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Perez AA, Goronzy IN, Blanco MR, Guo JK, Guttman M. ChIP-DIP: A multiplexed method for mapping hundreds of proteins to DNA uncovers diverse regulatory elements controlling gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571730. [PMID: 38187704 PMCID: PMC10769186 DOI: 10.1101/2023.12.14.571730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Gene expression is controlled by the dynamic localization of thousands of distinct regulatory proteins to precise regions of DNA. Understanding this cell-type specific process has been a goal of molecular biology for decades yet remains challenging because most current DNA-protein mapping methods study one protein at a time. To overcome this, we developed ChIP-DIP (ChIP Done In Parallel), a split-pool based method that enables simultaneous, genome-wide mapping of hundreds of diverse regulatory proteins in a single experiment. We demonstrate that ChIP-DIP generates highly accurate maps for all classes of DNA-associated proteins, including histone modifications, chromatin regulators, transcription factors, and RNA Polymerases. Using these data, we explore quantitative combinations of protein localization on genomic DNA to define distinct classes of regulatory elements and their functional activity. Our data demonstrate that ChIP-DIP enables the generation of 'consortium level', context-specific protein localization maps within any molecular biology lab.
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Zhao D, Zhang M, Huang S, Liu Q, Zhu S, Li Y, Jiang W, Kiss DL, Cao Q, Zhang L, Chen K. CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells. Nucleic Acids Res 2022; 50:12186-12201. [PMID: 36408932 PMCID: PMC9757051 DOI: 10.1093/nar/gkac1090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/19/2022] [Indexed: 11/22/2022] Open
Abstract
Despite being a member of the chromodomain helicase DNA-binding protein family, little is known about the exact role of CHD6 in chromatin remodeling or cancer disease. Here we show that CHD6 binds to chromatin to promote broad nucleosome eviction for transcriptional activation of many cancer pathways. By integrating multiple patient cohorts for bioinformatics analysis of over a thousand prostate cancer datasets, we found CHD6 expression elevated in prostate cancer and associated with poor prognosis. Further comprehensive experiments demonstrated that CHD6 regulates oncogenicity of prostate cancer cells and tumor development in a murine xenograft model. ChIP-Seq for CHD6, along with MNase-Seq and RNA-Seq, revealed that CHD6 binds on chromatin to evict nucleosomes from promoters and gene bodies for transcriptional activation of oncogenic pathways. These results demonstrated a key function of CHD6 in evicting nucleosomes from chromatin for transcriptional activation of prostate cancer pathways.
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Affiliation(s)
- Dongyu Zhao
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Min Zhang
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Shaodong Huang
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Qi Liu
- Department of Urology, and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sen Zhu
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yanqiang Li
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Weihua Jiang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Daniel L Kiss
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Qi Cao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Urology, and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kaifu Chen
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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Hu J, Yu Y. Epigenetic response profiles into environmental epigenotoxicant screening and health risk assessment: A critical review. CHEMOSPHERE 2019; 226:259-272. [PMID: 30933735 DOI: 10.1016/j.chemosphere.2019.03.096] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The epigenome may be an important interface between exposure to environmental contaminants and adverse outcome on human health. Many environmental pollutants deregulate gene expression and promote diseases by modulating the epigenome. Adverse epigenetic responses have been widely used for risk assessment of chemical substances. Various pollutants, including trace elements and persistent organic pollutants, have been detected frequently in the environment. Epigenetic toxicity of environmental matrices including water, air, soil, and food cannot be ignored. This review provides a comprehensive overview of epigenetic effects of pollutants and environmental matrices. We start with an overview of the mechanisms of epigenetic regulation and the effects of several types of environmental pollutants (trace elements, persistent organic pollutants, endocrine disrupting chemicals, and volatile organic pollutants) on epigenetic modulation. We then discuss the epigenetic responses to environmental water, air, and soil based on in vivo and in vitro assays. Finally, we discuss recommendations to promote the incorporation of epigenotoxicity into contamination screening and health risk assessment.
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Affiliation(s)
- Junjie Hu
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Yingxin Yu
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, Guangdong, PR China.
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Girgis HZ, Velasco A, Reyes ZE. HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures. BMC Bioinformatics 2018; 19:310. [PMID: 30176808 PMCID: PMC6122555 DOI: 10.1186/s12859-018-2312-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 08/14/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Histone modifications play important roles in gene regulation, heredity, imprinting, and many human diseases. The histone code is complex and consists of more than 100 marks. Therefore, biologists need computational tools to characterize general signatures representing the distributions of tens of chromatin marks around thousands of regions. RESULTS To this end, we developed a software tool, HebbPlot, which utilizes a Hebbian neural network in learning a general chromatin signature from regions with a common function. Hebbian networks can learn the associations between tens of marks and thousands of regions. HebbPlot presents a signature as a digital image, which can be easily interpreted. Moreover, signatures produced by HebbPlot can be compared quantitatively. We validated HebbPlot in six case studies. The results of these case studies are novel or validating results already reported in the literature, indicating the accuracy of HebbPlot. Our results indicate that promoters have a directional chromatin signature; several marks tend to stretch downstream or upstream. H3K4me3 and H3K79me2 have clear directional distributions around active promoters. In addition, the signatures of high- and low-CpG promoters are different; H3K4me3, H3K9ac, and H3K27ac are the most different marks. When we studied the signatures of enhancers active in eight tissues, we observed that these signatures are similar, but not identical. Further, we identified some histone modifications - H3K36me3, H3K79me1, H3K79me2, and H4K8ac - that are associated with coding regions of active genes. Other marks - H4K12ac, H3K14ac, H3K27me3, and H2AK5ac - were found to be weakly associated with coding regions of inactive genes. CONCLUSIONS This study resulted in a novel software tool, HebbPlot, for learning and visualizing the chromatin signature of a genetic element. Using HebbPlot, we produced a visual catalog of the signatures of multiple genetic elements in 57 cell types available through the Roadmap Epigenomics Project. Furthermore, we made a progress toward a functional catalog consisting of 22 histone marks. In sum, HebbPlot is applicable to a wide array of studies, facilitating the deciphering of the histone code.
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Affiliation(s)
- Hani Z. Girgis
- Tandy School of Computer Science, University of Tulsa, 800 South Tucker Drive, Tulsa, 74104-9700 OK USA
| | - Alfredo Velasco
- Tandy School of Computer Science, University of Tulsa, 800 South Tucker Drive, Tulsa, 74104-9700 OK USA
| | - Zachary E. Reyes
- Tandy School of Computer Science, University of Tulsa, 800 South Tucker Drive, Tulsa, 74104-9700 OK USA
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Lu J, Xu D, Jiang Y, Kong S, Shen Z, Xia S, Lu L. Integrated analysis of mRNA and viral miRNAs in the kidney of Carassius auratus gibelio response to cyprinid herpesvirus 2. Sci Rep 2017; 7:13787. [PMID: 29062054 PMCID: PMC5653811 DOI: 10.1038/s41598-017-14217-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 10/06/2017] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding single stranded RNAs that play crucial roles in numerous biological processes. Vertebrate herpesviruses encode multiple viral miRNAs that modulate host and viral genes. However, the roles of viral miRNAs in lower vertebrates have not been fully determined. Here, we used high-throughput sequencing to analyse the miRNA and mRNA expression profiles of Carassius auratus gibelio in response to infection by cyprinid herpesvirus 2 (CyHV-2). RNA sequencing obtained 26,664 assembled transcripts, including 2,912 differentially expressed genes. Based on small RNA sequencing and secondary structure predictions, we identified 17 CyHV-2 encoded miRNAs, among which 14 were validated by stem-loop quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) and eight were validated by northern blotting. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of miRNAs-mRNA pairs revealed diverse affected immune signalling pathways, including the RIG-I-like receptor and JAK-STAT pathways. Finally, we presented four genes involved in RIG-I-like pathways, including host gene IRF3, RBMX, PIN1, viral gene ORF4, which are negatively regulated by CyHV-2 encoded miRNA miR-C4. The present study is the first to provide a comprehensive overview of viral miRNA-mRNA co-regulation, which might have a key role in controlling post-transcriptomic regulation during CyHV-2 infection.
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Affiliation(s)
- Jianfei Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
| | - Dan Xu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
- Key Laboratory of Agriculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, P. R. China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, P. R. China
| | - Yousheng Jiang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
- Key Laboratory of Agriculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, P. R. China
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, P. R. China
| | - Shanyun Kong
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
| | - Zhaoyuan Shen
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
| | - Siyao Xia
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China
| | - Liqun Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, P. R. China.
- Key Laboratory of Agriculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, P. R. China.
- National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, P. R. China.
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Mauser R, Kungulovski G, Keup C, Reinhardt R, Jeltsch A. Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state. Epigenetics Chromatin 2017; 10:45. [PMID: 28946896 PMCID: PMC5613355 DOI: 10.1186/s13072-017-0153-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/18/2017] [Indexed: 12/14/2022] Open
Abstract
Background Histone post-translational modifications (PTMs) play central roles in chromatin-templated processes. Combinations of two or more histone PTMs form unique interfaces for readout and recruitment of chromatin interacting complexes, but the genome-wide mapping of coexisting histone PTMs remains an experimentally difficult task. Results We introduce here a novel type of affinity reagents consisting of two fused recombinant histone modification interacting domains (HiMIDs) for direct detection of doubly modified chromatin. To develop the method, we fused the MPP8 chromodomain and DNMT3A PWWP domain which have a binding specificity for H3K9me3 and H3K36me2/3, respectively. We validate the novel reagent biochemically and in ChIP applications and show its specific interaction with H3K9me3–H3K36me2/3 doubly modified chromatin. Modification specificity was confirmed using mutant double-HiMIDs with inactivated methyllysine binding pockets. Using this novel tool, we mapped coexisting H3K9me3–H3K36me2/3 marks in human cells by chromatin interacting domain precipitation (CIDOP). CIDOP-seq data were validated by qPCR, sequential CIDOP/ChIP and by comparison with CIDOP- and ChIP-seq data obtained with single modification readers and antibodies. The genome-wide distribution of H3K9me3–H3K36me2/3 indicates that it represents a novel bivalent chromatin state, which is enriched in weakly transcribed chromatin segments and at ZNF274 and SetDB1 binding sites. Conclusions The application of double-HiMIDs allows the single-step study of co-occurrence and distribution of combinatorial chromatin marks. Our discovery of a novel H3K9me3–H3K36me2/3 bivalent chromatin state illustrates the power of this approach, and it will stimulate numerous follow-up studies on its biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0153-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebekka Mauser
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Goran Kungulovski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Corinna Keup
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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Anderson WD, Greenhalgh AD, Takwale A, David S, Vadigepalli R. Novel Influences of IL-10 on CNS Inflammation Revealed by Integrated Analyses of Cytokine Networks and Microglial Morphology. Front Cell Neurosci 2017; 11:233. [PMID: 28855862 PMCID: PMC5557777 DOI: 10.3389/fncel.2017.00233] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/25/2017] [Indexed: 01/16/2023] Open
Abstract
Coordinated interactions between cytokine signaling and morphological dynamics of microglial cells regulate neuroinflammation in CNS injury and disease. We found that pro-inflammatory cytokine gene expression in vivo showed a pronounced recovery following systemic LPS. We performed a novel multivariate analysis of microglial morphology and identified changes in specific morphological properties of microglia that matched the expression dynamics of pro-inflammatory cytokine TNFα. The adaptive recovery kinetics of TNFα expression and microglial soma size showed comparable profiles and dependence on anti-inflammatory cytokine IL-10 expression. The recovery of cytokine variations and microglial morphology responses to inflammation were negatively regulated by IL-10. Our novel morphological analysis of microglia is able to detect subtle changes and can be used widely. We implemented in silico simulations of cytokine network dynamics which showed—counter-intuitively, but in line with our experimental observations—that negative feedback from IL-10 was sufficient to impede the adaptive recovery of TNFα-mediated inflammation. Our integrative approach is a powerful tool to study changes in specific components of microglial morphology for insights into their functional states, in relation to cytokine network dynamics, during CNS injury and disease.
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Affiliation(s)
- Warren D Anderson
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson UniversityPhiladelphia, PA, United States
| | - Andrew D Greenhalgh
- Center for Research in Neuroscience, The Research Institute of the McGill University Health CenterMontreal, QC, Canada
| | - Aditya Takwale
- Center for Research in Neuroscience, The Research Institute of the McGill University Health CenterMontreal, QC, Canada
| | - Samuel David
- Center for Research in Neuroscience, The Research Institute of the McGill University Health CenterMontreal, QC, Canada
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson UniversityPhiladelphia, PA, United States
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Abstract
Understanding epigenetic processes holds immense promise for medical applications. Advances in Machine Learning (ML) are critical to realize this promise. Previous studies used epigenetic data sets associated with the germline transmission of epigenetic transgenerational inheritance of disease and novel ML approaches to predict genome-wide locations of critical epimutations. A combination of Active Learning (ACL) and Imbalanced Class Learning (ICL) was used to address past problems with ML to develop a more efficient feature selection process and address the imbalance problem in all genomic data sets. The power of this novel ML approach and our ability to predict epigenetic phenomena and associated disease is suggested. The current approach requires extensive computation of features over the genome. A promising new approach is to introduce Deep Learning (DL) for the generation and simultaneous computation of novel genomic features tuned to the classification task. This approach can be used with any genomic or biological data set applied to medicine. The application of molecular epigenetic data in advanced machine learning analysis to medicine is the focus of this review.
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Affiliation(s)
- Lawrence B Holder
- a School of Electrical Engineering and Computer Science , Washington State University , Pullman , WA , USA
| | - M Muksitul Haque
- a School of Electrical Engineering and Computer Science , Washington State University , Pullman , WA , USA.,b Center for Reproductive Biology, School of Biological Sciences , Washington State University , Pullman , WA , USA
| | - Michael K Skinner
- b Center for Reproductive Biology, School of Biological Sciences , Washington State University , Pullman , WA , USA
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Gandolfi F, Tramontano A. A computational approach for the functional classification of the epigenome. Epigenetics Chromatin 2017; 10:26. [PMID: 28515787 PMCID: PMC5433140 DOI: 10.1186/s13072-017-0131-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/26/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In the last decade, advanced functional genomics approaches and deep sequencing have allowed large-scale mapping of histone modifications and other epigenetic marks, highlighting functional relationships between chromatin organization and genome function. Here, we propose a novel approach to explore functional interactions between different epigenetic modifications and extract combinatorial profiles that can be used to annotate the chromatin in a finite number of functional classes. Our method is based on non-negative matrix factorization (NMF), an unsupervised learning technique originally employed to decompose high-dimensional data in a reduced number of meaningful patterns. We applied the NMF algorithm to a set of different epigenetic marks, consisting of ChIP-seq assays for multiple histone modifications, Pol II binding and chromatin accessibility assays from human H1 cells. RESULTS We identified a number of chromatin profiles that contain functional information and are biologically interpretable. We also observe that epigenetic profiles are characterized by specific genomic contexts and show significant association with distinct genomic features. Moreover, analysis of RNA-seq data reveals that distinct chromatin signatures correlate with the level of gene expression. CONCLUSIONS Overall, our study highlights the utility of NMF in studying functional relationships between different epigenetic modifications and may provide new biological insights for the interpretation of the chromatin dynamics.
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Affiliation(s)
- Francesco Gandolfi
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy
| | - Anna Tramontano
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy.,Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy
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Jiang X, Hu X, Xu W. Microbiome Data Representation by Joint Nonnegative Matrix Factorization with Laplacian Regularization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:353-359. [PMID: 28368813 DOI: 10.1109/tcbb.2015.2440261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microbiome datasets are often comprised of different representations or views which provide complementary information to understand microbial communities, such as metabolic pathways, taxonomic assignments, and gene families. Data integration methods including approaches based on nonnegative matrix factorization (NMF) combine multi-view data to create a comprehensive view of a given microbiome study by integrating multi-view information. In this paper, we proposed a novel variant of NMF which called Laplacian regularized joint non-negative matrix factorization (LJ-NMF) for integrating functional and phylogenetic profiles from HMP. We compare the performance of this method to other variants of NMF. The experimental results indicate that the proposed method offers an efficient framework for microbiome data analysis.
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Cieślik M, Bekiranov S. Genome-wide predictors of NF-κB recruitment and transcriptional activity. BioData Min 2015; 8:37. [PMID: 26617673 PMCID: PMC4661973 DOI: 10.1186/s13040-015-0071-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 11/18/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Inducible transcription factors (TFs) mediate transcriptional responses to environmental cues. In response to multiple inflammatory signals active NF-κB dimers enter the nucleus and trigger cell-type-, and stimulus-specific transcriptional programs. Although much is known about NF-κB inducing pathways and about locus-specific mechanisms of transcriptional control, it is poorly understood how the pre-existing chromatin landscape determines NF-κB target selection and activation. Specifically, it is not known which epigenetic marks and pre-bound TFs serve genome-wide as positive (negative) cues for active NF-κB. RESULTS We applied multivariate and combinatorial data mining techniques on a comprehensive dataset of DNA methylation, DNase I hypersensitivity, eight epigenetic marks, and 34 TFs to arrive at genome-wide patterns that predict NF-κB binding. Strikingly, we observed NF-κB recruitment to accessible and nucleosome-bound sites. Within nucleosomal DNA NF-κB binding was primed by H3K4me1 and H2A.Z, but also hyper-methylated DNA outside of promoters and CpG-islands. Many of these predictors showed combinatorial cooperativity and statistically significant interactions. Recruitment to pre-accessible sites was more frequent and influenced by chromatin-associated TFs. We observed that specific TF-combinations are greatly enriched for (or depleted of) NF-κB binding events. CONCLUSIONS We provide evidence of NF-κB binding within genomic regions that lack classical marks of activity. These pioneer binding events are relatively often associated with transcriptional regulation. Further, our predictive models indicate that specific combinations of epigenetic marks and transcription factors predetermine the NF-κB cistrome, supporting the feasibility of using statistical approaches to identify "histone codes".
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Affiliation(s)
- Marcin Cieślik
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia USA
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109 USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia USA
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Hamada M, Ono Y, Fujimaki R, Asai K. Learning chromatin states with factorized information criteria. Bioinformatics 2015; 31:2426-33. [PMID: 25810430 DOI: 10.1093/bioinformatics/btv163] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 03/16/2015] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION Recent studies have suggested that both the genome and the genome with epigenetic modifications, the so-called epigenome, play important roles in various biological functions, such as transcription and DNA replication, repair, and recombination. It is well known that specific combinations of histone modifications (e.g. methylations and acetylations) of nucleosomes induce chromatin states that correspond to specific functions of chromatin. Although the advent of next-generation sequencing (NGS) technologies enables measurement of epigenetic information for entire genomes at high-resolution, the variety of chromatin states has not been completely characterized. RESULTS In this study, we propose a method to estimate the chromatin states indicated by genome-wide chromatin marks identified by NGS technologies. The proposed method automatically estimates the number of chromatin states and characterize each state on the basis of a hidden Markov model (HMM) in combination with a recently proposed model selection technique, factorized information criteria. The method is expected to provide an unbiased model because it relies on only two adjustable parameters and avoids heuristic procedures as much as possible. Computational experiments with simulated datasets show that our method automatically learns an appropriate model, even in cases where methods that rely on Bayesian information criteria fail to learn the model structures. In addition, we comprehensively compare our method to ChromHMM on three real datasets and show that our method estimates more chromatin states than ChromHMM for those datasets.
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Affiliation(s)
- Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan, Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yukiteru Ono
- Information and Mathematical Science and Bioinformatics Co., Ltd., 4-21-1-601 Higashi-Ikebukuro, Toshima-ku, Tokyo 170-0013, Japan
| | - Ryohei Fujimaki
- Department of Media Analytics, NEC Laboratories America, 10080 North Wolfe Road, Suite SW3-350, Cupertino, CA 95014 and
| | - Kiyoshi Asai
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan
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Abstract
Osteosarcoma is the most common primary malignancy of bone, typically presenting in the first or second decade of life. Unfortunately, clinical outcomes for osteosarcoma patients have not substantially improved in over 30 years. This stagnation in therapeutic advances is perhaps explained by the genetic, epigenetic, and biological complexities of this rare tumor. In this review we provide a general background on the biology of osteosarcoma and the clinical status quo. We go on to enumerate the genetic and epigenetic defects identified in osteosarcoma. Finally, we discuss ongoing large-scale studies in the field and potential new therapies that are currently under investigation.
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Affiliation(s)
- James J. Morrow
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Chand Khanna
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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