and promises of the emerging field of epigenome editing, including applications for translational purposes, such as epigenetic therapy and regenerative medicine.
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Affiliation(s)
- Liad Holtzman
- Department of Biomedical Engineering and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; ,
| | - Charles A Gersbach
- Department of Biomedical Engineering and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; , .,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
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