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Zhang L, Li G, Zhang Y, Cheng Y, Roberts N, Glenn SE, DeZwaan-McCabe D, Rube HT, Manthey J, Coleman G, Vakulskas CA, Qi Y. Boosting genome editing efficiency in human cells and plants with novel LbCas12a variants. Genome Biol 2023; 24:102. [PMID: 37122009 PMCID: PMC10150537 DOI: 10.1186/s13059-023-02929-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/07/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND Cas12a (formerly known as Cpf1), the class II type V CRISPR nuclease, has been widely used for genome editing in mammalian cells and plants due to its distinct characteristics from Cas9. Despite being one of the most robust Cas12a nucleases, LbCas12a in general is less efficient than SpCas9 for genome editing in human cells, animals, and plants. RESULTS To improve the editing efficiency of LbCas12a, we conduct saturation mutagenesis in E. coli and identify 1977 positive point mutations of LbCas12a. We selectively assess the editing efficiency of 56 LbCas12a variants in human cells, identifying an optimal LbCas12a variant (RVQ: G146R/R182V/E795Q) with the most robust editing activity. We further test LbCas12a-RV, LbCas12a-RRV, and LbCas12a-RVQ in plants and find LbCas12a-RV has robust editing activity in rice and tomato protoplasts. Interestingly, LbCas12a-RRV, resulting from the stacking of RV and D156R, displays improved editing efficiency in stably transformed rice and poplar plants, leading to up to 100% editing efficiency in T0 plants of both plant species. Moreover, this high-efficiency editing occurs even at the non-canonical TTV PAM sites. CONCLUSIONS Our results demonstrate that LbCas12a-RVQ is a powerful tool for genome editing in human cells while LbCas12a-RRV confers robust genome editing in plants. Our study reveals the tremendous potential of these LbCas12a variants for advancing precision genome editing applications across a wide range of organisms.
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Affiliation(s)
- Liyang Zhang
- Integrated DNA Technologies, Coralville, IA, 52241, USA
- Current Address: Aera Therapeutics, 50 Northern Ave, Boston, MA, 02210, USA
| | - Gen Li
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
- Current Address: Syngenta, 9 Davis Dr, Research Triangle, NC, 27709, USA
| | - Yanhao Cheng
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | | | - Steve E Glenn
- Integrated DNA Technologies, Coralville, IA, 52241, USA
| | | | - H Tomas Rube
- Department of Applied Mathematics, University of California-Merced, Merced, CA, 95343, USA
| | - Jeff Manthey
- Integrated DNA Technologies, Coralville, IA, 52241, USA
| | - Gary Coleman
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
| | | | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.
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2
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Rube HT, Rastogi C, Feng S, Kribelbauer JF, Li A, Becerra B, Melo LAN, Do BV, Li X, Adam HH, Shah NH, Mann RS, Bussemaker HJ. Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning. Nat Biotechnol 2022; 40:1520-1527. [PMID: 35606422 PMCID: PMC9546773 DOI: 10.1038/s41587-022-01307-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 06/06/2021] [Accepted: 04/04/2022] [Indexed: 01/02/2023]
Abstract
Protein-ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions. Here we describe a flexible machine learning method, called ProBound, that accurately defines sequence recognition in terms of equilibrium binding constants or kinetic rates. This is achieved using a multi-layered maximum-likelihood framework that models both the molecular interactions and the data generation process. We show that ProBound quantifies transcription factor (TF) behavior with models that predict binding affinity over a range exceeding that of previous resources; captures the impact of DNA modifications and conformational flexibility of multi-TF complexes; and infers specificity directly from in vivo data such as ChIP-seq without peak calling. When coupled with an assay called KD-seq, it determines the absolute affinity of protein-ligand interactions. We also apply ProBound to profile the kinetics of kinase-substrate interactions. ProBound opens new avenues for decoding biological networks and rationally engineering protein-ligand interactions.
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Affiliation(s)
- H Tomas Rube
- Department of Bioengineering, University of California, Merced, Merced, CA, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Allyson Li
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Basheer Becerra
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lucas A N Melo
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Bach Viet Do
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Xiaoting Li
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Hammaad H Adam
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
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3
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Feng S, Rastogi C, Loker R, Glassford WJ, Tomas Rube H, Bussemaker HJ, Mann RS. Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors. Nat Commun 2022; 13:3808. [PMID: 35778382 PMCID: PMC9249852 DOI: 10.1038/s41467-022-31501-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 08/03/2021] [Accepted: 06/20/2022] [Indexed: 12/23/2022] Open
Abstract
In eukaryotes, members of transcription factor families often exhibit similar DNA binding properties in vitro, yet orchestrate paralog-specific gene regulatory networks in vivo. The serially homologous first (T1) and third (T3) thoracic legs of Drosophila, which are specified by the Hox proteins Scr and Ubx, respectively, offer a unique opportunity to address this paradox in vivo. Genome-wide analyses using epitope-tagged alleles of both Hox loci in the T1 and T3 leg imaginal discs, the precursors to the adult legs and ventral body regions, show that ~8% of Hox binding is paralog-specific. Binding specificity is mediated by interactions with distinct cofactors in different domains: the Hox cofactor Exd acts in the proximal domain and is necessary for Scr to bind many of its paralog-specific targets, while in the distal leg domain, the homeodomain protein Distal-less (Dll) enhances Scr binding to a different subset of loci. These findings reveal how Hox paralogs, and perhaps paralogs of other transcription factor families, orchestrate alternative downstream gene regulatory networks with the help of multiple, context-specific cofactors.
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Affiliation(s)
- Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ryan Loker
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Genetics and Development, Columbia University, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - William J Glassford
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - H Tomas Rube
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Bioengineering, University of California, Merced, CA, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, 10027, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, 10027, USA.
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4
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Zhang L, Rube HT, Vakulskas CA, Behlke MA, Bussemaker HJ, Pufall MA. Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes. Nucleic Acids Res 2020; 48:5037-5053. [PMID: 32315032 PMCID: PMC7229833 DOI: 10.1093/nar/gkaa231] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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] [Received: 11/27/2019] [Revised: 03/06/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
CRISPR RNA-guided endonucleases (RGEs) cut or direct activities to specific genomic loci, yet each has off-target activities that are often unpredictable. We developed a pair of simple in vitro assays to systematically measure the DNA-binding specificity (Spec-seq), catalytic activity specificity (SEAM-seq) and cleavage efficiency of RGEs. By separately quantifying binding and cleavage specificity, Spec/SEAM-seq provides detailed mechanistic insight into off-target activity. Feature-based models generated from Spec/SEAM-seq data for SpCas9 were consistent with previous reports of its in vitro and in vivo specificity, validating the approach. Spec/SEAM-seq is also useful for profiling less-well characterized RGEs. Application to an engineered SpCas9, HiFi-SpCas9, indicated that its enhanced target discrimination can be attributed to cleavage rather than binding specificity. The ortholog ScCas9, on the other hand, derives specificity from binding to an extended PAM. The decreased off-target activity of AsCas12a (Cpf1) appears to be primarily driven by DNA-binding specificity. Finally, we performed the first characterization of CasX specificity, revealing an all-or-nothing mechanism where mismatches can be bound, but not cleaved. Together, these applications establish Spec/SEAM-seq as an accessible method to rapidly and reliably evaluate the specificity of RGEs, Cas::gRNA pairs, and gain insight into the mechanism and thermodynamics of target discrimination.
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Affiliation(s)
- Liyang Zhang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Coralville, IA 52241, USA.,Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
| | - H Tomas Rube
- Department of Bioengineering, University of California, Merced, New York, NY 10027, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA.,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Coralville, IA 52241, USA
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5
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Kribelbauer JF, Loker RE, Feng S, Rastogi C, Abe N, Rube HT, Bussemaker HJ, Mann RS. Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins. Mol Cell 2020; 78:152-167.e11. [PMID: 32053778 DOI: 10.1016/j.molcel.2020.01.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 09/12/2019] [Revised: 12/01/2019] [Accepted: 01/27/2020] [Indexed: 01/09/2023]
Abstract
Eukaryotic transcription factors (TFs) form complexes with various partner proteins to recognize their genomic target sites. Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood. Here, we demonstrate that high-throughput in vitro DNA binding assays coupled with unbiased computational analysis provide unprecedented insight into how different DNA sequences select distinct compositions and configurations of homeodomain TF complexes. Using inferred knowledge about minor groove width readout, we design targeted protein mutations that destabilize homeodomain binding both in vitro and in vivo in a complex-specific manner. By performing parallel systematic evolution of ligands by exponential enrichment sequencing (SELEX-seq), chromatin immunoprecipitation sequencing (ChIP-seq), RNA sequencing (RNA-seq), and Hi-C assays, we not only classify the majority of in vivo binding events in terms of complex composition but also infer complex-specific functions by perturbing the gene regulatory network controlled by a single complex.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ryan E Loker
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Namiko Abe
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - H Tomas Rube
- Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Richard S Mann
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Neuroscience, Columbia University, New York, NY 10027, USA.
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6
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Rube HT, Rastogi C, Kribelbauer JF, Bussemaker HJ. A unified approach for quantifying and interpreting DNA shape readout by transcription factors. Mol Syst Biol 2018; 14:e7902. [PMID: 29472273 PMCID: PMC5822049 DOI: 10.15252/msb.20177902] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 07/28/2017] [Revised: 01/26/2018] [Accepted: 01/31/2018] [Indexed: 01/07/2023] Open
Abstract
Transcription factors (TFs) interpret DNA sequence by probing the chemical and structural properties of the nucleotide polymer. DNA shape is thought to enable a parsimonious representation of dependencies between nucleotide positions. Here, we propose a unified mathematical representation of the DNA sequence dependence of shape and TF binding, respectively, which simplifies and enhances analysis of shape readout. First, we demonstrate that linear models based on mononucleotide features alone account for 60-70% of the variance in minor groove width, roll, helix twist, and propeller twist. This explains why simple scoring matrices that ignore all dependencies between nucleotide positions can partially account for DNA shape readout by a TF Adding dinucleotide features as sequence-to-shape predictors to our model, we can almost perfectly explain the shape parameters. Building on this observation, we developed a post hoc analysis method that can be used to analyze any mechanism-agnostic protein-DNA binding model in terms of shape readout. Our insights provide an alternative strategy for using DNA shape information to enhance our understanding of how cis-regulatory codes are interpreted by the cellular machinery.
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Affiliation(s)
- H Tomas Rube
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Program in Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA
| | - Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
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7
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Zhang L, Martini GD, Rube HT, Kribelbauer JF, Rastogi C, FitzPatrick VD, Houtman JC, Bussemaker HJ, Pufall MA. SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site. Genome Res 2017; 28:111-121. [PMID: 29196557 PMCID: PMC5749176 DOI: 10.1101/gr.222844.117] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 11/22/2017] [Indexed: 11/28/2022]
Abstract
The DNA-binding interfaces of the androgen (AR) and glucocorticoid (GR) receptors are virtually identical, yet these transcription factors share only about a third of their genomic binding sites and regulate similarly distinct sets of target genes. To address this paradox, we determined the intrinsic specificities of the AR and GR DNA-binding domains using a refined version of SELEX-seq. We developed an algorithm, SelexGLM, that quantifies binding specificity over a large (31-bp) binding site by iteratively fitting a feature-based generalized linear model to SELEX probe counts. This analysis revealed that the DNA-binding preferences of AR and GR homodimers differ significantly, both within and outside the 15-bp core binding site. The relative preference between the two factors can be tuned over a wide range by changing the DNA sequence, with AR more sensitive to sequence changes than GR. The specificity of AR extends to the regions flanking the core 15-bp site, where isothermal calorimetry measurements reveal that affinity is augmented by enthalpy-driven readout of poly(A) sequences associated with narrowed minor groove width. We conclude that the increased specificity of AR is correlated with more enthalpy-driven binding than GR. The binding models help explain differences in AR and GR genomic binding and provide a biophysical rationale for how promiscuous binding by GR allows functional substitution for AR in some castration-resistant prostate cancers.
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Affiliation(s)
- Liyang Zhang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Gabriella D Martini
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - H Tomas Rube
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Vincent D FitzPatrick
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Jon C Houtman
- Department of Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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8
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Kim M, Kreig A, Lee CY, Rube HT, Calvert J, Song JS, Myong S. Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA. Nucleic Acids Res 2016; 44:4807-17. [PMID: 27095201 PMCID: PMC4889947 DOI: 10.1093/nar/gkw272] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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] [Received: 02/19/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
G-quadruplex (GQ) is a four-stranded DNA structure that can be formed in guanine-rich sequences. GQ structures have been proposed to regulate diverse biological processes including transcription, replication, translation and telomere maintenance. Recent studies have demonstrated the existence of GQ DNA in live mammalian cells and a significant number of potential GQ forming sequences in the human genome. We present a systematic and quantitative analysis of GQ folding propensity on a large set of 438 GQ forming sequences in double-stranded DNA by integrating fluorescence measurement, single-molecule imaging and computational modeling. We find that short minimum loop length and the thymine base are two main factors that lead to high GQ folding propensity. Linear and Gaussian process regression models further validate that the GQ folding potential can be predicted with high accuracy based on the loop length distribution and the nucleotide content of the loop sequences. Our study provides important new parameters that can inform the evaluation and classification of putative GQ sequences in the human genome.
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Affiliation(s)
- Minji Kim
- Department of Electrical and Computer Engineering, University of Illinois; 306 N. Wright St. Urbana, IL 61801, USA Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA
| | - Alex Kreig
- Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA
| | - Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University; 3400 N. Charles St. Baltimore, MD 21218 USA
| | - H Tomas Rube
- Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jacob Calvert
- Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA School of Mathematics, University of Bristol; University Walk, Bristol BS8 1TW, UK
| | - Jun S Song
- Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA Department of Physics, University of Illinois; 1110 West Green Street, Urbana, IL 61801-3080, USA Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St. Urbana, IL 61801, USA
| | - Sua Myong
- Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA Department of Biophysics, Johns Hopkins University; 3400 N. Charles St. Baltimore, MD 21218 USA Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St. Urbana, IL 61801, USA
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9
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Bell RJA, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song JS, Costello JF. Understanding TERT Promoter Mutations: A Common Path to Immortality. Mol Cancer Res 2016; 14:315-23. [PMID: 26941407 PMCID: PMC4852159 DOI: 10.1158/1541-7786.mcr-16-0003] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/24/2016] [Indexed: 12/23/2022]
Abstract
Telomerase (TERT) activation is a fundamental step in tumorigenesis. By maintaining telomere length, telomerase relieves a main barrier on cellular lifespan, enabling limitless proliferation driven by oncogenes. The recently discovered, highly recurrent mutations in the promoter of TERT are found in over 50 cancer types, and are the most common mutation in many cancers. Transcriptional activation of TERT, via promoter mutation or other mechanisms, is the rate-limiting step in production of active telomerase. Although TERT is expressed in stem cells, it is naturally silenced upon differentiation. Thus, the presence of TERT promoter mutations may shed light on whether a particular tumor arose from a stem cell or more differentiated cell type. It is becoming clear that TERT mutations occur early during cellular transformation, and activate the TERT promoter by recruiting transcription factors that do not normally regulate TERT gene expression. This review highlights the fundamental and widespread role of TERT promoter mutations in tumorigenesis, including recent progress on their mechanism of transcriptional activation. These somatic promoter mutations, along with germline variation in the TERT locus also appear to have significant value as biomarkers of patient outcome. Understanding the precise molecular mechanism of TERT activation by promoter mutation and germline variation may inspire novel cancer cell-specific targeted therapies for a large number of cancer patients.
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Affiliation(s)
- Robert J A Bell
- Department of Neurological Surgery, University of California, San Francisco, California
| | - H Tomas Rube
- Department of Biological Sciences, Columbia University, New York, New York
| | - Ana Xavier-Magalhães
- Department of Neurological Surgery, University of California, San Francisco, California. Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal. ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal. ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal
| | - Andrew Mancini
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Jun S Song
- Departments of Bioengineering and Physics, University of Illinois, Urbana-Champaign, Illinois
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, California.
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10
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Rube HT, Lee W, Hejna M, Chen H, Yasui DH, Hess JF, LaSalle JM, Song JS, Gong Q. Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nat Commun 2016; 7:11025. [PMID: 27008915 PMCID: PMC4820824 DOI: 10.1038/ncomms11025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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] [Received: 11/17/2015] [Accepted: 02/15/2016] [Indexed: 01/24/2023] Open
Abstract
Methyl-CpG binding protein 2 (MeCP2) is critical for proper brain development and
expressed at near-histone levels in neurons, but the mechanism of its genomic
localization remains poorly understood. Using high-resolution MeCP2-binding data, we
show that DNA sequence features alone can predict binding with 88% accuracy.
Integrating MeCP2 binding and DNA methylation in a probabilistic graphical model, we
demonstrate that previously reported genome-wide association with methylation is in
part due to MeCP2's affinity to GC-rich chromatin, a result replicated using
published data. Furthermore, MeCP2 co-localizes with nucleosomes. Finally, MeCP2
binding downstream of promoters correlates with increased expression in
Mecp2-deficient neurons. MeCP2 is critical for proper brain development, and mutations in the
gene encoding MeCP2 are responsible for several neurological disorders. Here, the
authors show that the previously reported genome-wide preference of MeCP2 to methylated
CpGs is in part due to MeCP2's affinity to GC-rich chromatin.
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Affiliation(s)
- H Tomas Rube
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Champaign, Illinois 61801, USA.,Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Wooje Lee
- Department of Cell Biology and Human Anatomy, University of California School of Medicine, Davis, California 95616, USA.,Division of Life Sciences, Korea University, Seoul 136-713, Korea
| | - Miroslav Hejna
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Huaiyang Chen
- Department of Cell Biology and Human Anatomy, University of California School of Medicine, Davis, California 95616, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, University of California School of Medicine, Davis, California 95616, USA
| | - John F Hess
- Department of Cell Biology and Human Anatomy, University of California School of Medicine, Davis, California 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, University of California School of Medicine, Davis, California 95616, USA
| | - Jun S Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Champaign, Illinois 61801, USA.,Department of Bioengineering, University of Illinois, Urbana-Champaign, Champaign, Illinois 61801, USA.,Department of Biostatistics and Epidemiology, University of California, San Francisco, California 94158, USA
| | - Qizhi Gong
- Department of Cell Biology and Human Anatomy, University of California School of Medicine, Davis, California 95616, USA
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11
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Jin H, Rube HT, Song JS. Categorical spectral analysis of periodicity in nucleosomal DNA. Nucleic Acids Res 2016; 44:2047-57. [PMID: 26893354 PMCID: PMC4797311 DOI: 10.1093/nar/gkw101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/09/2016] [Indexed: 12/26/2022] Open
Abstract
DNA helical twist imposes geometric constraints on the location of histone–DNA interaction sites along nucleosomal DNA. Certain 10.5-bp periodic nucleotides in phase with these geometric constraints have been suggested to facilitate nucleosome positioning. However, the extent of nucleotide periodicity in nucleosomal DNA and its significance in directing nucleosome positioning still remain unclear. We clarify these issues by applying categorical spectral analysis to high-resolution nucleosome maps in two yeast species. We find that only a small fraction of nucleosomal sequences contain significant 10.5-bp periodicity. We further develop a spectral decomposition method to show that the previously observed periodicity in aligned nucleosomal sequences mainly results from proper phasing among nucleosomal sequences, and not from a preponderant occurrence of periodicity within individual sequences. Importantly, we show that this phasing may arise from the histones’ proclivity for putting preferred nucleotides at some of the evenly spaced histone–DNA contact points with respect to the dyad axis. We demonstrate that 10.5-bp periodicity, when present, significantly facilitates rotational, but not translational, nucleosome positioning. Finally, although periodicity only moderately affects nucleosome occupancy genome wide, reduced periodicity is an evolutionarily conserved signature of nucleosome-depleted regions around transcription start/termination sites.
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Affiliation(s)
- Hu Jin
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - H Tomas Rube
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Jun S Song
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
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12
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Bell R, Rube HT, Kreig A, Mancini A, Fouse S, Nagarajan R, Choi S, Hong C, He D, Pekmezci M, Wiencke J, Wrensch M, Chang S, Walsh K, Myong S, Song J, Costello J. GENO-07A MECHANISM OF MUTANT TERT PROMOTER ACTIVATION SHARED ACROSS CANCER TYPES. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov215.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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13
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Bell RJA, Rube HT, Kreig A, Mancini A, Fouse SD, Nagarajan RP, Choi S, Hong C, He D, Pekmezci M, Wiencke JK, Wrensch MR, Chang SM, Walsh KM, Myong S, Song JS, Costello JF. Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. Science 2015; 348:1036-9. [PMID: 25977370 PMCID: PMC4456397 DOI: 10.1126/science.aab0015] [Citation(s) in RCA: 389] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/04/2015] [Indexed: 12/12/2022]
Abstract
Reactivation of telomerase reverse transcriptase (TERT) expression enables cells to overcome replicative senescence and escape apoptosis, which are fundamental steps in the initiation of human cancer. Multiple cancer types, including up to 83% of glioblastomas (GBMs), harbor highly recurrent TERT promoter mutations of unknown function but specific to two nucleotide positions. We identified the functional consequence of these mutations in GBMs to be recruitment of the multimeric GA-binding protein (GABP) transcription factor specifically to the mutant promoter. Allelic recruitment of GABP is consistently observed across four cancer types, highlighting a shared mechanism underlying TERT reactivation. Tandem flanking native E26 transformation-specific motifs critically cooperate with these mutations to activate TERT, probably by facilitating GABP heterotetramer binding. GABP thus directly links TERT promoter mutations to aberrant expression in multiple cancers.
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Affiliation(s)
- Robert J A Bell
- Department of Neurological Surgery, University of California, San Francisco, CA. Department of Biostatistics and Epidemiology, University of California, San Francisco, CA
| | - H Tomas Rube
- Department of Physics, University of Illinois, Urbana-Champaign, IL. Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL
| | - Alex Kreig
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL. Department of Bioengineering, University of Illinois, Urbana-Champaign, IL
| | - Andrew Mancini
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Shaun D Fouse
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Raman P Nagarajan
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Serah Choi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Daniel He
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Melike Pekmezci
- Department of Anatomic Pathology, University of California San Francisco Medical School, San Francisco, CA 94143, USA
| | - John K Wiencke
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA. Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Margaret R Wrensch
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA. Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Kyle M Walsh
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sua Myong
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL. Department of Bioengineering, University of Illinois, Urbana-Champaign, IL
| | - Jun S Song
- Department of Biostatistics and Epidemiology, University of California, San Francisco, CA. Department of Physics, University of Illinois, Urbana-Champaign, IL. Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL. Department of Bioengineering, University of Illinois, Urbana-Champaign, IL.
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA.
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14
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Abstract
Statistical positioning, the localization of nucleosomes packed against a fixed barrier, is conjectured to explain the array of well-positioned nucleosomes at the 5′ end of genes, but the extent and precise implications of statistical positioning in vivo are unclear. We examine this hypothesis quantitatively and generalize the idea to include moving barriers as well as nucleosomes actively packed against a barrier. Early experiments noted a similarity between the nucleosome profile aligned and averaged across genes and that predicted by statistical positioning; however, we demonstrate that aligning random nucleosomes also generates the same profile, calling the previous interpretation into question. New rigorous results reformulate statistical positioning as predictions on the variance structure of nucleosome locations in individual genes. In particular, a quantity termed the variance gradient, describing the change in variance between adjacent nucleosomes, is tested against recent high-throughput nucleosome sequencing data. Constant variance gradients provide support for generalized statistical positioning in ∼50% of long genes. Genes that deviate from predictions have high nucleosome turnover and cell-to-cell gene expression variability. The observed variance gradient suggests an effective nucleosome size of 158 bp, instead of the commonly perceived 147 bp. Our analyses thus clarify the role of statistical positioning in vivo.
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Affiliation(s)
- H Tomas Rube
- Institute for Human Genetics, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143-0794, USA, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143-0794, USA, Department of Epidemiology and Biostatistics, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143-0794, USA and Department of Bioengineering and Therapeutic Sciences, University of California, 513 Parnassus Avenue, Box 0794, San Francisco, CA 94143-0794, USA
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