1
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Li M, Yao T, Lin W, Hinckley WE, Galli M, Muchero W, Gallavotti A, Chen JG, Huang SSC. Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors. Nat Commun 2023; 14:2600. [PMID: 37147307 PMCID: PMC10163045 DOI: 10.1038/s41467-023-38096-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/15/2023] [Indexed: 05/07/2023] Open
Abstract
Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.
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Affiliation(s)
- Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wanru Lin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Will E Hinckley
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Shao-Shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
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2
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Morin A, Chu ECP, Sharma A, Adrian-Hamazaki A, Pavlidis P. Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets. Genome Res 2023; 33:763-778. [PMID: 37308292 PMCID: PMC10317128 DOI: 10.1101/gr.277273.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Mapping the gene targets of chromatin-associated transcription regulators (TRs) is a major goal of genomics research. ChIP-seq of TRs and experiments that perturb a TR and measure the differential abundance of gene transcripts are a primary means by which direct relationships are tested on a genomic scale. It has been reported that there is a poor overlap in the evidence across gene regulation strategies, emphasizing the need for integrating results from multiple experiments. Although research consortia interested in gene regulation have produced a valuable trove of high-quality data, there is an even greater volume of TR-specific data throughout the literature. In this study, we show a workflow for the identification, uniform processing, and aggregation of ChIP-seq and TR perturbation experiments for the ultimate purpose of ranking human and mouse TR-target interactions. Focusing on an initial set of eight regulators (ASCL1, HES1, MECP2, MEF2C, NEUROD1, PAX6, RUNX1, and TCF4), we identified 497 experiments suitable for analysis. We used this corpus to examine data concordance, to identify systematic patterns of the two data types, and to identify putative orthologous interactions between human and mouse. We build upon commonly used strategies to forward a procedure for aggregating and combining these two genomic methodologies, assessing these rankings against independent literature-curated evidence. Beyond a framework extensible to other TRs, our work also provides empirically ranked TR-target listings, as well as transparent experiment-level gene summaries for community use.
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Affiliation(s)
- Alexander Morin
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Eric Ching-Pan Chu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Aman Sharma
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Alex Adrian-Hamazaki
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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3
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Radak M, Ghamari N, Fallahi H. Common factors among three types of cells aged in mice. Biogerontology 2023; 24:363-375. [PMID: 37081236 DOI: 10.1007/s10522-023-10035-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/05/2023] [Indexed: 04/22/2023]
Abstract
The greatest risk factor for the formation of numerous significant chronic disorders is aging. Understanding the core molecular underpinnings of aging can help to slow down the inevitable process. Systematic study of gene expression or DNA methylation data is possible at the transcriptomics and epigenetics levels. DNA methylation and gene expression are both affected by aging. Gene expression is an important element in the aging of Homo sapiens. In this work, we evaluated the expression of differentially expressed genes (DEGs), proteins, and transcription factors (TFs) in three different types of cells in mice: antibody-secreting cells, cardiac mesenchymal stromal cells, and skeletal muscle cells. The goal of this article is to uncover a common cause during aging among these cells in order to increase understanding about establishing complete techniques for preventing aging and improving people's quality of life. We conducted a comprehensive network-based investigation to establish which genes and proteins are shared by the three different types of aged cells. Our findings clearly indicated that aging induces gene dysregulation in immune, pharmacological, and apoptotic pathways. Furthermore, our research developed a list of hub genes with differential expression in aging responses that should be investigated further to discover viable anti-aging treatments.
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Affiliation(s)
- Mehran Radak
- Department of Biology, School of Sciences, Razi University, Baq-e-Abrisham, 6714967346, Kermanshah, Islamic Republic of Iran
| | - Nakisa Ghamari
- Department of Biology, School of Sciences, Razi University, Baq-e-Abrisham, 6714967346, Kermanshah, Islamic Republic of Iran
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Baq-e-Abrisham, 6714967346, Kermanshah, Islamic Republic of Iran.
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4
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Zheng H, Wang S, Li X, Hu H. INSISTC: Incorporating network structure information for single-cell type classification. Genomics 2022; 114:110480. [PMID: 36075505 DOI: 10.1016/j.ygeno.2022.110480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 11/27/2022]
Abstract
Uncovering gene regulatory mechanisms in individual cells can provide insight into cell heterogeneity and function. Recent accumulated Single-Cell RNA-Seq data have made it possible to analyze gene regulation at single-cell resolution. Understanding cell-type-specific gene regulation can assist in more accurate cell type and state identification. Computational approaches utilizing such relationships are under development. Methods pioneering in integrating gene regulatory mechanism discovery with cell-type classification encounter challenges such as determine gene regulatory relationships and incorporate gene regulatory network structure. To fill this gap, we developed INSISTC, a computational method to incorporate gene regulatory network structure information for single-cell type classification. INSISTC is capable of identifying cell-type-specific gene regulatory mechanisms while performing single-cell type classification. INSISTC demonstrated its accuracy in cell type classification and its potential for providing insight into molecular mechanisms specific to individual cells. In comparison with the alternative methods, INSISTC demonstrated its complementary performance for gene regulation interpretation.
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Affiliation(s)
- Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Saidi Wang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA.
| | - Haiyan Hu
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA.
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5
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Islam MK, Islam MR, Rahman MH, Islam MZ, Amin MA, Ahmed KR, Rahman MA, Moni MA, Kim B. Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma. Pharmaceutics 2022; 14:1573. [PMID: 36015199 PMCID: PMC9413912 DOI: 10.3390/pharmaceutics14081573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 12/01/2022] Open
Abstract
Expanding data suggest that glioblastoma is accountable for the growing prevalence of various forms of stroke formation, such as ischemic stroke and moyamoya disease. However, the underlying deterministic details are still unspecified. Bioinformatics approaches are designed to investigate the relationships between two pathogens as well as fill this study void. Glioblastoma is a form of cancer that typically occurs in the brain or spinal cord and is highly destructive. A stroke occurs when a brain region starts to lose blood circulation and prevents functioning. Moyamoya disorder is a recurrent and recurring arterial disorder of the brain. To begin, adequate gene expression datasets on glioblastoma, ischemic stroke, and moyamoya disease were gathered from various repositories. Then, the association between glioblastoma, ischemic stroke, and moyamoya was established using the existing pipelines. The framework was developed as a generalized workflow to allow for the aggregation of transcriptomic gene expression across specific tissue; Gene Ontology (GO) and biological pathway, as well as the validation of such data, are carried out using enrichment studies such as protein-protein interaction and gold benchmark databases. The results contribute to a more profound knowledge of the disease mechanisms and unveil the projected correlations among the diseases.
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Affiliation(s)
- Md Khairul Islam
- Department of Information & Communication Technology, Islamic University, Kushtia 7003, Bangladesh; (M.K.I.); (M.R.I.); (M.Z.I.)
| | - Md Rakibul Islam
- Department of Information & Communication Technology, Islamic University, Kushtia 7003, Bangladesh; (M.K.I.); (M.R.I.); (M.Z.I.)
| | - Md Habibur Rahman
- Department of Computer Science & Engineering, Islamic University, Kushtia 7003, Bangladesh;
| | - Md Zahidul Islam
- Department of Information & Communication Technology, Islamic University, Kushtia 7003, Bangladesh; (M.K.I.); (M.R.I.); (M.Z.I.)
| | - Md Al Amin
- Department of Computer Science & Engineering, Prime University, Dhaka 1216, Bangladesh;
| | - Kazi Rejvee Ahmed
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 02447, Korea;
| | - Md Ataur Rahman
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 02447, Korea;
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Mohammad Ali Moni
- School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 02447, Korea;
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea
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6
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Simonett SP, Shin S, Herring JA, Bacher R, Smith LA, Dong C, Rabaglia ME, Stapleton DS, Schueler KL, Choi J, Bernstein MN, Turkewitz DR, Perez-Cervantes C, Spaeth J, Stein R, Tessem JS, Kendziorski C, Keleş S, Moskowitz IP, Keller MP, Attie AD. Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation. J Clin Invest 2021; 131:e144833. [PMID: 34491912 PMCID: PMC8553569 DOI: 10.1172/jci144833] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
The transcription factor NFATC2 induces β cell proliferation in mouse and human islets. However, the genomic targets that mediate these effects have not been identified. We expressed active forms of Nfatc2 and Nfatc1 in human islets. By integrating changes in gene expression with genomic binding sites for NFATC2, we identified approximately 2200 transcriptional targets of NFATC2. Genes induced by NFATC2 were enriched for transcripts that regulate the cell cycle and for DNA motifs associated with the transcription factor FOXP. Islets from an endocrine-specific Foxp1, Foxp2, and Foxp4 triple-knockout mouse were less responsive to NFATC2-induced β cell proliferation, suggesting the FOXP family works to regulate β cell proliferation in concert with NFATC2. NFATC2 induced β cell proliferation in both mouse and human islets, whereas NFATC1 did so only in human islets. Exploiting this species difference, we identified approximately 250 direct transcriptional targets of NFAT in human islets. This gene set enriches for cell cycle-associated transcripts and includes Nr4a1. Deletion of Nr4a1 reduced the capacity of NFATC2 to induce β cell proliferation, suggesting that much of the effect of NFATC2 occurs through its induction of Nr4a1. Integration of noncoding RNA expression, chromatin accessibility, and NFATC2 binding sites enabled us to identify NFATC2-dependent enhancer loci that mediate β cell proliferation.
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Affiliation(s)
- Shane P. Simonett
- Biochemistry Department, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Sunyoung Shin
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Jacob A. Herring
- Nutrition, Dietetics and Food Science Department, Brigham Young University, Provo, Utah, USA
| | - Rhonda Bacher
- Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Linsin A. Smith
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Chenyang Dong
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Mary E. Rabaglia
- Biochemistry Department, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Donnie S. Stapleton
- Biochemistry Department, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Kathryn L. Schueler
- Biochemistry Department, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Jeea Choi
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | | | - Daniel R. Turkewitz
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Carlos Perez-Cervantes
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Jason Spaeth
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Roland Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeffery S. Tessem
- Nutrition, Dietetics and Food Science Department, Brigham Young University, Provo, Utah, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Sündüz Keleş
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ivan P. Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Mark P. Keller
- Biochemistry Department, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Alan D. Attie
- Biochemistry Department, University of Wisconsin–Madison, Madison, Wisconsin, USA
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7
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Kang R, Tan Z, Lang M, Jin L, Zhang Y, Zhang Y, Guo T, Guo Z. EnhFFL: A database of enhancer mediated feed-forward loops for human and mouse. PRECISION CLINICAL MEDICINE 2021; 4:129-135. [PMID: 35694152 PMCID: PMC8982537 DOI: 10.1093/pcmedi/pbab006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 12/17/2022] Open
Abstract
Feed-forward loops (FFLs) are thought to be one of the most common and important classes of transcriptional network motifs involved in various diseases. Enhancers are cis-regulatory elements that positively regulate protein-coding genes or microRNAs (miRNAs) by recruiting DNA-binding transcription factors (TFs). However, a comprehensive resource to identify, store, and analyze the FFLs of typical enhancer and super-enhancer FFLs is not currently available. Here, we present EnhFFL, an online database to provide a data resource for users to browse and search typical enhancer and super-enhancer FFLs. The current database covers 46 280/7000 TF-enhancer-miRNA FFLs, 9997/236 enhancer-miRNA-gene FFLs, 3 561 164/3 193 182 TF-enhancer-gene FFLs, and 1259/235 TF-enhancer feed-back loops (FBLs) across 91 tissues/cell lines of human and mouse, respectively. Users can browse loops by selecting species, types of tissue/cell line, and types of FFLs. EnhFFL supports searching elements including name/ID, genomic location, and the conservation of miRNA target genes. We also developed tools for users to screen customized FFLs using the threshold of q value as well as the confidence score of miRNA target genes. Disease and functional enrichment analysis showed that master miRNAs that are widely engaged in FFLs including TF-enhancer-miRNAs and enhancer-miRNA-genes are significantly involved in tumorigenesis. Database URL:http://lcbb.swjtu.edu.cn/EnhFFL/.
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Affiliation(s)
- Ran Kang
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Zhengtang Tan
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Mei Lang
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Linqi Jin
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Yin Zhang
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Yiming Zhang
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Tailin Guo
- College of Medicine, Southwest Jiaotong University, Chengdu 610031, China
| | - Zhiyun Guo
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu 610031, China
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8
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Minchington TG, Griffiths-Jones S, Papalopulu N. Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback. Sci Rep 2020; 10:12960. [PMID: 32737375 PMCID: PMC7395740 DOI: 10.1038/s41598-020-69791-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023] Open
Abstract
Concepts from dynamical systems theory, including multi-stability, oscillations, robustness and stochasticity, are critical for understanding gene regulation during cell fate decisions, inflammation and stem cell heterogeneity. However, the prevalence of the structures within gene networks that drive these dynamical behaviours, such as autoregulation or feedback by microRNAs, is unknown. We integrate transcription factor binding site (TFBS) and microRNA target data to generate a gene interaction network across 28 human tissues. This network was analysed for motifs capable of driving dynamical gene expression, including oscillations. Identified autoregulatory motifs involve 56% of transcription factors (TFs) studied. TFs that autoregulate have more interactions with microRNAs than non-autoregulatory genes and 89% of autoregulatory TFs were found in dual feedback motifs with a microRNA. Both autoregulatory and dual feedback motifs were enriched in the network. TFs that autoregulate were highly conserved between tissues. Dual feedback motifs with microRNAs were also conserved between tissues, but less so, and TFs regulate different combinations of microRNAs in a tissue-dependent manner. The study of these motifs highlights ever more genes that have complex regulatory dynamics. These data provide a resource for the identification of TFs which regulate the dynamical properties of human gene expression.
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Affiliation(s)
- Thomas G Minchington
- School of Medical Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Nancy Papalopulu
- School of Medical Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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9
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Sauta E, Demartini A, Vitali F, Riva A, Bellazzi R. A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks. BMC Bioinformatics 2020; 21:219. [PMID: 32471360 PMCID: PMC7257163 DOI: 10.1186/s12859-020-3510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/22/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among transcription factors (TFs) and their target genes, with a method able to handle both the high number of interacting variables and the noise in the available heterogeneous experimental sources of information. RESULTS In this work, we propose a data fusion approach that exploits the integration of complementary omics-data as prior knowledge within a Bayesian framework, in order to learn and model large-scale transcriptional networks. We develop a hybrid structure-learning algorithm able to jointly combine TFs ChIP-Sequencing data and gene expression compendia to reconstruct TRNs in a genome-wide perspective. Applying our method to high-throughput data, we verified its ability to deal with the complexity of a genomic TRN, providing a snapshot of the synergistic TFs regulatory activity. Given the noisy nature of data-driven prior knowledge, which potentially contains incorrect information, we also tested the method's robustness to false priors on a benchmark dataset, comparing the proposed approach to other regulatory network reconstruction algorithms. We demonstrated the effectiveness of our framework by evaluating structural commonalities of our learned genomic network with other existing networks inferred by different DNA binding information-based methods. CONCLUSIONS This Bayesian omics-data fusion based methodology allows to gain a genome-wide picture of the transcriptional interplay, helping to unravel key hierarchical transcriptional interactions, which could be subsequently investigated, and it represents a promising learning approach suitable for multi-layered genomic data integration, given its robustness to noisy sources and its tailored framework for handling high dimensional data.
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Affiliation(s)
- Elisabetta Sauta
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.
| | - Andrea Demartini
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Francesca Vitali
- Center for Biomedical Informatics and Biostatistics, Dept. of Medicine, The University of Arizona Health Sciences, 1230 Cherry Ave, Tucson, AZ, 85719, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
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10
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Qin Q, Fan J, Zheng R, Wan C, Mei S, Wu Q, Sun H, Brown M, Zhang J, Meyer CA, Liu XS. Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. Genome Biol 2020; 21:32. [PMID: 32033573 PMCID: PMC7007693 DOI: 10.1186/s13059-020-1934-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 01/13/2020] [Indexed: 12/21/2022] Open
Abstract
We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identifying the perturbed TRs.
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Affiliation(s)
- Qian Qin
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
- Center of Molecular Medicine, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Jingyu Fan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Rongbin Zheng
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Changxin Wan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Shenglin Mei
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Qiu Wu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Hanfei Sun
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Jing Zhang
- Stem Cell Translational Research Center, Tongji Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200065, China.
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
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11
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Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2. Sci Rep 2019; 9:19697. [PMID: 31873146 PMCID: PMC6927953 DOI: 10.1038/s41598-019-56171-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Excitatory neurons of the mammalian cerebral cortex are organized into six functional layers characterized by unique patterns of connectivity, as well as distinctive physiological and morphological properties. Cortical layers appear after a highly regulated migration process in which cells move from the deeper, proliferative zone toward the superficial layers. Importantly, defects in this radial migration process have been implicated in neurodevelopmental and psychiatric diseases. Here we report that during the final stages of migration, transcription factor Neurogenic Differentiation 2 (Neurod2) contributes to terminal cellular localization within the cortical plate. In mice, in utero knockdown of Neurod2 resulted in reduced numbers of neurons localized to the uppermost region of the developing cortex, also termed the primitive cortical zone. Our ChIP-Seq and RNA-Seq analyses of genes regulated by NEUROD2 in the developing cortex identified a number of key target genes with known roles in Reelin signaling, a critical regulator of neuronal migration. Our focused analysis of regulation of the Reln gene, encoding the extracellular ligand REELIN, uncovered NEUROD2 binding to conserved E-box elements in multiple introns. Furthermore, we demonstrate that knockdown of NEUROD2 in primary cortical neurons resulted in a strong increase in Reln gene expression at the mRNA level, as well as a slight upregulation at the protein level. These data reveal a new role for NEUROD2 during the late stages of neuronal migration, and our analysis of its genomic targets offers new genes with potential roles in cortical lamination.
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12
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Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Rep 2019; 23:297-312.e12. [PMID: 29617668 PMCID: PMC5906131 DOI: 10.1016/j.celrep.2018.03.064] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/12/2018] [Accepted: 03/15/2018] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts. Hundreds of lncRNAs target cancer genes and pathways in each tumor context lncRNA copy numbers are predictive of target cancer gene dysregulation Most lncRNAs are predicted to be transcriptional or post-transcriptional specialists lncRNAs are predicted to synergistically regulate proliferation pathways in cancer
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13
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Nicol B, Grimm SA, Gruzdev A, Scott GJ, Ray MK, Yao HHC. Genome-wide identification of FOXL2 binding and characterization of FOXL2 feminizing action in the fetal gonads. Hum Mol Genet 2019; 27:4273-4287. [PMID: 30212841 DOI: 10.1093/hmg/ddy312] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/30/2018] [Indexed: 12/16/2022] Open
Abstract
The identity of the gonads is determined by which fate, ovarian granulosa cell or testicular Sertoli cell, the bipotential somatic cell precursors choose to follow. In most vertebrates, the conserved transcription factor FOXL2 contributes to the fate of granulosa cells. To understand FOXL2 functions during gonad differentiation, we performed genome-wide analysis of FOXL2 chromatin occupancy in fetal ovaries and established a genetic mouse model that forces Foxl2 expression in the fetal testis. When FOXL2 was ectopically expressed in the somatic cell precursors in the fetal testis, FOXL2 was sufficient to repress Sertoli cell differentiation, ultimately resulting in partial testis-to-ovary sex-reversal. Combining genome-wide analysis of FOXL2 binding in the fetal ovary with transcriptomic analyses of our Foxl2 gain-of-function and previously published Foxl2 loss-of-function models, we identified potential pathways responsible for the feminizing action of FOXL2. Finally, comparison of FOXL2 genome-wide occupancy in the fetal ovary with testis-determining factor SOX9 genome-wide occupancy in the fetal testis revealed extensive overlaps, implying that antagonistic signals between FOXL2 and SOX9 occur at the chromatin level.
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Affiliation(s)
- Barbara Nicol
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sara A Grimm
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Artiom Gruzdev
- Knockout Mouse Core Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Greg J Scott
- Knockout Mouse Core Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Manas K Ray
- Knockout Mouse Core Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Humphrey H-C Yao
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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14
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Müller S, Glaß M, Singh AK, Haase J, Bley N, Fuchs T, Lederer M, Dahl A, Huang H, Chen J, Posern G, Hüttelmaier S. IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner. Nucleic Acids Res 2019; 47:375-390. [PMID: 30371874 PMCID: PMC6326824 DOI: 10.1093/nar/gky1012] [Citation(s) in RCA: 256] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/09/2018] [Accepted: 10/17/2018] [Indexed: 12/13/2022] Open
Abstract
The oncofetal mRNA-binding protein IGF2BP1 and the transcriptional regulator SRF modulate gene expression in cancer. In cancer cells, we demonstrate that IGF2BP1 promotes the expression of SRF in a conserved and N6-methyladenosine (m6A)-dependent manner by impairing the miRNA-directed decay of the SRF mRNA. This results in enhanced SRF-dependent transcriptional activity and promotes tumor cell growth and invasion. At the post-transcriptional level, IGF2BP1 sustains the expression of various SRF-target genes. The majority of these SRF/IGF2BP1-enhanced genes, including PDLIM7 and FOXK1, show conserved upregulation with SRF and IGF2BP1 synthesis in cancer. PDLIM7 and FOXK1 promote tumor cell growth and were reported to enhance cell invasion. Consistently, 35 SRF/IGF2BP1-dependent genes showing conserved association with SRF and IGF2BP1 expression indicate a poor overall survival probability in ovarian, liver and lung cancer. In conclusion, these findings identify the SRF/IGF2BP1-, miRNome- and m6A-dependent control of gene expression as a conserved oncogenic driver network in cancer.
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Affiliation(s)
- Simon Müller
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford protein center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Markus Glaß
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford protein center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Anurag K Singh
- Institute for Physiological Chemistry, Medical Faculty, Martin Luther University Halle-Wittenberg, 06114 Halle (Saale), Germany
| | - Jacob Haase
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford protein center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Nadine Bley
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford protein center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Tommy Fuchs
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford protein center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Marcell Lederer
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford protein center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
| | - Andreas Dahl
- Deep Sequencing Group, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden
| | - Huilin Huang
- Department of Systems Biology, City of Hope, Monrovia, CA 91016, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Jianjun Chen
- Department of Systems Biology, City of Hope, Monrovia, CA 91016, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA
| | - Guido Posern
- Institute for Physiological Chemistry, Medical Faculty, Martin Luther University Halle-Wittenberg, 06114 Halle (Saale), Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford protein center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
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15
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O'Connor T, Bodén M, Bailey TL. CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data. Nucleic Acids Res 2018; 45:e19. [PMID: 28204599 PMCID: PMC5389714 DOI: 10.1093/nar/gkw956] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 09/30/2016] [Accepted: 10/10/2016] [Indexed: 12/18/2022] Open
Abstract
Identifying the genomic regions and regulatory factors that control the transcription of genes is an important, unsolved problem. The current method of choice predicts transcription factor (TF) binding sites using chromatin immunoprecipitation followed by sequencing (ChIP-seq), and then links the binding sites to putative target genes solely on the basis of the genomic distance between them. Evidence from chromatin conformation capture experiments shows that this approach is inadequate due to long-distance regulation via chromatin looping. We present CisMapper, which predicts the regulatory targets of a TF using the correlation between a histone mark at the TF's bound sites and the expression of each gene across a panel of tissues. Using both chromatin conformation capture and differential expression data, we show that CisMapper is more accurate at predicting the target genes of a TF than the distance-based approaches currently used, and is particularly advantageous for predicting the long-range regulatory interactions typical of tissue-specific gene expression. CisMapper also predicts which TF binding sites regulate a given gene more accurately than using genomic distance. Unlike distance-based methods, CisMapper can predict which transcription start site of a gene is regulated by a particular binding site of the TF.
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Affiliation(s)
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Timothy L Bailey
- Department of Pharmacology, University of Nevada School of Medicine, Reno, NV 89557-0357, USA
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16
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Roswall P, Bocci M, Bartoschek M, Li H, Kristiansen G, Jansson S, Lehn S, Sjölund J, Reid S, Larsson C, Eriksson P, Anderberg C, Cortez E, Saal LH, Orsmark-Pietras C, Cordero E, Haller BK, Häkkinen J, Burvenich IJG, Lim E, Orimo A, Höglund M, Rydén L, Moch H, Scott AM, Eriksson U, Pietras K. Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling. Nat Med 2018. [PMID: 29529015 PMCID: PMC5896729 DOI: 10.1038/nm.4494] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Breast tumors of the basal-like, hormone receptor-negative, subtype remain an unmet clinical challenge, as patients exhibit a high rate of recurrence and poor survival. Co-evolution of the malignant mammary epithelium and its underlying stroma instigates cancer-associated fibroblasts (CAFs) to endorse most, if not all, hallmarks of cancer progression. Here, we delineate a previously unappreciated role for CAFs as determinants of the molecular subtype of breast cancer. We identified a paracrine cross-talk between cancer cells expressing platelet-derived growth factor (PDGF)-CC and CAFs expressing the cognate receptors in human basal-like mammary carcinomas. Genetic or pharmacological intervention with PDGF-CC activity in mouse models of cancer resulted in conversion of basal-like breast cancers into a hormone receptor-positive state that conferred sensitivity to endocrine therapy in previously impervious tumors. We conclude that specification of the basal-like subtype of breast cancer is under microenvironmental control and therapeutically actionable in order to achieve sensitivity to endocrine therapy.
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Affiliation(s)
- Pernilla Roswall
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Matteo Bocci
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Michael Bartoschek
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Hong Li
- Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Sara Jansson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Sophie Lehn
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jonas Sjölund
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Steven Reid
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Pontus Eriksson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Charlotte Anderberg
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Eliane Cortez
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Lao H Saal
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | | | - Eugenia Cordero
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bengt Kristian Haller
- Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jari Häkkinen
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ingrid J G Burvenich
- Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,University of New South Wales, Sydney, New South Wales, Australia
| | - Akira Orimo
- Department of Pathology and Oncology, Juntendo University School of Medicine, Tokyo, Japan
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Lisa Rydén
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Andrew M Scott
- Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Ulf Eriksson
- Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kristian Pietras
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
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17
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Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P. Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression. Nat Ecol Evol 2018; 2:152-163. [PMID: 29180706 PMCID: PMC5733139 DOI: 10.1038/s41559-017-0377-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/10/2017] [Indexed: 02/02/2023]
Abstract
To gain insight into how mammalian gene expression is controlled by rapidly evolving regulatory elements, we jointly analysed promoter and enhancer activity with downstream transcription levels in liver samples from 15 species. Genes associated with complex regulatory landscapes generally exhibit high expression levels that remain evolutionarily stable. While the number of regulatory elements is the key driver of transcriptional output and resilience, regulatory conservation matters: elements active across mammals most effectively stabilize gene expression. In contrast, recently evolved enhancers typically contribute weakly, consistent with their high evolutionary plasticity. These effects are observed across the entire mammalian clade and are robust to potential confounders, such as the gene expression level. Using liver as a representative somatic tissue, our results illuminate how the evolutionary stability of gene expression is profoundly entwined with both the number and conservation of surrounding promoters and enhancers.
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Affiliation(s)
- Camille Berthelot
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique UMR8197, Institut National de la Santé et de la Recherche Médicale U1024, 46 Rue d'Ulm, 75230, Paris, Cedex 05, France
| | - Diego Villar
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Julie E Horvath
- Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, 27707, USA
- North Carolina Museum of Natural Sciences, Raleigh, NC, 27601, USA
- Evolutionary Anthropology Department, Duke University, Durham, NC, 27707, USA
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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18
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Essebier A, Lamprecht M, Piper M, Bodén M. Bioinformatics approaches to predict target genes from transcription factor binding data. Methods 2017; 131:111-119. [DOI: 10.1016/j.ymeth.2017.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/29/2017] [Accepted: 09/03/2017] [Indexed: 12/28/2022] Open
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19
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Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. PLoS Comput Biol 2017; 13:e1005340. [PMID: 28103241 PMCID: PMC5289608 DOI: 10.1371/journal.pcbi.1005340] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 02/02/2017] [Accepted: 01/03/2017] [Indexed: 01/12/2023] Open
Abstract
Gene expression regulators, such as transcription factors (TFs) and microRNAs (miRNAs), have varying regulatory targets based on the tissue and physiological state (context) within which they are expressed. While the emergence of regulator-characterizing experiments has inferred the target genes of many regulators across many contexts, methods for transferring regulator target genes across contexts are lacking. Further, regulator target gene lists frequently are not curated or have permissive inclusion criteria, impairing their use. Here, we present a method called iterative Contextual Transcriptional Activity Inference of Regulators (icTAIR) to resolve these issues. icTAIR takes a regulator’s previously-identified target gene list and combines it with gene expression data from a context, quantifying that regulator’s activity for that context. It then calculates the correlation between each listed target gene’s expression and the quantitative score of regulatory activity, removes the uncorrelated genes from the list, and iterates the process until it derives a stable list of refined target genes. To validate and demonstrate icTAIR’s power, we use it to refine the MSigDB c3 database of TF, miRNA and unclassified motif target gene lists for breast cancer. We then use its output for survival analysis with clinicopathological multivariable adjustment in 7 independent breast cancer datasets covering 3,430 patients. We uncover many novel prognostic regulators that were obscured prior to refinement, in particular NFY, and offer a detailed look at the composition and relationships among the breast cancer prognostic regulome. We anticipate icTAIR will be of general use in contextually refining regulator target genes for discoveries across many contexts. The icTAIR algorithm can be downloaded from https://github.com/icTAIR. Gene expression regulators, such as transcription factors and microRNAs, are critical actors in cellular physiology and pathophysiology and act by modulating the expression levels of sets of target genes. Given their significance, numerous experiments have sought to characterize the specific target genes of specific regulators, which in turn has led to regulator target gene list databases. Unfortunately, these lists are plagued by poor curation and validation. Further, all lists suffer from the fundamental issue that regulator targets vary across tissue type and physiological state, or “context”, making them poor for conducting downstream, context-specific analyses. To address this issue, here we present a method called icTAIR that contextually-refines regulator target gene lists. To demonstrate its value, we use icTAIR to take the largest-available database of regulator target gene lists, refine it for the breast cancer context, and use both the pre-refined and refined lists for downstream survival analyses in over 3,400 tumors. We find that icTAIR improves the statistical power of the analyses by multiple orders of magnitude. This in turn lets us map the relational network of breast cancer regulators and identify regulators with prognostic effects even after clinicopathological adjustment. We anticipate icTAIR will be broadly useful in regulator studies.
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20
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Yang CC, Chen MH, Lin SY, Andrews EH, Cheng C, Liu CC, Chen JJW. Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data. BMC Genomics 2017; 18:61. [PMID: 28068916 PMCID: PMC5223348 DOI: 10.1186/s12864-016-3450-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/21/2016] [Indexed: 01/18/2023] Open
Abstract
Background Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mammalian two-hybrid experiments or data mining. Lately, a wealth of ChIP-seq data on human TFs under different experiment conditions are available, making it possible to investigate condition-specific (cell type and/or physiologic state) TF complexes and their target genes. Results Here, we developed a systematic pipeline to infer Condition-Specific Targets of human TF-TF complexes (called the CST pipeline) by integrating ChIP-seq data and TF motifs. In total, we predicted 2,392 TF complexes and 13,504 high-confidence or 127,994 low-confidence regulatory interactions amongst TF complexes and their target genes. We validated our predictions by (i) comparing predicted TF complexes to external TF complex databases, (ii) validating selected target genes of TF complexes using ChIP-qPCR and RT-PCR experiments, and (iii) analysing target genes of select TF complexes using gene ontology enrichment to demonstrate the accuracy of our work. Finally, the predicted results above were integrated and employed to construct a CST database. Conclusions We built up a methodology to construct the CST database, which contributes to the analysis of transcriptional regulation and the identification of novel TF-TF complex formation in a certain condition. This database also allows users to visualize condition-specific TF regulatory networks through a user-friendly web interface. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3450-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chia-Chun Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, No. 250, Kuo-Kuang Rd., 40227, Taichung, Taiwan
| | - Min-Hsuan Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Sheng-Yi Lin
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, No. 250, Kuo-Kuang Rd., 40227, Taichung, Taiwan
| | - Erik H Andrews
- Department of Genetics, Geisel School of Medicine at Dartmouth, 03755, Hanover, NH, USA
| | - Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, 03755, Hanover, NH, USA. .,Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, 03766, Lebanon, NH, USA.
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan. .,Institute of Biomedical Sciences, National Chung Hsing University, No. 250, Kuo-Kuang Rd., 40227, Taichung, Taiwan. .,Agricultural Biotechnology Centre, National Chung Hsing University, Taichung, Taiwan.
| | - Jeremy J W Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan. .,Institute of Biomedical Sciences, National Chung Hsing University, No. 250, Kuo-Kuang Rd., 40227, Taichung, Taiwan. .,Agricultural Biotechnology Centre, National Chung Hsing University, Taichung, Taiwan.
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21
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Investigating the specific core genetic-and-epigenetic networks of cellular mechanisms involved in human aging in peripheral blood mononuclear cells. Oncotarget 2017; 7:8556-79. [PMID: 26895224 PMCID: PMC4890987 DOI: 10.18632/oncotarget.7388] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/03/2016] [Indexed: 12/26/2022] Open
Abstract
Aging is an inevitable part of life for humans, and slowing down the aging process has become a main focus of human endeavor. Here, we applied a systems biology approach to construct protein-protein interaction networks, gene regulatory networks, and epigenetic networks, i.e. genetic and epigenetic networks (GENs), of elderly individuals and young controls. We then compared these GENs to extract aging mechanisms using microarray data in peripheral blood mononuclear cells, microRNA (miRNA) data, and database mining. The core GENs of elderly individuals and young controls were obtained by applying principal network projection to GENs based on Principal Component Analysis. By comparing the core networks, we identified that to overcome the accumulated mutation of genes in the aging process the transcription factor JUN can be activated by stress signals, including the MAPK signaling, T-cell receptor signaling, and neurotrophin signaling pathways through DNA methylation of BTG3, G0S2, and AP2B1 and the regulations of mir-223 let-7d, and mir-130a. We also address the aging mechanisms in old men and women. Furthermore, we proposed that drugs designed to target these DNA methylated genes or miRNAs may delay aging. A multiple drug combination comprising phenylalanine, cholesterol, and palbociclib was finally designed for delaying the aging process.
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22
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Sauta E, Demartini A, Vitali F, Riva A, Bellazzi R. Data Fusion Approach for Learning Transcriptional Bayesian Networks. Artif Intell Med 2017. [DOI: 10.1007/978-3-319-59758-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Hou M, Tang X, Tian F, Shi F, Liu F, Gao G. AnnoLnc: a web server for systematically annotating novel human lncRNAs. BMC Genomics 2016; 17:931. [PMID: 27852242 PMCID: PMC5112684 DOI: 10.1186/s12864-016-3287-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 11/10/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have been shown to play essential roles in almost every important biological process through multiple mechanisms. Although the repertoire of human lncRNAs has rapidly expanded, their biological function and regulation remain largely elusive, calling for a systematic and integrative annotation tool. RESULTS Here we present AnnoLnc ( http://annolnc.cbi.pku.edu.cn ), a one-stop portal for systematically annotating novel human lncRNAs. Based on more than 700 data sources and various tool chains, AnnoLnc enables a systematic annotation covering genomic location, secondary structure, expression patterns, transcriptional regulation, miRNA interaction, protein interaction, genetic association and evolution. An intuitive web interface is available for interactive analysis through both desktops and mobile devices, and programmers can further integrate AnnoLnc into their pipeline through standard JSON-based Web Service APIs. CONCLUSIONS To the best of our knowledge, AnnoLnc is the only web server to provide on-the-fly and systematic annotation for newly identified human lncRNAs. Compared with similar tools, the annotation generated by AnnoLnc covers a much wider spectrum with intuitive visualization. Case studies demonstrate the power of AnnoLnc in not only rediscovering known functions of human lncRNAs but also inspiring novel hypotheses.
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Affiliation(s)
- Mei Hou
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China
| | - Xing Tang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China.,Present address: Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Feng Tian
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P.R. China
| | - Fangyuan Shi
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China
| | - Fenglin Liu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China.
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24
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Liu C, Rohart F, Simpson PT, Khanna KK, Ragan MA, Lê Cao KA. Integrating Multi-omics Data to Dissect Mechanisms of DNA repair Dysregulation in Breast Cancer. Sci Rep 2016; 6:34000. [PMID: 27666291 PMCID: PMC5036051 DOI: 10.1038/srep34000] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/01/2016] [Indexed: 12/20/2022] Open
Abstract
DNA repair genes and pathways that are transcriptionally dysregulated in cancer provide the first line of evidence for the altered DNA repair status in tumours, and hence have been explored intensively as a source for biomarker discovery. The molecular mechanisms underlying DNA repair dysregulation, however, have not been systematically investigated in any cancer type. In this study, we performed a statistical analysis to dissect the roles of DNA copy number alteration (CNA), DNA methylation (DM) at gene promoter regions and the expression changes of transcription factors (TFs) in the differential expression of individual DNA repair genes in normal versus tumour breast samples. These gene-level results were summarised at pathway level to assess whether different DNA repair pathways are affected in distinct manners. Our results suggest that CNA and expression changes of TFs are major causes of DNA repair dysregulation in breast cancer, and that a subset of the identified TFs may exert global impacts on the dysregulation of multiple repair pathways. Our work hence provides novel insights into DNA repair dysregulation in breast cancer. These insights improve our understanding of the molecular basis of the DNA repair biomarkers identified thus far, and have potential to inform future biomarker discovery.
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Affiliation(s)
- Chao Liu
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia
| | - Florian Rohart
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Peter T Simpson
- UQ Centre for Clinical Research and School of Medicine, The University of Queensland, Herston, QLD 4101, Australia
| | - Kum Kum Khanna
- QIMR-Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia
| | - Kim-Anh Lê Cao
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
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25
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Ehrlichia chaffeensis TRP32 is a Nucleomodulin that Directly Regulates Expression of Host Genes Governing Differentiation and Proliferation. Infect Immun 2016; 84:3182-3194. [PMID: 27572329 DOI: 10.1128/iai.00657-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ehrlichia chaffeensis is an obligately intracellular bacterium that reprograms the mononuclear phagocyte through diverse effector-host interactions to modulate numerous host cell processes, including transcription. In a previous study, we reported that E. chaffeensis TRP32, a type 1 secreted effector, interacts with multiple host nucleus-associated proteins and also auto-activates reporter gene expression in yeast. In this study, we demonstrate that TRP32 is a nucleomodulin that binds host DNA and alters host gene transcription. TRP32 enters the host cell nucleus via a noncanonical translocation mechanism that involves phosphorylation of Y179 located in a C-terminal tri-tyrosine motif. Both genistein and mutation of Y179 inhibited TRP32 nuclear entry. An electromobility shift assay (EMSA) demonstrated TRP32 host DNA binding via its tandem repeat domain. TRP32 DNA binding and motif preference were further confirmed by supershift assays, as well as competition and mutant probe analyses. Using ChIP-Seq, we determined that TRP32 binds a G-rich motif primarily within ±500 bp of the gene transcription start site. An ontology analysis identified genes involved in processes such as immune cell differentiation, chromatin remodeling, and RNA transcription and processing, as primary TRP32 targets. TRP32 bound genes (n=1223) were distributed on all chromosomes and included several global regulators of proliferation and inflammation such as FOS and JUN, AKT3 and NRAS, and non-coding RNA genes, miRNA 21 and miRNA 142. TRP32 target genes were differentially regulated during infection, the majority of which were repressed, and direct repression/activation of these genes by TRP32 was confirmed in vitro with a cellular luciferase reporter assay.
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26
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Yang CC, Andrews EH, Chen MH, Wang WY, Chen JJW, Gerstein M, Liu CC, Cheng C. iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data. BMC Genomics 2016; 17:632. [PMID: 27519564 PMCID: PMC4983039 DOI: 10.1186/s12864-016-2963-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/22/2016] [Indexed: 11/12/2022] Open
Abstract
Background Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP’s output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. Description To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server (http://syslab3.nchu.edu.tw/iTAR/) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. Conclusions The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the characteristic binding profiles and the density plot of normalized regulatory scores. The iTAR web server is a useful tool in identifying TF target genes from ChIP-seq/ChIP-chip data and discovering biological insights. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2963-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chia-Chun Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402, Taiwan.,Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Erik H Andrews
- Geisel School of Medicine at Dartmouth, Institute for Quantitative Biomedical Sciences, Lebanon, NH, 03766, USA
| | - Min-Hsuan Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, Taichung, 402, Taiwan
| | - Wan-Yu Wang
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Jeremy J W Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, Taichung, 402, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, 260 Whitney Avenue, New Haven, CT, 06520, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT, 06520, USA
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan. .,Institute of Biomedical Sciences, National Chung Hsing University, Taichung, 402, Taiwan. .,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan.
| | - Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA. .,Geisel School of Medicine at Dartmouth, Institute for Quantitative Biomedical Sciences, Lebanon, NH, 03766, USA. .,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03766, USA.
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27
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Hombach D, Schwarz JM, Robinson PN, Schuelke M, Seelow D. A systematic, large-scale comparison of transcription factor binding site models. BMC Genomics 2016; 17:388. [PMID: 27209209 PMCID: PMC4875604 DOI: 10.1186/s12864-016-2729-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/06/2016] [Indexed: 11/10/2022] Open
Abstract
Background The modelling of gene regulation is a major challenge in biomedical research. This process is dominated by transcription factors (TFs) and mutations in their binding sites (TFBSs) may cause the misregulation of genes, eventually leading to disease. The consequences of DNA variants on TF binding are modelled in silico using binding matrices, but it remains unclear whether these are capable of accurately representing in vivo binding. In this study, we present a systematic comparison of binding models for 82 human TFs from three freely available sources: JASPAR matrices, HT-SELEX-generated models and matrices derived from protein binding microarrays (PBMs). We determined their ability to detect experimentally verified “real” in vivo TFBSs derived from ENCODE ChIP-seq data. As negative controls we chose random downstream exonic sequences, which are unlikely to harbour TFBS. All models were assessed by receiver operating characteristics (ROC) analysis. Results While the area-under-curve was low for most of the tested models with only 47 % reaching a score of 0.7 or higher, we noticed strong differences between the various position-specific scoring matrices with JASPAR and HT-SELEX models showing higher success rates than PBM-derived models. In addition, we found that while TFBS sequences showed a higher degree of conservation than randomly chosen sequences, there was a high variability between individual TFBSs. Conclusions Our results show that only few of the matrix-based models used to predict potential TFBS are able to reliably detect experimentally confirmed TFBS. We compiled our findings in a freely accessible web application called ePOSSUM (http:/mutationtaster.charite.de/ePOSSUM/) which uses a Bayes classifier to assess the impact of genetic alterations on TF binding in user-defined sequences. Additionally, ePOSSUM provides information on the reliability of the prediction using our test set of experimentally confirmed binding sites. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2729-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniela Hombach
- Department of Neuropaediatrics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jana Marie Schwarz
- Department of Neuropaediatrics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Schuelke
- Department of Neuropaediatrics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik Seelow
- Department of Neuropaediatrics, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany. .,Berliner Institut für Gesundheitsforschung / Berlin Institute of Health, Berlin, Germany.
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28
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Chen X, Jung JG, Shajahan-Haq AN, Clarke R, Shih IM, Wang Y, Magnani L, Wang TL, Xuan J. ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles. Nucleic Acids Res 2016; 44:e65. [PMID: 26704972 PMCID: PMC4838354 DOI: 10.1093/nar/gkv1491] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/16/2015] [Accepted: 12/09/2015] [Indexed: 11/16/2022] Open
Abstract
Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq) has greatly improved the reliability with which transcription factor binding sites (TFBSs) can be identified from genome-wide profiling studies. Many computational tools are developed to detect binding events or peaks, however the robust detection of weak binding events remains a challenge for current peak calling tools. We have developed a novel Bayesian approach (ChIP-BIT) to reliably detect TFBSs and their target genes by jointly modeling binding signal intensities and binding locations of TFBSs. Specifically, a Gaussian mixture model is used to capture both binding and background signals in sample data. As a unique feature of ChIP-BIT, background signals are modeled by a local Gaussian distribution that is accurately estimated from the input data. Extensive simulation studies showed a significantly improved performance of ChIP-BIT in target gene prediction, particularly for detecting weak binding signals at gene promoter regions. We applied ChIP-BIT to find target genes from NOTCH3 and PBX1 ChIP-seq data acquired from MCF-7 breast cancer cells. TF knockdown experiments have initially validated about 30% of co-regulated target genes identified by ChIP-BIT as being differentially expressed in MCF-7 cells. Functional analysis on these genes further revealed the existence of crosstalk between Notch and Wnt signaling pathways.
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Affiliation(s)
- Xi Chen
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA 22203, USA
| | - Jin-Gyoung Jung
- Department of Pathology, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB-II, Baltimore, MD 21231, USA
| | - Ayesha N Shajahan-Haq
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington, DC 20057, USA
| | - Robert Clarke
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington, DC 20057, USA
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB-II, Baltimore, MD 21231, USA
| | - Yue Wang
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA 22203, USA
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, ICTEM building, Hammersmith Hospital, DuCane Road, London W120NN, UK
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB-II, Baltimore, MD 21231, USA
| | - Jianhua Xuan
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA 22203, USA
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29
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Zhu L, Guo WL, Deng SP, Huang DS. ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:55-63. [PMID: 26886732 DOI: 10.1109/tcbb.2015.2465893] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating them independently, several recent studies have convincingly demonstrated that a wealth of scientific insights can be gained by integrative analysis of these ChIP-seq data. However, when used for the purpose of integrative analysis, a serious drawback of current ChIP-seq technique is that it is still expensive and time-consuming to generate ChIP-seq datasets of high standard. Most researchers are therefore unable to obtain complete ChIP-seq data for several TFs in a wide variety of cell lines, which considerably limits the understanding of transcriptional regulation pattern. In this paper, we propose a novel method called ChIP-PIT to overcome the aforementioned limitation. In ChIP-PIT, ChIP-seq data corresponding to a diverse collection of cell types, TFs and genes are fused together using the three-mode pair-wise interaction tensor (PIT) model, and the prediction of unperformed ChIP-seq experimental results is formulated as a tensor completion problem. Computationally, we propose efficient first-order method based on extensions of coordinate descent method to learn the optimal solution of ChIP-PIT, which makes it particularly suitable for the analysis of massive scale ChIP-seq data. Experimental evaluation the ENCODE data illustrate the usefulness of the proposed model.
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30
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Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A. Testing and Validation of Computational Methods for Mass Spectrometry. J Proteome Res 2015; 15:809-14. [PMID: 26549429 DOI: 10.1021/acs.jproteome.5b00852] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High-throughput methods based on mass spectrometry (proteomics, metabolomics, lipidomics, etc.) produce a wealth of data that cannot be analyzed without computational methods. The impact of the choice of method on the overall result of a biological study is often underappreciated, but different methods can result in very different biological findings. It is thus essential to evaluate and compare the correctness and relative performance of computational methods. The volume of the data as well as the complexity of the algorithms render unbiased comparisons challenging. This paper discusses some problems and challenges in testing and validation of computational methods. We discuss the different types of data (simulated and experimental validation data) as well as different metrics to compare methods. We also introduce a new public repository for mass spectrometric reference data sets ( http://compms.org/RefData ) that contains a collection of publicly available data sets for performance evaluation for a wide range of different methods.
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Affiliation(s)
- Laurent Gatto
- Computational Proteomics Unit and Cambridge Centre for Proteomics, University of Cambridge , Cambridge CB2 1QR, United Kingdom
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins University , Baltimore, Maryland 21205, United States.,Institute of Genetic Medicine, Johns Hopkins University , Baltimore, Maryland 21205, United States
| | - Michael R Hoopmann
- Institute for Systems Biology , Seattle, Washington 98109, United States
| | - Henning Hermjakob
- European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.,National Center for Protein Sciences , Beijing, China
| | - Oliver Kohlbacher
- Quantitative Biology Center, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany.,Center for Bioinformatics, Universität Tübingen , Sand 14, 72076 Tübingen, Germany.,Dept. of Computer Science, Universität Tübingen , Sand 14, 72076 Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology , Spemannstr. 35, 72076 Tübingen, Germany
| | - Andreas Beyer
- CECAD, University of Cologne , 50931 Cologne, Germany
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31
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Bhargava A, Herzel H, Ananthasubramaniam B. Mining for novel candidate clock genes in the circadian regulatory network. BMC SYSTEMS BIOLOGY 2015; 9:78. [PMID: 26576534 PMCID: PMC4650315 DOI: 10.1186/s12918-015-0227-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Most physiological processes in mammals are temporally regulated by means of a master circadian clock in the brain and peripheral oscillators in most other tissues. A transcriptional-translation feedback network of clock genes produces near 24 h oscillations in clock gene and protein expression. Here, we aim to identify novel additions to the clock network using a meta-analysis of public chromatin immunoprecipitation sequencing (ChIP-seq), proteomics and protein-protein interaction data starting from a published list of 1000 genes with robust transcriptional rhythms and circadian phenotypes of knockdowns. RESULTS We identified 20 candidate genes including nine known clock genes that received significantly high scores and were also robust to the relative weights assigned to different data types. Our scoring was consistent with the original ranking of the 1000 genes, but also provided novel complementary insights. Candidate genes were enriched for genes expressed in a circadian manner in multiple tissues with regulation driven mainly by transcription factors BMAL1 and REV-ERB α,β. Moreover, peak transcription of candidate genes was remarkably consistent across tissues. While peaks of the 1000 genes were distributed uniformly throughout the day, candidate gene peaks were strongly concentrated around dusk. Finally, we showed that binding of specific transcription factors to a gene promoter was predictive of peak transcription at a certain time of day and discuss combinatorial phase regulation. CONCLUSIONS Combining complementary publicly-available data targeting different levels of regulation within the circadian network, we filtered the original list and found 11 novel robust candidate clock genes. Using the criteria of circadian proteomic expression, circadian expression in multiple tissues and independent gene knockdown data, we propose six genes (Por, Mtss1, Dgat2, Pim3, Ppp1r3b, Upp2) involved in metabolism and cancer for further experimental investigation. The availability of public high-throughput databases makes such meta-analysis a promising approach to test consistency between sources and tap their entire potential.
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Affiliation(s)
- Anuprabha Bhargava
- Institute for Theoretical Biology, Charité Universitätsmedizin, Phillipstr. 13, Haus 4, Berlin, 10115, Germany.
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Invalidenstr. 43, Berlin, 10115, Germany.
| | - Bharath Ananthasubramaniam
- Institute for Theoretical Biology, Charité Universitätsmedizin, Phillipstr. 13, Haus 4, Berlin, 10115, Germany.
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32
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Bayam E, Sahin GS, Guzelsoy G, Guner G, Kabakcioglu A, Ince-Dunn G. Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation. BMC Genomics 2015; 16:681. [PMID: 26341353 PMCID: PMC4560887 DOI: 10.1186/s12864-015-1882-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/26/2015] [Indexed: 12/03/2022] Open
Abstract
Background Cellular differentiation programs are controlled, to a large extent, by the combinatorial functioning of specific transcription factors. Cortical projection neurons constitute the major excitatory neuron population within the cortex and mediate long distance communication between the cortex and other brain regions. Our understanding of effector transcription factors and their downstream transcriptional programs that direct the differentiation process of cortical projection neurons is far from complete. Results In this study, we carried out a ChIP-Seq (chromatin-immunoprecipitation and sequencing) analysis of NEUROD2, an effector transcription factor expressed in lineages of cortical projection neurons during the peak of cortical excitatory neurogenesis. Our results suggest that during cortical development NEUROD2 targets key genes that are required for Reelin signaling, a major pathway that regulates the migration of neurons from germinal zones to their final layers of residence within the cortex. We also find that NEUROD2 binds to a large set of genes with functions in layer-specific differentiation and in axonal pathfinding of cortical projection neurons. Conclusions Our analysis of in vivo NEUROD2 target genes offers mechanistic insight into signaling pathways that regulate neuronal migration and axon guidance and identifies genes that are likely to be required for proper cortical development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1882-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Efil Bayam
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
| | - Gulcan Semra Sahin
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey. .,Present Address: Neuroscience Department, Washington State University, Pullman, WA, 99164, USA.
| | - Gizem Guzelsoy
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
| | - Gokhan Guner
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
| | - Alkan Kabakcioglu
- Physics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
| | - Gulayse Ince-Dunn
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
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33
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Stein C, Bardet AF, Roma G, Bergling S, Clay I, Ruchti A, Agarinis C, Schmelzle T, Bouwmeester T, Schübeler D, Bauer A. YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers. PLoS Genet 2015; 11:e1005465. [PMID: 26295846 PMCID: PMC4546604 DOI: 10.1371/journal.pgen.1005465] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/23/2015] [Indexed: 12/30/2022] Open
Abstract
YAP1 is a major effector of the Hippo pathway and a well-established oncogene. Elevated YAP1 activity due to mutations in Hippo pathway components or YAP1 amplification is observed in several types of human cancers. Here we investigated its genomic binding landscape in YAP1-activated cancer cells, as well as in non-transformed cells. We demonstrate that TEAD transcription factors mediate YAP1 chromatin-binding genome-wide, further explaining their dominant role as primary mediators of YAP1-transcriptional activity. Moreover, we show that YAP1 largely exerts its transcriptional control via distal enhancers that are marked by H3K27 acetylation and that YAP1 is necessary for this chromatin mark at bound enhancers and the activity of the associated genes. This work establishes YAP1-mediated transcriptional regulation at distal enhancers and provides an expanded set of target genes resulting in a fundamental source to study YAP1 function in a normal and cancer setting. The YAP1/Hippo signaling pathway is a key regulator of organ size and tissue homeostasis, and its dysregulation is linked to cancer development. Elevated activity of YAP1, a transcriptional coactivator and well-established oncogene has been reported to occur in human cancers. Comprehensive identification of YAP1 regulated genes and its mode of action will be of high importance to uncover YAP1 biology that could be exploited for a therapeutic intervention. To this end, we performed genome-wide analyses to identify YAP1 occupied sites in cancer cell lines representing different YAP1/Hippo pathway tumor etiologies and in non-transformed fibroblasts. Our data demonstrate that YAP1 activity is mediated predominantly via TEAD transcription factors supporting the importance of TEADs as main mediators of YAP1-coactivator activity. We further show that YAP1 and TEAD1 exert their transcriptional control via binding to enhancers, leading to characteristic chromatin changes and distal activation of genes. By linking enhancers to genes, we provide a list of novel YAP1 target genes in an oncogenic setting that we show can readily be exploited in tumor classification and provides a foundation for further investigations.
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Affiliation(s)
- Claudia Stein
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Anaïs Flore Bardet
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sebastian Bergling
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Ieuan Clay
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Alexandra Ruchti
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Claudia Agarinis
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tobias Schmelzle
- Oncology, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tewis Bouwmeester
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Faculty of Sciences, Basel, Switzerland
- * E-mail: (DS); (AB)
| | - Andreas Bauer
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
- * E-mail: (DS); (AB)
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Santhanam B, Cai H, Devreotes PN, Shaulsky G, Katoh-Kurasawa M. The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium. Nat Commun 2015; 6:7551. [PMID: 26144553 PMCID: PMC4506546 DOI: 10.1038/ncomms8551] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/20/2015] [Indexed: 12/11/2022] Open
Abstract
In many systems, including the social amoeba Dictyostelium discoideum, development is often marked by dynamic morphological and transcriptional changes orchestrated by key transcription factors. However, efforts to examine sequential genome-wide changes of gene regulation in developmental processes have been fairly limited. Here we report the developmental regulatory dynamics of GtaC, a GATA-type zinc-finger transcription factor, through the analyses of serial ChIP- and RNA-sequencing data. GtaC is essential for developmental progression, decoding extracellular cAMP pulses during early development and may play a role in mediating cell-type differentiation at later stages. We find that GtaC exhibits temporally distinctive DNA-binding patterns concordant with each developmental stage. We identify direct GtaC targets and observe cotemporaneous GtaC-binding and developmental expression regulation. Our results suggest that GtaC regulates multiple physiological processes as Dictyostelium transitions from a group of unicellular amoebae to an integrated multicellular organism. Development involves dynamic transcriptional changes. By serial ChIP- and RNA-sequencing, here, the authors show that GtaC, a GATA type transcription factor, exhibits temporally distinctive DNA binding and regulation of gene expression concordant with the development in the social amoeba Dictyostelium discoideum.
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Affiliation(s)
- Balaji Santhanam
- 1] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Huaqing Cai
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Peter N Devreotes
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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35
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Assembly of a comprehensive regulatory network for the mammalian circadian clock: a bioinformatics approach. PLoS One 2015; 10:e0126283. [PMID: 25945798 PMCID: PMC4422523 DOI: 10.1371/journal.pone.0126283] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/31/2015] [Indexed: 12/12/2022] Open
Abstract
By regulating the timing of cellular processes, the circadian clock provides a way to adapt physiology and behaviour to the geophysical time. In mammals, a light-entrainable master clock located in the suprachiasmatic nucleus (SCN) controls peripheral clocks that are present in virtually every body cell. Defective circadian timing is associated with several pathologies such as cancer and metabolic and sleep disorders. To better understand the circadian regulation of cellular processes, we developed a bioinformatics pipeline encompassing the analysis of high-throughput data sets and the exploitation of published knowledge by text-mining. We identified 118 novel potential clock-regulated genes and integrated them into an existing high-quality circadian network, generating the to-date most comprehensive network of circadian regulated genes (NCRG). To validate particular elements in our network, we assessed publicly available ChIP-seq data for BMAL1, REV-ERBα/β and RORα/γ proteins and found strong evidence for circadian regulation of Elavl1, Nme1, Dhx6, Med1 and Rbbp7 all of which are involved in the regulation of tumourigenesis. Furthermore, we identified Ncl and Ddx6, as targets of RORγ and REV-ERBα, β, respectively. Most interestingly, these genes were also reported to be involved in miRNA regulation; in particular, NCL regulates several miRNAs, all involved in cancer aggressiveness. Thus, NCL represents a novel potential link via which the circadian clock, and specifically RORγ, regulates the expression of miRNAs, with particular consequences in breast cancer progression. Our findings bring us one step forward towards a mechanistic understanding of mammalian circadian regulation, and provide further evidence of the influence of circadian deregulation in cancer.
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36
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Mathelier A, Lefebvre C, Zhang AW, Arenillas DJ, Ding J, Wasserman WW, Shah SP. Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas. Genome Biol 2015; 16:84. [PMID: 25903198 PMCID: PMC4467049 DOI: 10.1186/s13059-015-0648-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/07/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND With the rapid increase of whole-genome sequencing of human cancers, an important opportunity to analyze and characterize somatic mutations lying within cis-regulatory regions has emerged. A focus on protein-coding regions to identify nonsense or missense mutations disruptive to protein structure and/or function has led to important insights; however, the impact on gene expression of mutations lying within cis-regulatory regions remains under-explored. We analyzed somatic mutations from 84 matched tumor-normal whole genomes from B-cell lymphomas with accompanying gene expression measurements to elucidate the extent to which these cancers are disrupted by cis-regulatory mutations. RESULTS We characterize mutations overlapping a high quality set of well-annotated transcription factor binding sites (TFBSs), covering a similar portion of the genome as protein-coding exons. Our results indicate that cis-regulatory mutations overlapping predicted TFBSs are enriched in promoter regions of genes involved in apoptosis or growth/proliferation. By integrating gene expression data with mutation data, our computational approach culminates with identification of cis-regulatory mutations most likely to participate in dysregulation of the gene expression program. The impact can be measured along with protein-coding mutations to highlight key mutations disrupting gene expression and pathways in cancer. CONCLUSIONS Our study yields specific genes with disrupted expression triggered by genomic mutations in either the coding or the regulatory space. It implies that mutated regulatory components of the genome contribute substantially to cancer pathways. Our analyses demonstrate that identifying genomically altered cis-regulatory elements coupled with analysis of gene expression data will augment biological interpretation of mutational landscapes of cancers.
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Affiliation(s)
- Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada.
| | - Calvin Lefebvre
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada. .,Bioinformatics Graduate Program, University of British Columbia, Vancouver, V5Z 1L3, BC, Canada.
| | - Allen W Zhang
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada. .,Bioinformatics Graduate Program, University of British Columbia, Vancouver, V5Z 1L3, BC, Canada.
| | - David J Arenillas
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada.
| | - Jiarui Ding
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada. .,Department of Computer Science, University of British Columbia, Vancouver, V6T 1Z4, BC, Canada.
| | - Wyeth W Wasserman
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada.
| | - Sohrab P Shah
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, G227-2211, BC, Canada.
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Fattori J, Indolfo NDC, Campos JCLDO, Videira NB, Bridi AV, Doratioto TR, Assis MAD, Figueira ACM. Investigation of Interactions between DNA and Nuclear Receptors: A Review of the Most Used Methods. NUCLEAR RECEPTOR RESEARCH 2014. [DOI: 10.11131/2014/101090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Juliana Fattori
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Nathalia de Carvalho Indolfo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | | | - Natália Bernardi Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Aline Villanova Bridi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Tábata Renée Doratioto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Michelle Alexandrino de Assis
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
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Angelini C, Costa V. Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems. Front Cell Dev Biol 2014; 2:51. [PMID: 25364758 PMCID: PMC4207007 DOI: 10.3389/fcell.2014.00051] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 09/01/2014] [Indexed: 11/15/2022] Open
Abstract
The availability of omic data produced from international consortia, as well as from worldwide laboratories, is offering the possibility both to answer long-standing questions in biomedicine/molecular biology and to formulate novel hypotheses to test. However, the impact of such data is not fully exploited due to a limited availability of multi-omic data integration tools and methods. In this paper, we discuss the interplay between gene expression and epigenetic markers/transcription factors. We show how integrating ChIP-seq and RNA-seq data can help to elucidate gene regulatory mechanisms. In particular, we discuss the two following questions: (i) Can transcription factor occupancies or histone modification data predict gene expression? (ii) Can ChIP-seq and RNA-seq data be used to infer gene regulatory networks? We propose potential directions for statistical data integration. We discuss the importance of incorporating underestimated aspects (such as alternative splicing and long-range chromatin interactions). We also highlight the lack of data benchmarks and the need to develop tools for data integration from a statistical viewpoint, designed in the spirit of reproducible research.
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Affiliation(s)
- Claudia Angelini
- Istituto per le Applicazioni del Calcolo "M. Picone" - CNR Napoli, Italy ; Computational and Biology Open Laboratory (ComBOlab) Napoli, Italy
| | - Valerio Costa
- Computational and Biology Open Laboratory (ComBOlab) Napoli, Italy ; Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR Napoli, Italy
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Pechenick DA, Payne JL, Moore JH. Phenotypic robustness and the assortativity signature of human transcription factor networks. PLoS Comput Biol 2014; 10:e1003780. [PMID: 25121490 PMCID: PMC4133045 DOI: 10.1371/journal.pcbi.1003780] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 06/30/2014] [Indexed: 11/21/2022] Open
Abstract
Many developmental, physiological, and behavioral processes depend on the precise expression of genes in space and time. Such spatiotemporal gene expression phenotypes arise from the binding of sequence-specific transcription factors (TFs) to DNA, and from the regulation of nearby genes that such binding causes. These nearby genes may themselves encode TFs, giving rise to a transcription factor network (TFN), wherein nodes represent TFs and directed edges denote regulatory interactions between TFs. Computational studies have linked several topological properties of TFNs — such as their degree distribution — with the robustness of a TFN's gene expression phenotype to genetic and environmental perturbation. Another important topological property is assortativity, which measures the tendency of nodes with similar numbers of edges to connect. In directed networks, assortativity comprises four distinct components that collectively form an assortativity signature. We know very little about how a TFN's assortativity signature affects the robustness of its gene expression phenotype to perturbation. While recent theoretical results suggest that increasing one specific component of a TFN's assortativity signature leads to increased phenotypic robustness, the biological context of this finding is currently limited because the assortativity signatures of real-world TFNs have not been characterized. It is therefore unclear whether these earlier theoretical findings are biologically relevant. Moreover, it is not known how the other three components of the assortativity signature contribute to the phenotypic robustness of TFNs. Here, we use publicly available DNaseI-seq data to measure the assortativity signatures of genome-wide TFNs in 41 distinct human cell and tissue types. We find that all TFNs share a common assortativity signature and that this signature confers phenotypic robustness to model TFNs. Lastly, we determine the extent to which each of the four components of the assortativity signature contributes to this robustness. The cells of living organisms do not concurrently express their entire complement of genes. Instead, they regulate their gene expression, and one consequence of this is the potential for different cells to adopt different stable gene expression patterns. For example, the development of an embryo necessitates that cells alter their gene expression patterns in order to differentiate. These gene expression phenotypes are largely robust to genetic mutation, and one source of this robustness may reside in the network structure of interacting molecules that underlie genetic regulation. Theoretical studies of regulatory networks have linked network structure to robustness; however, it is also necessary to more extensively characterize real-world regulatory networks in order to understand which structural properties may be biologically meaningful. We recently used theoretical models to show that a particular structural property, degree assortativity, is linked to robustness. Here, we measure the assortativity of human regulatory networks in 41 distinct cell and tissue types. We then develop a theoretical framework to explore how this structural property affects robustness, and we find that the gene expression phenotypes of human regulatory networks are more robust than expected by chance alone.
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Affiliation(s)
- Dov A. Pechenick
- Computational Genetics Laboratory, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Joshua L. Payne
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Jason H. Moore
- Computational Genetics Laboratory, Dartmouth College, Hanover, New Hampshire, United States of America
- * E-mail:
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Biased, non-equivalent gene-proximal and -distal binding motifs of orphan nuclear receptor TR4 in primary human erythroid cells. PLoS Genet 2014; 10:e1004339. [PMID: 24811540 PMCID: PMC4014424 DOI: 10.1371/journal.pgen.1004339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 03/17/2014] [Indexed: 02/04/2023] Open
Abstract
We previously reported that TR2 and TR4 orphan nuclear receptors bind to direct repeat (DR) elements in the ε- and γ-globin promoters, and act as molecular anchors for the recruitment of epigenetic corepressors of the multifaceted DRED complex, thereby leading to ε- and γ-globin transcriptional repression during definitive erythropoiesis. Other than the ε- and γ-globin and the GATA1 genes, TR4-regulated target genes in human erythroid cells remain unknown. Here, we identified TR4 binding sites genome-wide using chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) as human primary CD34+ hematopoietic progenitors differentiated progressively to late erythroid precursors. We also performed whole transcriptome analyses by RNA-seq to identify TR4 downstream targets after lentiviral-mediated TR4 shRNA knockdown in erythroid cells. Analyses from combined ChIP-seq and RNA-seq datasets indicate that DR1 motifs are more prevalent in the proximal promoters of TR4 direct target genes, which are involved in basic biological functions (e.g., mRNA processing, ribosomal assembly, RNA splicing and primary metabolic processes). In contrast, other non-DR1 repeat motifs (DR4, ER6 and IR1) are more prevalent at gene-distal TR4 binding sites. Of these, approximately 50% are also marked with epigenetic chromatin signatures (such as P300, H3K27ac, H3K4me1 and H3K27me3) associated with enhancer function. Thus, we hypothesize that TR4 regulates gene transcription via gene-proximal DR1 sites as TR4/TR2 heterodimers, while it can associate with novel nuclear receptor partners (such as RXR) to bind to distant non-DR1 consensus sites. In summary, this study reveals that the TR4 regulatory network is far more complex than previously appreciated and that TR4 regulates basic, essential biological processes during the terminal differentiation of human erythroid cells. Sequential genome-wide binding studies investigated by deep sequencing (ChIP-seq) represent a powerful tool for investigating the temporal sequence of gene activation and repression events that take place as cells differentiate. Here, we report the binding of an “orphan” nuclear receptor (one for which no ligand has been identified) to its cognate genomic regulatory sites and perform the functional analysis to validate its downstream targets as precursor cells differentiate from very early human hematopoietic progenitors into red blood cells. We discovered that when this receptor is bound at gene proximal promoters, it recognizes a different DNA sequence than when it binds to more distant regulatory sites (enhancers and silencers). Since this receptor can either activate or repress specific target genes, the data suggest the intriguing possibility that the two different modes of DNA recognition may reflect association of the receptor with different partner molecules when regulating gene expression from proximal or distal sequences.
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