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Kribelbauer JF, Laptenko O, Chen S, Martini GD, Freed-Pastor WA, Prives C, Mann RS, Bussemaker HJ. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes. Cell Rep 2018; 19:2383-2395. [PMID: 28614722 DOI: 10.1016/j.celrep.2017.05.069] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 04/07/2017] [Accepted: 05/22/2017] [Indexed: 01/25/2023] Open
Abstract
Although DNA modifications play an important role in gene regulation, the underlying mechanisms remain elusive. We developed EpiSELEX-seq to probe the sensitivity of transcription factor binding to DNA modification in vitro using massively parallel sequencing. Feature-based modeling quantifies the effect of cytosine methylation (5mC) on binding free energy in a position-specific manner. Application to the human bZIP proteins ATF4 and C/EBPβ and three different Pbx-Hox complexes shows that 5mCpG can both increase and decrease affinity, depending on where the modification occurs within the protein-DNA interface. The TF paralogs tested vary in their methylation sensitivity, for which we provide a structural rationale. We show that 5mCpG can also enhance in vitro p53 binding and provide evidence for increased in vivo p53 occupancy at methylated binding sites, correlating with primed enhancer histone marks. Our results establish a powerful strategy for dissecting the epigenomic modulation of protein-DNA interactions and their role in gene regulation.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Siying Chen
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Gabriella D Martini
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - William A Freed-Pastor
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Richard S Mann
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA.
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Weng YL, An R, Cassin J, Joseph J, Mi R, Wang C, Zhong C, Jin SG, Pfeifer GP, Bellacosa A, Dong X, Hoke A, He Z, Song H, Ming GL. An Intrinsic Epigenetic Barrier for Functional Axon Regeneration. Neuron 2017; 94:337-346.e6. [PMID: 28426967 PMCID: PMC6007997 DOI: 10.1016/j.neuron.2017.03.034] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 02/05/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022]
Abstract
Mature neurons in the adult peripheral nervous system can effectively switch from a dormant state with little axonal growth to robust axon regeneration upon injury. The mechanisms by which injury unlocks mature neurons' intrinsic axonal growth competence are not well understood. Here, we show that peripheral sciatic nerve lesion in adult mice leads to elevated levels of Tet3 and 5-hydroxylmethylcytosine in dorsal root ganglion (DRG) neurons. Functionally, Tet3 is required for robust axon regeneration of DRG neurons and behavioral recovery. Mechanistically, peripheral nerve injury induces DNA demethylation and upregulation of multiple regeneration-associated genes in a Tet3- and thymine DNA glycosylase-dependent fashion in DRG neurons. In addition, Pten deletion-induced axon regeneration of retinal ganglion neurons in the adult CNS is attenuated upon Tet1 knockdown. Together, our study suggests an epigenetic barrier that can be removed by active DNA demethylation to permit axon regeneration in the adult mammalian nervous system.
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Affiliation(s)
- Yi-Lan Weng
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ran An
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200040, China
| | - Jessica Cassin
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Pre-doctoral Human Genetics Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jessica Joseph
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ruifa Mi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chen Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Chun Zhong
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Seung-Gi Jin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gerd P. Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ahmet Hoke
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Pre-doctoral Human Genetics Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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