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Azpeitia E, Wagner A. Short Residence Times of DNA-Bound Transcription Factors Can Reduce Gene Expression Noise and Increase the Transmission of Information in a Gene Regulation System. Front Mol Biosci 2020; 7:67. [PMID: 32411721 PMCID: PMC7198700 DOI: 10.3389/fmolb.2020.00067] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/25/2020] [Indexed: 12/14/2022] Open
Abstract
Gene expression noise is not just ubiquitous but also variable, and we still do not understand some of the most elementary factors that affect it. Among them is the residence time of a transcription factor (TF) on DNA, the mean time that a DNA-bound TF remains bound. Here, we use a stochastic model of transcriptional regulation to study how residence time affects the gene expression noise that arises when a TF induces gene expression. We find that the effect of residence time on gene expression noise depends on the TF’s concentration and its affinity to DNA, which determine the level of induction of the gene. At high levels of induction, residence time has no effect on gene expression noise. However, as the level of induction decreases, short residence times reduce gene expression noise. The reason is that fast on-off TF binding dynamics prevent long periods where proteins are predominantly synthesized or degraded, which can cause excessive fluctuations in gene expression. As a consequence, short residence times can help a gene regulation system acquire information about the cellular environment it operates in. Our predictions are consistent with the observation that experimentally measured residence times are usually modest and lie between seconds to minutes.
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Affiliation(s)
- Eugenio Azpeitia
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Centro de Ciencias Matemáticas, UNAM, Morelia, Mexico
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Santa Fe Institute, Santa Fe, NM, United States
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2
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Ryan NM, Morris SW, Porteous DJ, Taylor MS, Evans KL. SuRFing the genomics wave: an R package for prioritising SNPs by functionality. Genome Med 2014; 6:79. [PMID: 25400697 PMCID: PMC4224693 DOI: 10.1186/s13073-014-0079-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/26/2014] [Indexed: 12/16/2022] Open
Abstract
Identifying functional non-coding variants is one of the greatest unmet challenges in genetics. To help address this, we introduce an R package, SuRFR, which integrates functional annotation and prior biological knowledge to prioritise candidate functional variants. SuRFR is publicly available, modular, flexible, fast, and simple to use. We demonstrate that SuRFR performs with high sensitivity and specificity and provide a widely applicable and scalable benchmarking dataset for model training and validation. Website: http://www.cgem.ed.ac.uk/resources/
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Affiliation(s)
- Niamh M Ryan
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK ; Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ UK
| | - Martin S Taylor
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK ; Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ UK
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Miranda TB, Morris SA, Hager GL. Complex genomic interactions in the dynamic regulation of transcription by the glucocorticoid receptor. Mol Cell Endocrinol 2013; 380:16-24. [PMID: 23499945 PMCID: PMC3724757 DOI: 10.1016/j.mce.2013.03.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/26/2013] [Accepted: 03/03/2013] [Indexed: 12/13/2022]
Abstract
The glucocorticoid receptor regulates transcriptional output through complex interactions with the genome. These events require continuous remodeling of chromatin, interactions of the glucocorticoid receptor with chaperones and other accessory factors, and recycling of the receptor by the proteasome. Therefore, the cohort of factors expressed in a particular cell type can determine the physiological outcome upon treatment with glucocorticoid hormones. In addition, circadian and ultradian cycling of hormones can also affect GR response. Here we will discuss revision of the classical static model of GR binding to response elements to incorporate recent findings from single cell and genome-wide analyses of GR regulation. We will highlight how these studies have changed our views on the dynamics of GR recruitment and its modulation of gene expression.
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Basu U, Romao JM, Guan LL. Adipogenic transcriptome profiling using high throughput technologies. J Genomics 2013; 1:22-8. [PMID: 25031652 PMCID: PMC4091434 DOI: 10.7150/jgen.3781] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The recent technological innovations in the area of functional genomics, gene expression/transcriptomic profiling can provide new insights to understand the molecular basis of adipogenesis. The focus of this review is to highlight the recent advances in our understanding of the complex interplay of gene expression events and the regulatory mechanisms of adipogenesis in mouse cell lines, humans and farm animals. All these studies have employed the availability of constantly evolving high throughput 'omics' technologies including microarrays, RNA-Seq, chromatin immunoprecipitation, next generation sequencing, RNAi, miRNA profiling and quantitative PCR arrays.
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Affiliation(s)
- Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Josue Moura Romao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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Madrigal P, Krajewski P. Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data. Front Genet 2012; 3:230. [PMID: 23118738 PMCID: PMC3484326 DOI: 10.3389/fgene.2012.00230] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 10/13/2012] [Indexed: 12/16/2022] Open
Affiliation(s)
- Pedro Madrigal
- Laboratory of Biometry, Institute of Plant Genetics, Polish Academy of Sciences Poznań, Poland
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6
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Grøntved L, Hager GL. Impact of chromatin structure on PR signaling: transition from local to global analysis. Mol Cell Endocrinol 2012; 357:30-6. [PMID: 21958695 PMCID: PMC3290724 DOI: 10.1016/j.mce.2011.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 09/02/2011] [Indexed: 01/16/2023]
Abstract
The progesterone receptor (PR) interacts with chromatin in a highly dynamic manner that requires ongoing chromatin remodeling, interaction with chaparones and activity of the proteasome. Here we discuss dynamic interaction of steroid receptor with chromatin, with special attention not only to PR but also to the glucocorticoid receptor (GR), as these receptors share many similarities regarding interaction with, and remodeling of, chromatin. Both receptors can bind nucleosomal DNA and have accordingly been described as pioneering factors. However recent genomic approaches (ChIP-seq and DHS-seq) show that a large fraction of receptor binding events occur at pre-accessible chromatin. Thus factors which generate and maintain accessible chromatin during development, and in fully differentiated tissue, contribute a major fraction of receptor tissue specificity. In addition, chromosome conformation capture techniques suggest that steroid receptors preferentially sequester within distinct nuclear hubs. We will integrate dynamic studies from single cells and genomic studies from cell populations, and discuss how genomic approaches have reshaped our current understanding of mechanisms that control steroid receptor interaction with chromatin.
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Affiliation(s)
- Lars Grøntved
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892
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Abstract
Recent high-throughput sequencing technologies have opened the door for genome-wide characterization of chromatin features at an unprecedented resolution. Chromatin accessibility is an important property that regulates protein binding and other nuclear processes. Here, we describe computational methods to analyze chromatin accessibility using DNaseI hypersensitivity by sequencing (DNaseI-seq). Although there are numerous bioinformatic tools to analyze ChIP-seq data, our statistical algorithm was developed specifically to identify significantly accessible genomic regions by handling features of DNaseI hypersensitivity. Without prior knowledge of relevant protein factors, one can discover genome-wide chromatin remodeling events associated with specific conditions or differentiation stages from quantitative analysis of DNaseI hypersensitivity. By performing appropriate subsequent computational analyses on a select subset of remodeled sites, it is also possible to extract information about putative factors that may bind to specific DNA elements within DNaseI hypersensitive sites. These approaches enabled by DNaseI-seq represent a powerful new methodology that reveals mechanisms of transcriptional regulation.
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Affiliation(s)
- Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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8
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Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis. EMBO J 2011; 30:1459-72. [PMID: 21427703 DOI: 10.1038/emboj.2011.65] [Citation(s) in RCA: 275] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 02/17/2011] [Indexed: 12/27/2022] Open
Abstract
Adipogenesis is tightly controlled by a complex network of transcription factors acting at different stages of differentiation. Peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein (C/EBP) family members are key regulators of this process. We have employed DNase I hypersensitive site analysis to investigate the genome-wide changes in chromatin structure that accompany the binding of adipogenic transcription factors. These analyses revealed a dramatic and dynamic modulation of the chromatin landscape during the first hours of adipocyte differentiation that coincides with cooperative binding of multiple early transcription factors (including glucocorticoid receptor, retinoid X receptor, Stat5a, C/EBPβ and -δ) to transcription factor 'hotspots'. Our results demonstrate that C/EBPβ marks a large number of these transcription factor 'hotspots' before induction of differentiation and chromatin remodelling and is required for their establishment. Furthermore, a subset of early remodelled C/EBP-binding sites persists throughout differentiation and is later occupied by PPARγ, indicating that early C/EBP family members, in addition to their well-established role in activation of PPARγ transcription, may act as pioneering factors for PPARγ binding.
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Ryu S, Joshi N, McDonnell K, Woo J, Choi H, Gao D, McCombie WR, Mittal V. Discovery of novel human breast cancer microRNAs from deep sequencing data by analysis of pri-microRNA secondary structures. PLoS One 2011; 6:e16403. [PMID: 21346806 PMCID: PMC3035615 DOI: 10.1371/journal.pone.0016403] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 12/20/2010] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression and contribute to a
variety of biological processes. Abnormal miRNA expression has been reported in
various diseases including pathophysiology of breast cancer, where they regulate
protumorigenic processes including vascular invasiveness, estrogen receptor
status, chemotherapy resistance, invasion and metastasis. The miRBase sequence
database, a public repository for newly discovered miRNAs, has grown rapidly
with approximately >10,000 entries to date. Despite this rapid growth, many
miRNAs have not yet been validated, and several others are yet to be identified.
A lack of a full complement of miRNAs has imposed limitations on recognizing
their important roles in cancer, including breast cancer. Using deep sequencing
technology, we have identified 189 candidate novel microRNAs in human breast
cancer cell lines with diverse tumorigenic potential. We further show that
analysis of 500-nucleotide pri-microRNA secondary structure constitutes a
reliable method to predict bona fide miRNAs as judged by experimental
validation. Candidate novel breast cancer miRNAs with stem lengths of greater
than 30 bp resulted in the generation of precursor and mature sequences
in vivo. On the other hand, candidates with stem length
less than 30 bp were less efficient in producing mature miRNA. This approach may
be used to predict which candidate novel miRNA would qualify as bona fide miRNAs
from deep sequencing data with approximately 90% accuracy.
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Affiliation(s)
- Seongho Ryu
- Department of Cardiothoracic Surgery, Weill Cornell Medical College of
Cornell University, New York, New York, United States of America
- Department of Cell and Developmental Biology, Weill Cornell Medical
College of Cornell University, New York, New York, United States of
America
| | - Natasha Joshi
- Department of Cardiothoracic Surgery, Weill Cornell Medical College of
Cornell University, New York, New York, United States of America
- Department of Cell and Developmental Biology, Weill Cornell Medical
College of Cornell University, New York, New York, United States of
America
| | - Kevin McDonnell
- Department of Cardiothoracic Surgery, Weill Cornell Medical College of
Cornell University, New York, New York, United States of America
- Department of Cell and Developmental Biology, Weill Cornell Medical
College of Cornell University, New York, New York, United States of
America
| | - Jongchan Woo
- Laboratory of Plant Molecular Biology, Rockefeller University, New York,
New York, United States of America
| | - Hyejin Choi
- Department of Cardiothoracic Surgery, Weill Cornell Medical College of
Cornell University, New York, New York, United States of America
- Department of Cell and Developmental Biology, Weill Cornell Medical
College of Cornell University, New York, New York, United States of
America
| | - Dingcheng Gao
- Department of Cardiothoracic Surgery, Weill Cornell Medical College of
Cornell University, New York, New York, United States of America
- Department of Cell and Developmental Biology, Weill Cornell Medical
College of Cornell University, New York, New York, United States of
America
| | | | - Vivek Mittal
- Department of Cardiothoracic Surgery, Weill Cornell Medical College of
Cornell University, New York, New York, United States of America
- Department of Cell and Developmental Biology, Weill Cornell Medical
College of Cornell University, New York, New York, United States of
America
- * E-mail:
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10
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Biddie SC, John S, Hager GL. Genome-wide mechanisms of nuclear receptor action. Trends Endocrinol Metab 2010; 21:3-9. [PMID: 19800253 PMCID: PMC2818176 DOI: 10.1016/j.tem.2009.08.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 08/19/2009] [Accepted: 08/21/2009] [Indexed: 01/11/2023]
Abstract
Nuclear receptors are involved in a myriad of physiological processes, responding to ligands and binding to DNA at sequence-specific cis-regulatory elements. This binding occurs in the context of chromatin, a critical factor in regulating eukaryotic transcription. Recent high-throughput assays have examined nuclear receptor action genome-wide, advancing our understanding of receptor binding to regulatory elements. Here, we discuss current knowledge of genome-wide response element occupancy by receptors and the function of transcription factor networks in regulating nuclear receptor action. We highlight emerging roles for the epigenome, chromatin remodeling, histone modification, histone variants and long-range chromosomal interactions in nuclear receptor binding and receptor-dependent gene regulation. These mechanisms contribute importantly to the action of nuclear receptors in health and disease.
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Affiliation(s)
- Simon C. Biddie
- Laboratory of Receptor Biology and Gene Expression, Building 41, Rm B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, The Dorothy Hodgkin Building, University of Bristol, Whitson Street, Bristol, BS1 3NY United Kingdom
| | - Sam John
- Laboratory of Receptor Biology and Gene Expression, Building 41, Rm B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, Building 41, Rm B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
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