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Riley TR, Lazarovici A, Mann RS, Bussemaker HJ. Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE. eLife 2015; 4:e06397. [PMID: 26701911 PMCID: PMC4758951 DOI: 10.7554/elife.06397] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 12/20/2015] [Indexed: 01/26/2023] Open
Abstract
Transcription factors are crucial regulators of gene expression. Accurate quantitative definition of their intrinsic DNA binding preferences is critical to understanding their biological function. High-throughput in vitro technology has recently been used to deeply probe the DNA binding specificity of hundreds of eukaryotic transcription factors, yet algorithms for analyzing such data have not yet fully matured. Here, we present a general framework (FeatureREDUCE) for building sequence-to-affinity models based on a biophysically interpretable and extensible model of protein-DNA interaction that can account for dependencies between nucleotides within the binding interface or multiple modes of binding. When training on protein binding microarray (PBM) data, we use robust regression and modeling of technology-specific biases to infer specificity models of unprecedented accuracy and precision. We provide quantitative validation of our results by comparing to gold-standard data when available.
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Affiliation(s)
- Todd R Riley
- Department of Biological Sciences, Columbia University, New York, United States
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biology, University of Massachusetts Boston, Boston, United States
| | - Allan Lazarovici
- Department of Biological Sciences, Columbia University, New York, United States
- Department of Electrical Engineering, Columbia University, New York, United States
| | - Richard S Mann
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, United States
- Department of Systems Biology, Columbia University, New York, United States
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Dantas Machado AC, Zhou T, Rao S, Goel P, Rastogi C, Lazarovici A, Bussemaker HJ, Rohs R. Evolving insights on how cytosine methylation affects protein-DNA binding. Brief Funct Genomics 2015; 14:61-73. [PMID: 25319759 PMCID: PMC4303714 DOI: 10.1093/bfgp/elu040] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Many anecdotal observations exist of a regulatory effect of DNA methylation on gene expression. However, in general, the underlying mechanisms of this effect are poorly understood. In this review, we summarize what is currently known about how this important, but mysterious, epigenetic mark impacts cellular functions. Cytosine methylation can abrogate or enhance interactions with DNA-binding proteins, or it may have no effect, depending on the context. Despite being only a small chemical change, the addition of a methyl group to cytosine can affect base readout via hydrophobic contacts in the major groove and shape readout via electrostatic contacts in the minor groove. We discuss the recent discovery that CpG methylation increases DNase I cleavage at adjacent positions by an order of magnitude through altering the local 3D DNA shape and the possible implications of this structural insight for understanding the methylation sensitivity of transcription factors (TFs). Additionally, 5-methylcytosines change the stability of nucleosomes and, thus, affect the local chromatin structure and access of TFs to genomic DNA. Given these complexities, it seems unlikely that the influence of DNA methylation on protein-DNA binding can be captured in a small set of general rules. Hence, data-driven approaches may be essential to gain a better understanding of these mechanisms.
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Ghosh HS, Ceribelli M, Matos I, Lazarovici A, Bussemaker HJ, Lasorella A, Hiebert SW, Liu K, Staudt LM, Reizis B. ETO family protein Mtg16 regulates the balance of dendritic cell subsets by repressing Id2. ACTA ACUST UNITED AC 2014; 211:1623-35. [PMID: 24980046 PMCID: PMC4113936 DOI: 10.1084/jem.20132121] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dendritic cells (DCs) comprise two major subsets, the interferon (IFN)-producing plasmacytoid DCs (pDCs) and antigen-presenting classical DCs (cDCs). The development of pDCs is promoted by E protein transcription factor E2-2, whereas E protein antagonist Id2 is specifically absent from pDCs. Conversely, Id2 is prominently expressed in cDCs and promotes CD8(+) cDC development. The mechanisms that control the balance between E and Id proteins during DC subset specification remain unknown. We found that the loss of Mtg16, a transcriptional cofactor of the ETO protein family, profoundly impaired pDC development and pDC-dependent IFN response. The residual Mtg16-deficient pDCs showed aberrant phenotype, including the expression of myeloid marker CD11b. Conversely, the development of cDC progenitors (pre-DCs) and of CD8(+) cDCs was enhanced. Genome-wide expression and DNA-binding analysis identified Id2 as a direct target of Mtg16. Mtg16-deficient cDC progenitors and pDCs showed aberrant induction of Id2, and the deletion of Id2 facilitated the impaired development of Mtg16-deficient pDCs. Thus, Mtg16 promotes pDC differentiation and restricts cDC development in part by repressing Id2, revealing a cell-intrinsic mechanism that controls subset balance during DC development.
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Affiliation(s)
- Hiyaa S Ghosh
- Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032
| | - Michele Ceribelli
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ines Matos
- Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032
| | - Allan Lazarovici
- Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032
| | - Harmen J Bussemaker
- Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032
| | - Anna Lasorella
- Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Kang Liu
- Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032
| | - Louis M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Boris Reizis
- Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032
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Gray BF, Kalliadasis S, Lazarovici A, Macaskill C, Merkin JH, Scott SK. The suppression of an exothermic branched–chain flame through endothermic reaction and radical scavenging. Proc Math Phys Eng Sci 2002. [DOI: 10.1098/rspa.2002.0961] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- B. F. Gray
- School of Mathematics and Statistics, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - A. Lazarovici
- Department of Applied Mathematics, Leeds LS2 9JT, UK
| | - C. Macaskill
- School of Mathematics and Statistics, University of Sydney, Sydney, New South Wales 2006, Australia
| | - J. H. Merkin
- Department of Applied Mathematics, Leeds LS2 9JT, UK
| | - S. K. Scott
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
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