1
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Hauck JS, Moon D, Jiang X, Wang ME, Zhao Y, Xu L, Quang H, Butler W, Chen M, Macias E, Gao X, He Y, Huang J. Heat shock factor 1 directly regulates transsulfuration pathway to promote prostate cancer proliferation and survival. Commun Biol 2024; 7:9. [PMID: 38172561 PMCID: PMC10764307 DOI: 10.1038/s42003-023-05727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
There are limited therapeutic options for patients with advanced prostate cancer (PCa). We previously found that heat shock factor 1 (HSF1) expression is increased in PCa and is an actionable target. In this manuscript, we identify that HSF1 regulates the conversion of homocysteine to cystathionine in the transsulfuration pathway by altering levels of cystathionine-β-synthase (CBS). We find that HSF1 directly binds the CBS gene and upregulates CBS mRNA levels. Targeting CBS decreases PCa growth and induces tumor cell death while benign prostate cells are largely unaffected. Combined inhibition of HSF1 and CBS results in more pronounced inhibition of PCa cell proliferation and reduction of transsulfuration pathway metabolites. Combination of HSF1 and CBS knockout decreases tumor size for a small cell PCa xenograft mouse model. Our study thus provides new insights into the molecular mechanism of HSF1 function and an effective therapeutic strategy against advanced PCa.
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Affiliation(s)
- J Spencer Hauck
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Room 301M, Duke South DUMC 3712, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - David Moon
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Room 301M, Duke South DUMC 3712, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - Xue Jiang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Room 301M, Duke South DUMC 3712, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - Mu-En Wang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Room 301M, Duke South DUMC 3712, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - Yue Zhao
- Department of Pathology, College of Basic Medical Sciences, and the First Hospital of China Medical University, No.77 Puhe Road, Shenyang North New Area, 110122, Shenyang, China
| | - Lingfan Xu
- Urology Department, First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, 230001, Hefei, China
| | - Holly Quang
- Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Ave One Baylor Plaza, Houston, TX, 77030, USA
| | - William Butler
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Room 301M, Duke South DUMC 3712, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - Ming Chen
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Room 301M, Duke South DUMC 3712, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - Everardo Macias
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Room 301M, Duke South DUMC 3712, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - Xia Gao
- Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Ave One Baylor Plaza, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, 1100 Bates Ave Baylor College of Medicine, Houston, TX, USA
| | - Yiping He
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Room 301M, Duke South DUMC 3712, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - Jiaoti Huang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Room 301M, Duke South DUMC 3712, 40 Duke Medicine Circle, Durham, NC, 27710, USA.
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2
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Wolpe JB, Martins AL, Guertin MJ. Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling. NAR Genom Bioinform 2023; 5:lqad054. [PMID: 37274120 PMCID: PMC10236359 DOI: 10.1093/nargab/lqad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/02/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023] Open
Abstract
Chromatin accessibility assays have revolutionized the field of transcription regulation by providing single-nucleotide resolution measurements of regulatory features such as promoters and transcription factor binding sites. ATAC-seq directly measures how well the Tn5 transposase accesses chromatinized DNA. Tn5 has a complex sequence bias that is not effectively scaled with traditional bias-correction methods. We model this complex bias using a rule ensemble machine learning approach that integrates information from many input k-mers proximal to the ATAC sequence reads. We effectively characterize and correct single-nucleotide sequence biases and regional sequence biases of the Tn5 enzyme. Correction of enzymatic sequence bias is an important step in interpreting chromatin accessibility assays that aim to infer transcription factor binding and regulatory activity of elements in the genome.
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Affiliation(s)
- Jacob B Wolpe
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - André L Martins
- Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA
| | - Michael J Guertin
- Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA
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3
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Alexandari AM, Horton CA, Shrikumar A, Shah N, Li E, Weilert M, Pufall MA, Zeitlinger J, Fordyce PM, Kundaje A. De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540401. [PMID: 37214836 PMCID: PMC10197627 DOI: 10.1101/2023.05.11.540401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Transcription factors (TF) are proteins that bind DNA in a sequence-specific manner to regulate gene transcription. Despite their unique intrinsic sequence preferences, in vivo genomic occupancy profiles of TFs differ across cellular contexts. Hence, deciphering the sequence determinants of TF binding, both intrinsic and context-specific, is essential to understand gene regulation and the impact of regulatory, non-coding genetic variation. Biophysical models trained on in vitro TF binding assays can estimate intrinsic affinity landscapes and predict occupancy based on TF concentration and affinity. However, these models cannot adequately explain context-specific, in vivo binding profiles. Conversely, deep learning models, trained on in vivo TF binding assays, effectively predict and explain genomic occupancy profiles as a function of complex regulatory sequence syntax, albeit without a clear biophysical interpretation. To reconcile these complementary models of in vitro and in vivo TF binding, we developed Affinity Distillation (AD), a method that extracts thermodynamic affinities de-novo from deep learning models of TF chromatin immunoprecipitation (ChIP) experiments by marginalizing away the influence of genomic sequence context. Applied to neural networks modeling diverse classes of yeast and mammalian TFs, AD predicts energetic impacts of sequence variation within and surrounding motifs on TF binding as measured by diverse in vitro assays with superior dynamic range and accuracy compared to motif-based methods. Furthermore, AD can accurately discern affinities of TF paralogs. Our results highlight thermodynamic affinity as a key determinant of in vivo binding, suggest that deep learning models of in vivo binding implicitly learn high-resolution affinity landscapes, and show that these affinities can be successfully distilled using AD. This new biophysical interpretation of deep learning models enables high-throughput in silico experiments to explore the influence of sequence context and variation on both intrinsic affinity and in vivo occupancy.
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Affiliation(s)
- Amr M. Alexandari
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | | | - Avanti Shrikumar
- Department of Earth System Science, Stanford University, Stanford, CA 94305
| | - Nilay Shah
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Eileen Li
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Miles A. Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA
- The University of Kansas Medical Center, Kansas City, KS, USA
| | - Polly M. Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- ChEM-H Institute, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94110
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
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4
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Chyr J, Zhang Z, Chen X, Zhou X. PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines. Comput Struct Biotechnol J 2021; 19:2870-2880. [PMID: 34093998 PMCID: PMC8142020 DOI: 10.1016/j.csbj.2021.05.013] [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: 02/21/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 10/26/2022] Open
Abstract
Topologically associating domains, or TADs, play important roles in genome organization and gene regulation; however, they are often altered in diseases. High-throughput chromatin conformation capturing assays, such as Hi-C, can capture domains of increased interactions, and TADs and boundaries can be identified using well-established analytical tools. However, generating Hi-C data is expensive. In our study, we addressed the relationship between multi-omics data and higher-order chromatin structures using a newly developed machine-learning model called PredTAD. Our tool uses already-available and cost-effective datatypes such as transcription factor and histone modification ChIPseq data. Specifically, PredTAD utilizes both epigenetic and genetic features as well as neighboring information to classify the entire human genome as boundary or non-boundary regions. Our tool can predict boundary changes between normal and breast cancer genomes. Among the most important features for predicting boundary alterations were CTCF, subunits of cohesin (RAD21 and SMC3), and chromosome number, suggesting their roles in conserved and dynamic boundaries formation. Upon further analysis, we observed that genes near altered TAD boundaries were found to be involved in several important breast cancer signaling pathways such as Ras, Jak-STAT, and estrogen signaling pathways. We also discovered a TAD boundary alteration that contributes to RET oncogene overexpression. PredTAD can also successfully predict TAD boundary changes in other conditions and diseases. In conclusion, our newly developed machine learning tool allowed for a more complete understanding of the dynamic 3D chromatin structures involved in signaling pathway activation, altered gene expression, and disease state in breast cancer cells.
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Affiliation(s)
- Jacqueline Chyr
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
| | - Zhigang Zhang
- School of Information Management and Statistics, Hubei University of Economics, Wuhan, Hubei 430205 China
| | - Xi Chen
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
| | - Xiaobo Zhou
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
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5
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Srivastava D, Mahony S. Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194443. [PMID: 31639474 PMCID: PMC7166147 DOI: 10.1016/j.bbagrm.2019.194443] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/21/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022]
Abstract
Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TF's intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modifications in the same cell type. However, since concurrent chromatin may itself be a consequence of TF binding, chromatin landscapes measured prior to TF activation provide more useful insights into how cell type-specific TF binding events became established in the first place. Here, we review the various sequence and chromatin determinants of cell type-specific TF binding specificity. We identify the current challenges and opportunities associated with computational approaches to characterizing, imputing, and predicting cell type-specific TF binding patterns. We further focus on studies that characterize TF binding in dynamic regulatory settings, and we discuss how these studies are leading to a more complex and nuanced understanding of dynamic protein-DNA binding activities. We propose that TF binding activities at individual sites can be viewed along a two-dimensional continuum of local sequence and chromatin context. Under this view, cell type-specific TF binding activities may result from either strongly favorable sequence features or strongly favorable chromatin context.
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Affiliation(s)
- Divyanshi Srivastava
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America.
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6
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Harada AE, Burton RS. Consequences of HSF knockdown on gene expression during the heat shock response in Tigriopus californicus. J Exp Biol 2020; 223:jeb208611. [PMID: 31915203 DOI: 10.1242/jeb.208611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/30/2019] [Indexed: 12/16/2022]
Abstract
Although the existence of a cellular heat shock response is nearly universal, its relationship to organismal thermal tolerance is not completely understood. Many of the genes involved are known to be regulated by the highly conserved heat shock transcription factor-1 (HSF-1), yet the regulatory network is not fully characterized. Here, we investigated the role of HSF-1 in gene expression following thermal stress using knockdown of HSF-1 by RNA interference in the intertidal copepod Tigriopus californicus We observed some evidence for decreased transcription of heat shock protein genes following knockdown, supporting the widely acknowledged role of HSF-1 in the heat shock response. However, the majority of differentially expressed genes between the control and HSF-1 knockdown groups were upregulated, suggesting that HSF-1 normally functions to repress their expression. Differential expression observed in genes related to chitin and cuticle formation lends support to previous findings that these processes are highly regulated following heat stress. We performed a genome scan and identified a set of 396 genes associated with canonical heat shock elements. RNA-seq data did not find those genes to be more highly represented in our HSF-1 knockdown treatment, indicating that requirements for binding and interaction of HSF-1 with a given gene are not simply predicted by the presence of HSF-1 binding sites. Further study of the pathways implicated by these results and future comparisons among populations of T. californicus may help us understand the role and importance of HSF-1 in the heat shock response and, more broadly, in organismal thermal tolerance.
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Affiliation(s)
- Alice E Harada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
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7
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Cohen DM, Lim HW, Won KJ, Steger DJ. Shared nucleotide flanks confer transcriptional competency to bZip core motifs. Nucleic Acids Res 2019; 46:8371-8384. [PMID: 30085281 PMCID: PMC6144830 DOI: 10.1093/nar/gky681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/17/2018] [Indexed: 12/31/2022] Open
Abstract
Sequence-specific DNA binding recruits transcription factors (TFs) to the genome to regulate gene expression. Here, we perform high resolution mapping of CEBP proteins to determine how sequence dictates genomic occupancy. We demonstrate a fundamental difference between the sequence repertoire utilized by CEBPs in vivo versus the palindromic sequence preference reported by classical in vitro models, by identifying a palindromic motif at <1% of the genomic binding sites. On the native genome, CEBPs bind a diversity of related 10 bp sequences resulting from the fusion of degenerate and canonical half-sites. Altered DNA specificity of CEBPs in cells occurs through heterodimerization with other bZip TFs, and approximately 40% of CEBP-binding sites in primary human cells harbor motifs characteristic of CEBP heterodimers. In addition, we uncover an important role for sequence bias at core-motif-flanking bases for CEBPs and demonstrate that flanking bases regulate motif function across mammalian bZip TFs. Favorable flanking bases confer efficient TF occupancy and transcriptional activity, and DNA shape may explain how the flanks alter TF binding. Importantly, motif optimization within the 10-mer is strongly correlated with cell-type-independent recruitment of CEBPβ, providing key insight into how sequence sub-optimization affects genomic occupancy of widely expressed CEBPs across cell types.
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Affiliation(s)
- Daniel M Cohen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hee-Woong Lim
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyoung-Jae Won
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - David J Steger
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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8
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Datta V, Hannenhalli S, Siddharthan R. ChIPulate: A comprehensive ChIP-seq simulation pipeline. PLoS Comput Biol 2019; 15:e1006921. [PMID: 30897079 PMCID: PMC6445533 DOI: 10.1371/journal.pcbi.1006921] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/02/2019] [Accepted: 03/04/2019] [Indexed: 12/17/2022] Open
Abstract
ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) is a high-throughput technique to identify genomic regions that are bound in vivo by a particular protein, e.g., a transcription factor (TF). Biological factors, such as chromatin state, indirect and cooperative binding, as well as experimental factors, such as antibody quality, cross-linking, and PCR biases, are known to affect the outcome of ChIP-seq experiments. However, the relative impact of these factors on inferences made from ChIP-seq data is not entirely clear. Here, via a detailed ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding detection, the sensitivity of inferred TF-DNA binding strength, and number of replicates needed to confidently infer binding strength. We find that the TF motif can be recovered despite poor and non-uniform extraction and PCR amplification efficiencies. The recovery of the motif is, however, affected to a larger extent by the fraction of sites that are either cooperatively or indirectly bound. Importantly, our simulations reveal that the number of ChIP-seq replicates needed to accurately measure in vivo occupancy at high-affinity sites is larger than the recommended community standards. Our results establish statistical limits on the accuracy of inferences of protein-DNA binding from ChIP-seq and suggest that increasing the mean extraction efficiency, rather than amplification efficiency, would better improve sensitivity. The source code and instructions for running ChIPulate can be found at https://github.com/vishakad/chipulate. DNA-binding proteins perform many key roles in biology, such as transcriptional regulation of gene expression and chromatin modification. ChIP-seq (Chromatin immunoprecipitation followed by high-throughput sequencing) is a widely used experimental technique to identify DNA-binding sites of specific proteins of interest, within cells, genome-wide. DNA fragments from genomic regions that are bound by a protein of interest, often a transcription factor (TF), are selectively extracted using specific antibodies, amplified using PCR, and sequenced. The sequences are mapped to the reference genome. Regions where many sequences map, called “peaks”, are used to infer the location of TF-bound loci (peaks), in vivo occupancy at those loci, and the sequence pattern (motif) to which the TF shows a binding affinity. But measurements of TF occupancy and motif inference are vulnerable to several biological and experimental sources of variation that are poorly understood and difficult to assess directly. Here, we simulate key steps of the ChIP-seq protocol with the aim of estimating the relative effects of various sources of variations on motif inference and binding affinity estimations. Besides providing specific insights and recommendations, we provide a general framework to simulate sequence reads in a ChIP-seq experiment, which should considerably aid in the development of software aimed at analyzing ChIP-seq data.
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Affiliation(s)
- Vishaka Datta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, TIFR, Bengaluru, Karnataka, India
- * E-mail:
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Rahul Siddharthan
- The Institute of Mathematical Sciences/HBNI, Taramani, Chennai, India
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9
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Sen SQ, Chanchani S, Southall TD, Doe CQ. Neuroblast-specific open chromatin allows the temporal transcription factor, Hunchback, to bind neuroblast-specific loci. eLife 2019; 8:44036. [PMID: 30694180 PMCID: PMC6377230 DOI: 10.7554/elife.44036] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/24/2019] [Indexed: 12/12/2022] Open
Abstract
Spatial and temporal cues are required to specify neuronal diversity, but how these cues are integrated in neural progenitors remains unknown. Drosophila progenitors (neuroblasts) are a good model: they are individually identifiable with relevant spatial and temporal transcription factors known. Here we test whether spatial/temporal factors act independently or sequentially in neuroblasts. We used Targeted DamID to identify genomic binding sites of the Hunchback temporal factor in two neuroblasts (NB5-6 and NB7-4) that make different progeny. Hunchback targets were different in each neuroblast, ruling out the independent specification model. Moreover, each neuroblast had distinct open chromatin domains, which correlated with differential Hb-bound loci in each neuroblast. Importantly, the Gsb/Pax3 spatial factor, expressed in NB5-6 but not NB7-4, had genomic binding sites correlated with open chromatin in NB5-6, but not NB7-4. Our data support a model in which early-acting spatial factors like Gsb establish neuroblast-specific open chromatin domains, leading to neuroblast-specific temporal factor binding and the production of different neurons in each neuroblast lineage. The human brain is considered to be the most complicated object in the universe, but it only takes a handful of stem cells to make one. The process depends on two types of information: signals separated across space and time. Spatial cues tell a stem cell what type of cell it is going to be, while temporal cues work as molecular clocks to generate a sequence of different neurons over time. Together, these cues generate the large array of cell types in the nervous system. Each stem cell occupies its own space in the developing body and receives its own spatial cues, but they all follow the same timeline. For example, proteins called transcription factors act as molecular clocks and interact with specific genes, telling the cell when to turn them on or off. The same series of transcription factors operates in different stem cells, but they have different effects. So far, it has been unclear whether spatial and temporal signals work independently or sequentially to generate new cell types. To find out, Sen et al. studied two distinct, developing stem cells in fruit flies, which receive different spatial signals. Transcription factors only work if they are able to get to their target genes. Cells can open or close access to different genes by changing the structure of the chromatin wrapping that surrounds the genes. In the experiments, a marker was used to reveal the areas of open chromatin in each of the cells. Another marker was used to track the transcription factors. The results showed that the areas of open chromatin varied between stem cells. Moreover, although both cells used the same transcription factor called Hunchback, it targeted different genes in each stem cell. This was due to changes in the chromatin wrapping: Hunchback only acted in areas where the chromatin was open. This suggests that the spatial cues first sculpt the chromatin, making some genes easier to get to than others. Then, the same transcription factors go to the accessible gene, which will differ from one stem cell to another. These findings help us to understand how different types of brain cells develop, which may also aid us in finding a way how to engineer specific cell types. If we could turn stem cells into different types of brain cells, it might help us to treat brain diseases. This may involve giving the right spatial signal before starting the temporal cues.
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Affiliation(s)
- Sonia Q Sen
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, United States
| | - Sachin Chanchani
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, United States
| | - Tony D Southall
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Chris Q Doe
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, United States
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10
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Gong Y, Cao R, Ding G, Hong S, Zhou W, Lu W, Damle M, Fang B, Wang CC, Qian J, Lie N, Lanzillotta C, Rabinowitz JD, Sun Z. Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle. Mol Cell Endocrinol 2018; 471:22-32. [PMID: 28554803 PMCID: PMC5702591 DOI: 10.1016/j.mce.2017.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 05/09/2017] [Accepted: 05/23/2017] [Indexed: 12/22/2022]
Abstract
Nuclear receptors regulate gene expression by differentially binding to coactivators or corepressors in a ligand-dependent manner, which further recruits a set of epigenome-modifying enzymes that remodel chromatin conformation. Histone acetylation is a major epigenomic change controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs). HDAC3 is the only HDAC that confers the enzymatic activity to the complexes nucleated by nuclear receptor corepressors NCoR and SMRT. To address the metabolic function of HDAC3, we have deleted it specifically in mouse skeletal muscles. We have performed the following omics profiling in skeletal muscles of these mice: (1) RNA-seq profiling of total RNA; (2) Global nuclear run-on (GRO-seq) analysis of nascent RNAs; (3) Chromatin immuno-precipitation (ChIP-seq) of HDAC3 at both early evening and early morning; (4) proteomics profiling with mass spectrometry; (5) snap-shot metabolomics profiling of water-soluble metabolites at the basal condition; (6) snap-shot metabolomics profiling of lipid species at the basal condition; (7) kinetic fluxomics analysis of glucose utilization using 13C6-glucose In vivo during treadmill running exercise. These approaches have provided several novel insights into how nuclear receptors regulate circadian rhythm of skeletal muscle fuel metabolism, which has been published elsewhere. Here we present the original datasets and technical details during the execution, analysis, and interpretation of these omics studies.
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Affiliation(s)
- Yingyun Gong
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Rui Cao
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Guolian Ding
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Sungguan Hong
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Wenjun Zhou
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
| | - Manashree Damle
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Bin Fang
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Chuhan C Wang
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Justin Qian
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Natasha Lie
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Cristina Lanzillotta
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
| | - Zheng Sun
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States.
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11
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Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization. PLoS One 2018; 13:e0199771. [PMID: 30016330 PMCID: PMC6049898 DOI: 10.1371/journal.pone.0199771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/13/2018] [Indexed: 11/19/2022] Open
Abstract
Transcription factors (TFs) often work cooperatively, where the binding of one TF to DNA enhances the binding affinity of a second TF to a nearby location. Such cooperative binding is important for activating gene expression from promoters and enhancers in both prokaryotic and eukaryotic cells. Existing methods to detect cooperative binding of a TF pair rely on analyzing the sequence that is bound. We propose a method that uses, instead, only ChIP-seq peak intensities and an expectation maximization (CPI-EM) algorithm. We validate our method using ChIP-seq data from cells where one of a pair of TFs under consideration has been genetically knocked out. Our algorithm relies on our observation that cooperative TF-TF binding is correlated with weak binding of one of the TFs, which we demonstrate in a variety of cell types, including E. coli, S. cerevisiae and M. musculus cells. We show that this method performs significantly better than a predictor based only on the ChIP-seq peak distance of the TFs under consideration. This suggests that peak intensities contain information that can help detect the cooperative binding of a TF pair. CPI-EM also outperforms an existing sequence-based algorithm in detecting cooperative binding. The CPI-EM algorithm is available at https://github.com/vishakad/cpi-em.
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12
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Guertin MJ, Cullen AE, Markowetz F, Holding AN. Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq. Nucleic Acids Res 2018; 46:e75. [PMID: 29672735 PMCID: PMC6093181 DOI: 10.1093/nar/gky252] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 03/15/2018] [Accepted: 03/28/2018] [Indexed: 11/17/2022] Open
Abstract
A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.
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Affiliation(s)
- Michael J Guertin
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Amy E Cullen
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0RE, UK
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0RE, UK
| | - Andrew N Holding
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0RE, UK
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13
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Rossi MJ, Lai WKM, Pugh BF. Genome-wide determinants of sequence-specific DNA binding of general regulatory factors. Genome Res 2018; 28:497-508. [PMID: 29563167 PMCID: PMC5880240 DOI: 10.1101/gr.229518.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/05/2018] [Indexed: 01/01/2023]
Abstract
General regulatory factors (GRFs), such as Reb1, Abf1, Rap1, Mcm1, and Cbf1, positionally organize yeast chromatin through interactions with a core consensus DNA sequence. It is assumed that sequence recognition via direct base readout suffices for specificity and that spurious nonfunctional sites are rendered inaccessible by chromatin. We tested these assumptions through genome-wide mapping of GRFs in vivo and in purified biochemical systems at near–base pair (bp) resolution using several ChIP-exo–based assays. We find that computationally predicted DNA shape features (e.g., minor groove width, helix twist, base roll, and propeller twist) that are not defined by a unique consensus sequence are embedded in the nonunique portions of GRF motifs and contribute critically to sequence-specific binding. This dual source specificity occurs at GRF sites in promoter regions where chromatin organization starts. Outside of promoter regions, strong consensus sites lack the shape component and consequently lack an intrinsic ability to bind cognate GRFs, without regard to influences from chromatin. However, sites having a weak consensus and low intrinsic affinity do exist in these regions but are rendered inaccessible in a chromatin environment. Thus, GRF site-specificity is achieved through integration of favorable DNA sequence and shape readouts in promoter regions and by chromatin-based exclusion from fortuitous weak sites within gene bodies. This study further revealed a severe G/C nucleotide cross-linking selectivity inherent in all formaldehyde-based ChIP assays, which includes ChIP-seq. However, for most tested proteins, G/C selectivity did not appreciably affect binding site detection, although it does place limits on the quantitativeness of occupancy levels.
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Affiliation(s)
- Matthew J Rossi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - William K M Lai
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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14
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Liu Y, Walavalkar NM, Dozmorov MG, Rich SS, Civelek M, Guertin MJ. Identification of breast cancer associated variants that modulate transcription factor binding. PLoS Genet 2017; 13:e1006761. [PMID: 28957321 PMCID: PMC5619690 DOI: 10.1371/journal.pgen.1006761] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 04/12/2017] [Indexed: 01/11/2023] Open
Abstract
Genome-wide association studies (GWAS) have discovered thousands loci associated with disease risk and quantitative traits, yet most of the variants responsible for risk remain uncharacterized. The majority of GWAS-identified loci are enriched for non-coding single-nucleotide polymorphisms (SNPs) and defining the molecular mechanism of risk is challenging. Many non-coding causal SNPs are hypothesized to alter transcription factor (TF) binding sites as the mechanism by which they affect organismal phenotypes. We employed an integrative genomics approach to identify candidate TF binding motifs that confer breast cancer-specific phenotypes identified by GWAS. We performed de novo motif analysis of regulatory elements, analyzed evolutionary conservation of identified motifs, and assayed TF footprinting data to identify sequence elements that recruit TFs and maintain chromatin landscape in breast cancer-relevant tissue and cell lines. We identified candidate causal SNPs that are predicted to alter TF binding within breast cancer-relevant regulatory regions that are in strong linkage disequilibrium with significantly associated GWAS SNPs. We confirm that the TFs bind with predicted allele-specific preferences using CTCF ChIP-seq data. We used The Cancer Genome Atlas breast cancer patient data to identify ANKLE1 and ZNF404 as the target genes of candidate TF binding site SNPs in the 19p13.11 and 19q13.31 GWAS-identified loci. These SNPs are associated with the expression of ZNF404 and ANKLE1 in breast tissue. This integrative analysis pipeline is a general framework to identify candidate causal variants within regulatory regions and TF binding sites that confer phenotypic variation and disease risk.
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Affiliation(s)
- Yunxian Liu
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ninad M. Walavalkar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United Statess of America
| | - Michael J. Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
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15
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Rieder LE, Koreski KP, Boltz KA, Kuzu G, Urban JA, Bowman SK, Zeidman A, Jordan WT, Tolstorukov MY, Marzluff WF, Duronio RJ, Larschan EN. Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMP. Genes Dev 2017; 31:1494-1508. [PMID: 28838946 PMCID: PMC5588930 DOI: 10.1101/gad.300855.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/25/2017] [Indexed: 01/13/2023]
Abstract
Rieder et al. report that conserved GA repeat cis elements within the bidirectional histone3–histone4 promoter direct histone locus body (HLB) formation in Drosophila. In addition, the CLAMP zinc finger protein binds these GA repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation. The conserved histone locus body (HLB) assembles prior to zygotic gene activation early during development and concentrates factors into a nuclear domain of coordinated histone gene regulation. Although HLBs form specifically at replication-dependent histone loci, the cis and trans factors that target HLB components to histone genes remained unknown. Here we report that conserved GA repeat cis elements within the bidirectional histone3–histone4 promoter direct HLB formation in Drosophila. In addition, the CLAMP (chromatin-linked adaptor for male-specific lethal [MSL] proteins) zinc finger protein binds these GA repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation. We demonstrated previously that CLAMP also promotes the formation of another domain of coordinated gene regulation: the dosage-compensated male X chromosome. Therefore, CLAMP binding to GA repeat motifs promotes the formation of two distinct domains of coordinated gene activation located at different places in the genome.
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Affiliation(s)
- Leila E Rieder
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kaitlin P Koreski
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Kara A Boltz
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Guray Kuzu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jennifer A Urban
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Sarah K Bowman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Anna Zeidman
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - William T Jordan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Michael Y Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Biology, University of North Carolina at Chapel Hill, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Biology, University of North Carolina at Chapel Hill, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Erica N Larschan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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16
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Wang P, Song H, Li C, Li P, Li A, Guan H, Hou L, Wang X. Genome-Wide Dissection of the Heat Shock Transcription Factor Family Genes in Arachis. FRONTIERS IN PLANT SCIENCE 2017; 8:106. [PMID: 28220134 PMCID: PMC5292572 DOI: 10.3389/fpls.2017.00106] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 01/18/2017] [Indexed: 05/21/2023]
Abstract
Heat shock transcription factors (Hsfs) are important transcription factors (TFs) in protecting plants from damages caused by various stresses. The released whole genome sequences of wild peanuts make it possible for genome-wide analysis of Hsfs in peanut. In this study, a total of 16 and 17 Hsf genes were identified from Arachis duranensis and A. ipaensis, respectively. We identified 16 orthologous Hsf gene pairs in both peanut species; however HsfXs was only identified from A. ipaensis. Orthologous pairs between two wild peanut species were highly syntenic. Based on phylogenetic relationship, peanut Hsfs were divided into groups A, B, and C. Selection pressure analysis showed that group B Hsf genes mainly underwent positive selection and group A Hsfs were affected by purifying selection. Small scale segmental and tandem duplication may play important roles in the evolution of these genes. Cis-elements, such as ABRE, DRE, and HSE, were found in the promoters of most Arachis Hsf genes. Five AdHsfs and two AiHsfs contained fungal elicitor responsive elements suggesting their involvement in response to fungi infection. These genes were differentially expressed in cultivated peanut under abiotic stress and Aspergillus flavus infection. AhHsf2 and AhHsf14 were significantly up-regulated after inoculation with A. flavus suggesting their possible role in fungal resistance.
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Affiliation(s)
- Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Changsheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Aiqin Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Hongshan Guan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- *Correspondence: Lei Hou
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- College of Life Sciences, Shandong Normal UniversityJinan, China
- Xingjun Wang
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17
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O'Malley RC, Huang SSC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell 2016; 165:1280-1292. [PMID: 27203113 PMCID: PMC4907330 DOI: 10.1016/j.cell.2016.04.038] [Citation(s) in RCA: 762] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/26/2016] [Accepted: 04/11/2016] [Indexed: 10/21/2022]
Abstract
The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TF-specific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.
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Affiliation(s)
- Ronan C O'Malley
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Shao-Shan Carol Huang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Liang Song
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Mathew G Lewsey
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Mary Galli
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Waksman Institute, Rutgers University, Piscataway, NJ 08854-8020, USA
| | - Andrea Gallavotti
- Waksman Institute, Rutgers University, Piscataway, NJ 08854-8020, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
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18
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Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, Lander ES, Engreitz JM. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science 2016; 354:769-773. [PMID: 27708057 DOI: 10.1126/science.aag2445] [Citation(s) in RCA: 390] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/21/2016] [Indexed: 11/03/2022]
Abstract
Gene expression in mammals is regulated by noncoding elements that can affect physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) to discover regulatory elements and identify their target genes. We assess >1 megabase of sequence in the vicinity of two essential transcription factors, MYC and GATA1, and identify nine distal enhancers that control gene expression and cellular proliferation. Quantitative features of chromatin state and chromosome conformation distinguish the seven enhancers that regulate MYC from other elements that do not, suggesting a strategy for predicting enhancer-promoter connectivity. This CRISPRi-based approach can be applied to dissect transcriptional networks and interpret the contributions of noncoding genetic variation to human disease.
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Affiliation(s)
- Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Rockwell Anyoha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Glen Munson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sharon R Grossman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.,Department of Biology, MIT, Cambridge, MA 02139, USA
| | | | - Michael Kane
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Computational and Systems Biology Program, MIT, Cambridge, MA 02139, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. .,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Department of Biology, MIT, Cambridge, MA 02139, USA
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19
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Li J, Chauve L, Phelps G, Brielmann RM, Morimoto RI. E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response. Genes Dev 2016; 30:2062-2075. [PMID: 27688402 PMCID: PMC5066613 DOI: 10.1101/gad.283317.116] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/06/2016] [Indexed: 01/08/2023]
Abstract
Heat-shock factor (HSF) is the master transcriptional regulator of the heat-shock response (HSR) and is essential for stress resilience. HSF is also required for metazoan development; however, its function and regulation in this process are poorly understood. Here, we characterize the genomic distribution and transcriptional activity of Caenorhabditis elegans HSF-1 during larval development and show that the developmental HSF-1 transcriptional program is distinct from the HSR. HSF-1 developmental activation requires binding of E2F/DP to a GC-rich motif that facilitates HSF-1 binding to a heat-shock element (HSE) that is degenerate from the consensus HSE sequence and adjacent to the E2F-binding site at promoters. In contrast, induction of the HSR is independent of these promoter elements or E2F/DP and instead requires a distinct set of tandem canonical HSEs. Together, E2F and HSF-1 directly regulate a gene network, including a specific subset of chaperones, to promote protein biogenesis and anabolic metabolism, which are essential in development.
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Affiliation(s)
- Jian Li
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Laetitia Chauve
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Grace Phelps
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Renée M Brielmann
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
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20
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Villa R, Schauer T, Smialowski P, Straub T, Becker PB. PionX sites mark the X chromosome for dosage compensation. Nature 2016; 537:244-248. [PMID: 27580037 DOI: 10.1038/nature19338] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/27/2016] [Indexed: 11/09/2022]
Abstract
The rules defining which small fraction of related DNA sequences can be selectively bound by a transcription factor are poorly understood. One of the most challenging tasks in DNA recognition is posed by dosage compensation systems that require the distinction between sex chromosomes and autosomes. In Drosophila melanogaster, the male-specific lethal dosage compensation complex (MSL-DCC) doubles the level of transcription from the single male X chromosome, but the nature of this selectivity is not known. Previous efforts to identify X-chromosome-specific target sequences were unsuccessful as the identified MSL recognition elements lacked discriminative power. Therefore, additional determinants such as co-factors, chromatin features, RNA and chromosome conformation have been proposed to refine targeting further. Here, using an in vitro genome-wide DNA binding assay, we show that recognition of the X chromosome is an intrinsic feature of the MSL-DCC. MSL2, the male-specific organizer of the complex, uses two distinct DNA interaction surfaces-the CXC and proline/basic-residue-rich domains-to identify complex DNA elements on the X chromosome. Specificity is provided by the CXC domain, which binds a novel motif defined by DNA sequence and shape. This motif characterizes a subclass of MSL2-binding sites, which we name PionX (pioneering sites on the X) as they appeared early during the recent evolution of an X chromosome in D. miranda and are the first chromosomal sites to be bound during de novo MSL-DCC assembly. Our data provide the first, to our knowledge, documented molecular mechanism through which the dosage compensation machinery distinguishes the X chromosome from an autosome. They highlight fundamental principles in the recognition of complex DNA elements by protein that will have a strong impact on many aspects of chromosome biology.
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Affiliation(s)
- Raffaella Villa
- Division of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Tamas Schauer
- Division of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Pawel Smialowski
- Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Tobias Straub
- Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Peter B Becker
- Division of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
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21
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Structures of HSF2 reveal mechanisms for differential regulation of human heat-shock factors. Nat Struct Mol Biol 2016; 23:147-54. [PMID: 26727490 PMCID: PMC4973471 DOI: 10.1038/nsmb.3150] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/25/2015] [Indexed: 02/07/2023]
Abstract
Heat Shock Transcription Factor (HSF) family members function in stress protection and in human disease including proteopathies, neurodegeneration and cancer. The mechanisms that drive distinct post-translational modifications, co-factor recruitment and target gene activation for specific HSF paralogs are unknown. We present high-resolution crystal structures of the human HSF2 DNA-binding domain (DBD) bound to DNA, revealing an unprecedented view of HSFs that provides insights into their unique biology. The HSF2 DBD structures resolve a novel carboxyl-terminal helix that directs the coiled-coil domain to wrap around DNA, exposing paralog-specific sequences of the DBD surface, for differential post-translational modifications and co-factor interactions. We further demonstrate a direct interaction between HSF1 and HSF2 through their coiled-coil domains. Together, these features provide a new model for HSF structure as the basis for differential and combinatorial regulation to influence the transcriptional response to cellular stress.
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22
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Kibet CK, Machanick P. Transcription factor motif quality assessment requires systematic comparative analysis. F1000Res 2015; 4:ISCB Comm J-1429. [PMID: 27092243 PMCID: PMC4821295 DOI: 10.12688/f1000research.7408.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 11/22/2022] Open
Abstract
Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
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Affiliation(s)
- Caleb Kipkurui Kibet
- Department of Computer Science and Research Unit in Bioinformatics (RUBi), Rhodes University, Grahamstown, South Africa
| | - Philip Machanick
- Department of Computer Science and Research Unit in Bioinformatics (RUBi), Rhodes University, Grahamstown, South Africa
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Kibet CK, Machanick P. Transcription factor motif quality assessment requires systematic comparative analysis. F1000Res 2015; 4:ISCB Comm J-1429. [PMID: 27092243 DOI: 10.12688/f1000research.7408.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/19/2015] [Indexed: 03/26/2024] Open
Abstract
Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. Finally, we demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
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Affiliation(s)
- Caleb Kipkurui Kibet
- Department of Computer Science and Research Unit in Bioinformatics (RUBi), Rhodes University, Grahamstown, South Africa
| | - Philip Machanick
- Department of Computer Science and Research Unit in Bioinformatics (RUBi), Rhodes University, Grahamstown, South Africa
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24
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Zhu B, Zhang W, Zhang T, Liu B, Jiang J. Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures. THE PLANT CELL 2015; 27:2415-26. [PMID: 26373455 PMCID: PMC4815101 DOI: 10.1105/tpc.15.00537] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/27/2015] [Indexed: 05/02/2023]
Abstract
Enhancers are important regulators of gene expression in eukaryotes. Enhancers function independently of their distance and orientation to the promoters of target genes. Thus, enhancers have been difficult to identify. Only a few enhancers, especially distant intergenic enhancers, have been identified in plants. We developed an enhancer prediction system based exclusively on the DNase I hypersensitive sites (DHSs) in the Arabidopsis thaliana genome. A set of 10,044 DHSs located in intergenic regions, which are away from any gene promoters, were predicted to be putative enhancers. We examined the functions of 14 predicted enhancers using the β-glucuronidase gene reporter. Ten of the 14 (71%) candidates were validated by the reporter assay. We also designed 10 constructs using intergenic sequences that are not associated with DHSs, and none of these constructs showed enhancer activities in reporter assays. In addition, the tissue specificity of the putative enhancers can be precisely predicted based on DNase I hypersensitivity data sets developed from different plant tissues. These results suggest that the open chromatin signature-based enhancer prediction system developed in Arabidopsis may serve as a universal system for enhancer identification in plants.
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Affiliation(s)
- Bo Zhu
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706 Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
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25
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Cohen DM, Won KJ, Nguyen N, Lazar MA, Chen CS, Steger DJ. ATF4 licenses C/EBPβ activity in human mesenchymal stem cells primed for adipogenesis. eLife 2015; 4:e06821. [PMID: 26111340 PMCID: PMC4501333 DOI: 10.7554/elife.06821] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/25/2015] [Indexed: 12/24/2022] Open
Abstract
A well-established cascade of transcription factor (TF) activity orchestrates adipogenesis in response to chemical cues, yet how cell-intrinsic determinants of differentiation such as cell shape and/or seeding density inform this transcriptional program remain enigmatic. Here, we uncover a novel mechanism licensing transcription in human mesenchymal stem cells (hMSCs) adipogenically primed by confluence. Prior to adipogenesis, confluency promotes heterodimer recruitment of the bZip TFs C/EBPβ and ATF4 to a non-canonical C/EBP DNA sequence. ATF4 depletion decreases both cell-density-dependent transcription and adipocyte differentiation. Global profiling in hMSCs and a novel cell-free assay reveals that ATF4 requires C/EBPβ for genomic binding at a motif distinct from that bound by the C/EBPβ homodimer. Our observations demonstrate that C/EBPβ bridges the transcriptional programs in naïve, confluent cells and early differentiating pre-adipocytes. Moreover, they suggest that homo- and heterodimer formation poise C/EBPβ to execute diverse and stage-specific transcriptional programs by exploiting an expanded motif repertoire.
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Affiliation(s)
- Daniel M Cohen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Kyoung-Jae Won
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Nha Nguyen
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Christopher S Chen
- Department of Biomedical Engineering, Boston University, Boston, United States
| | - David J Steger
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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26
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Gómez AV, Córdova G, Munita R, Parada GE, Barrios ÁP, Cancino GI, Álvarez AR, Andrés ME. Characterizing HSF1 Binding and Post-Translational Modifications of hsp70 Promoter in Cultured Cortical Neurons: Implications in the Heat-Shock Response. PLoS One 2015; 10:e0129329. [PMID: 26053851 PMCID: PMC4459960 DOI: 10.1371/journal.pone.0129329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 05/08/2015] [Indexed: 11/21/2022] Open
Abstract
Causes of lower induction of Hsp70 in neurons during heat shock are still a matter of debate. To further inquire into the mechanisms regulating Hsp70 expression in neurons, we studied the activity of Heat Shock Factor 1 (HSF1) and histone posttranslational modifications (PTMs) at the hsp70 promoter in rat cortical neurons. Heat shock induced a transient and efficient translocation of HSF1 to neuronal nuclei. However, no binding of HSF1 at the hsp70 promoter was detected while it bound to the hsp25 promoter in cortical neurons during heat shock. Histone PTMs analysis showed that the hsp70 promoter harbors lower levels of histone H3 and H4 acetylation in cortical neurons compared to PC12 cells under basal conditions. Transcriptomic profiling data analysis showed a predominant usage of cryptic transcriptional start sites at hsp70 gene in the rat cerebral cortex, compared with the whole brain. These data support a weaker activation of hsp70 canonical promoter. Heat shock increased H3Ac at the hsp70 promoter in PC12 cells, which correlated with increased Hsp70 expression while no modifications occurred at the hsp70 promoter in cortical neurons. Increased histone H3 acetylation by Trichostatin A led to hsp70 mRNA and protein induction in cortical neurons. In conclusion, we found that two independent mechanisms maintain a lower induction of Hsp70 in cortical neurons. First, HSF1 fails to bind specifically to the hsp70 promoter in cortical neurons during heat shock and, second, the hsp70 promoter is less accessible in neurons compared to non-neuronal cells due to histone deacetylases repression.
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Affiliation(s)
- Andrea V. Gómez
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
- * E-mail: (AVG); (MEA)
| | - Gonzalo Córdova
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Roberto Munita
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Guillermo E. Parada
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Álvaro P. Barrios
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Gonzalo I. Cancino
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - Alejandra R. Álvarez
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
| | - María E. Andrés
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins 340, Santiago, Chile
- * E-mail: (AVG); (MEA)
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27
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Abstract
Recent advances in experimental and computational methodologies are enabling ultra-high resolution genome-wide profiles of protein-DNA binding events. For example, the ChIP-exo protocol precisely characterizes protein-DNA cross-linking patterns by combining chromatin immunoprecipitation (ChIP) with 5' → 3' exonuclease digestion. Similarly, deeply sequenced chromatin accessibility assays (e.g. DNase-seq and ATAC-seq) enable the detection of protected footprints at protein-DNA binding sites. With these techniques and others, we have the potential to characterize the individual nucleotides that interact with transcription factors, nucleosomes, RNA polymerases and other regulatory proteins in a particular cellular context. In this review, we explain the experimental assays and computational analysis methods that enable high-resolution profiling of protein-DNA binding events. We discuss the challenges and opportunities associated with such approaches.
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Affiliation(s)
- Shaun Mahony
- a Department of Biochemistry & Molecular Biology , Center for Eukaryotic Gene Regulation, The Pennsylvania State University , University Park , PA , USA
| | - B Franklin Pugh
- a Department of Biochemistry & Molecular Biology , Center for Eukaryotic Gene Regulation, The Pennsylvania State University , University Park , PA , USA
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28
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Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A. Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods 2015; 12:433-8. [PMID: 25799441 PMCID: PMC4507281 DOI: 10.1038/nmeth.3329] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/24/2015] [Indexed: 12/26/2022]
Abstract
Modifications to the global run-on and sequencing (GRO-seq) protocol that enrich for 5'-capped RNAs can be used to reveal active transcriptional regulatory elements (TREs) with high accuracy. Here, we introduce discriminative regulatory-element detection from GRO-seq (dREG), a sensitive machine learning method that uses support vector regression to identify active TREs from GRO-seq data without requiring cap-based enrichment (https://github.com/Danko-Lab/dREG/). This approach allows TREs to be assayed together with gene expression levels and other transcriptional features in a single experiment. Predicted TREs are more enriched for several marks of transcriptional activation—including expression quantitative trait loci, disease-associated polymorphisms, acetylated histone 3 lysine 27 (H3K27ac) and transcription factor binding—than those identified by alternative functional assays. Using dREG, we surveyed TREs in eight human cell types and provide new insights into global patterns of TRE function.
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Affiliation(s)
- Charles G. Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY,USA
| | - Stephanie L. Hyland
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, USA
| | - Leighton J. Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Andre L. Martins
- Graduate Field in Computational Biology, Cornell University, Ithaca, NY, USA
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Hyung Won Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Vivian G. Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John T. Lis
- Graduate Field in Computational Biology, Cornell University, Ithaca, NY, USA
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY,USA
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29
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Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell 2015; 58:216-31. [PMID: 25818644 DOI: 10.1016/j.molcel.2015.02.023] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/09/2015] [Accepted: 02/19/2015] [Indexed: 12/28/2022]
Abstract
Chromosomes of metazoan organisms are partitioned in the interphase nucleus into discrete topologically associating domains (TADs). Borders between TADs are formed in regions containing active genes and clusters of architectural protein binding sites. The transcription of most genes is repressed after temperature stress in Drosophila. Here we show that temperature stress induces relocalization of architectural proteins from TAD borders to inside TADs, and this is accompanied by a dramatic rearrangement in the 3D organization of the nucleus. TAD border strength declines, allowing for an increase in long-distance inter-TAD interactions. Similar but quantitatively weaker effects are observed upon inhibition of transcription or depletion of individual architectural proteins. Heat shock-induced inter-TAD interactions result in increased contacts among enhancers and promoters of silenced genes, which recruit Pc and form Pc bodies in the nucleolus. These results suggest that the TAD organization of metazoan genomes is plastic and can be reconfigured quickly.
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30
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Unraveling determinants of transcription factor binding outside the core binding site. Genome Res 2015; 25:1018-29. [PMID: 25762553 PMCID: PMC4484385 DOI: 10.1101/gr.185033.114] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 03/04/2015] [Indexed: 11/25/2022]
Abstract
Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control of gene expression. Despite many advances in the characterization of sequence motifs recognized by TFs, our ability to quantitatively predict TF binding to different regulatory sequences is still limited. Here, we present a novel experimental assay termed BunDLE-seq that provides quantitative measurements of TF binding to thousands of fully designed sequences of 200 bp in length within a single experiment. Applying this binding assay to two yeast TFs, we demonstrate that sequences outside the core TF binding site profoundly affect TF binding. We show that TF-specific models based on the sequence or DNA shape of the regions flanking the core binding site are highly predictive of the measured differential TF binding. We further characterize the dependence of TF binding, accounting for measurements of single and co-occurring binding events, on the number and location of binding sites and on the TF concentration. Finally, by coupling our in vitro TF binding measurements, and another application of our method probing nucleosome formation, to in vivo expression measurements carried out with the same template sequences serving as promoters, we offer insights into mechanisms that may determine the different expression outcomes observed. Our assay thus paves the way to a more comprehensive understanding of TF binding to regulatory sequences and allows the characterization of TF binding determinants within and outside of core binding sites.
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31
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Siepel A, Arbiza L. Cis-regulatory elements and human evolution. Curr Opin Genet Dev 2014; 29:81-9. [PMID: 25218861 PMCID: PMC4258466 DOI: 10.1016/j.gde.2014.08.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/17/2014] [Accepted: 08/23/2014] [Indexed: 11/20/2022]
Abstract
Modification of gene regulation has long been considered an important force in human evolution, particularly through changes to cis-regulatory elements (CREs) that function in transcriptional regulation. For decades, however, the study of cis-regulatory evolution was severely limited by the available data. New data sets describing the locations of CREs and genetic variation within and between species have now made it possible to study CRE evolution much more directly on a genome-wide scale. Here, we review recent research on the evolution of CREs in humans based on large-scale genomic data sets. We consider inferences based on primate divergence, human polymorphism, and combinations of divergence and polymorphism. We then consider 'new frontiers' in this field stemming from recent research on transcriptional regulation.
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Affiliation(s)
- Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Leonardo Arbiza
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
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32
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Guertin MJ, Zhang X, Anguish L, Kim S, Varticovski L, Lis JT, Hager GL, Coonrod SA. Targeted H3R26 deimination specifically facilitates estrogen receptor binding by modifying nucleosome structure. PLoS Genet 2014; 10:e1004613. [PMID: 25211228 PMCID: PMC4161307 DOI: 10.1371/journal.pgen.1004613] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 07/18/2014] [Indexed: 12/17/2022] Open
Abstract
Transcription factor binding to DNA in vivo causes the recruitment of chromatin modifiers that can cause changes in chromatin structure, including the modification of histone tails. We previously showed that estrogen receptor (ER) target gene activation is facilitated by peptidylarginine deiminase 2 (PAD2)-catalyzed histone H3R26 deimination (H3R26Cit). Here we report that the genomic distributions of ER and H3R26Cit in breast cancer cells are strikingly coincident, linearly correlated, and observed as early as 2 minutes following estradiol treatment. The H3R26Cit profile is unlike that of previously described histone modifications and is characterized by sharp, narrow peaks. Paired-end MNase ChIP-seq indicates that the charge-neutral H3R26Cit modification facilitates ER binding to DNA by altering the fine structure of the nucleosome. Clinically, we find that PAD2 and H3R26Cit levels correlate with ER expression in breast tumors and that high PAD2 expression is associated with increased survival in ER+ breast cancer patients. These findings provide insight into how transcription factors gain access to nucleosomal DNA and implicate PAD2 as a novel therapeutic target for ER+ breast cancer. Transcription factors bind to DNA to activate and repress gene transcription. Many transcription factors, particularly nuclear receptors, associate with their cognate DNA element in a highly dynamic manner in vivo. Highly acetylated histone tails and DNase sensitive chromatin are amenable to the initial binding of transcription factors. Upon binding to DNA, transcription factor binding recruits remodelers and coactivators that can cause a concomitant increase in accessibility and acetylation. Herein, we show that estrogen receptor recruitment of a histone deiminase causes the positively charged H3R26 residue to be neutralized. This modification changes the fine structure of the nucleosome particle and facilitates estrogen receptor binding. Lastly, we find that high deiminase expression is associated with increased survival in estrogen receptor-positive breast cancer patients.
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Affiliation(s)
- Michael J. Guertin
- Lab of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Xuesen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail: (XZ); (SAC)
| | - Lynne Anguish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Sohyoung Kim
- Lab of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Lyuba Varticovski
- Lab of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland, United States of America
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Gordon L. Hager
- Lab of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Scott A. Coonrod
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail: (XZ); (SAC)
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33
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Jaeger AM, Makley LN, Gestwicki JE, Thiele DJ. Genomic heat shock element sequences drive cooperative human heat shock factor 1 DNA binding and selectivity. J Biol Chem 2014; 289:30459-30469. [PMID: 25204655 DOI: 10.1074/jbc.m114.591578] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The heat shock transcription factor 1 (HSF1) activates expression of a variety of genes involved in cell survival, including protein chaperones, the protein degradation machinery, anti-apoptotic proteins, and transcription factors. Although HSF1 activation has been linked to amelioration of neurodegenerative disease, cancer cells exhibit a dependence on HSF1 for survival. Indeed, HSF1 drives a program of gene expression in cancer cells that is distinct from that activated in response to proteotoxic stress, and HSF1 DNA binding activity is elevated in cycling cells as compared with arrested cells. Active HSF1 homotrimerizes and binds to a DNA sequence consisting of inverted repeats of the pentameric sequence nGAAn, known as heat shock elements (HSEs). Recent comprehensive ChIP-seq experiments demonstrated that the architecture of HSEs is very diverse in the human genome, with deviations from the consensus sequence in the spacing, orientation, and extent of HSE repeats that could influence HSF1 DNA binding efficacy and the kinetics and magnitude of target gene expression. To understand the mechanisms that dictate binding specificity, HSF1 was purified as either a monomer or trimer and used to evaluate DNA-binding site preferences in vitro using fluorescence polarization and thermal denaturation profiling. These results were compared with quantitative chromatin immunoprecipitation assays in vivo. We demonstrate a role for specific orientations of extended HSE sequences in driving preferential HSF1 DNA binding to target loci in vivo. These studies provide a biochemical basis for understanding differential HSF1 target gene recognition and transcription in neurodegenerative disease and in cancer.
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Affiliation(s)
- Alex M Jaeger
- Departments of Pharmacology and Cancer Biology and Duke University School of Medicine, Durham, North Carolina 27710
| | - Leah N Makley
- Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, California 94143
| | - Jason E Gestwicki
- Institute for Neurodegenerative Disease, University of California at San Francisco, San Francisco, California 94143
| | - Dennis J Thiele
- Departments of Pharmacology and Cancer Biology and Duke University School of Medicine, Durham, North Carolina 27710; Departments of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710 and.
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34
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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35
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Guertin MJ, Zhang X, Coonrod SA, Hager GL. Transient estrogen receptor binding and p300 redistribution support a squelching mechanism for estradiol-repressed genes. Mol Endocrinol 2014; 28:1522-33. [PMID: 25051172 DOI: 10.1210/me.2014-1130] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Proper gene regulation is essential for proper organismal development and appropriate responses to external stimuli. Specialized factors, termed master regulators, are often responsible for orchestrating the molecular events that result from signaling cascades. Master regulators coordinate the activation and repression of specific gene classes. Estrogen receptor α (ER) precipitates the signaling cascade that results from endogenous or exogenous estrogen hormones. ER is a classic transcriptional activator and the mechanisms by which ER coordinates gene activation are well characterized. However, it remains unclear how ER coordinates the immediate repression of genes. We integrated genomic transcription, chromosome looping, transcription factor binding, and chromatin structure data to analyze the molecular cascade that results from estradiol (E2)-induced signaling in human MCF-7 breast cancer cells and addressed the context-specific nature of gene regulation. We defined a class of genes that are immediately repressed upon estrogen stimulation, and we compared and contrasted the molecular characteristics of these repressed genes vs activated and unregulated genes. The most striking and unique feature of the repressed gene class is transient binding of ER at early time points after estrogen stimulation. We also found that p300, a coactivator and acetyltransferase, quantitatively redistributes from non-ER enhancers to ER enhancers after E2 treatment. These data support an extension of the classic physiological squelching model, whereby ER hijacks coactivators from repressed genes and redistributes the coactivators to ER enhancers that activate transcription.
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Affiliation(s)
- Michael J Guertin
- Laboratory of Receptor Biology and Gene Expression (M.J.G., G.L.H.), National Cancer Institute, Bethesda, Maryland 20892; State Key Laboratory of Reproductive Medicine (X.Z.), Nanjing Medical University, Nanjing 210029, China; and Baker Institute for Animal Health (X.Z., S.A.C.), College of Veterinary Medicine, Cornell University, Ithaca, New York 14853
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36
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Abstract
Instructions for when, where and to what level each gene should be expressed are encoded within regulatory sequences. The importance of motifs recognized by DNA-binding regulators has long been known, but their extensive characterization afforded by recent technologies only partly accounts for how regulatory instructions are encoded in the genome. Here, we review recent advances in our understanding of regulatory sequences that influence transcription and go beyond the description of motifs. We discuss how understanding different aspects of the sequence-encoded regulation can help to unravel the genotype-phenotype relationship, which would lead to a more accurate and mechanistic interpretation of personal genome sequences.
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Affiliation(s)
- Michal Levo
- Department of Molecular Cell Biology, and Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Segal
- Department of Molecular Cell Biology, and Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
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Zhang H, Gao L, Anandhakumar J, Gross DS. Uncoupling transcription from covalent histone modification. PLoS Genet 2014; 10:e1004202. [PMID: 24722509 PMCID: PMC3983032 DOI: 10.1371/journal.pgen.1004202] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/08/2014] [Indexed: 12/04/2022] Open
Abstract
It is widely accepted that transcriptional regulation of eukaryotic genes is intimately coupled to covalent modifications of the underlying chromatin template, and in certain cases the functional consequences of these modifications have been characterized. Here we present evidence that gene activation in the silent heterochromatin of the yeast Saccharomyces cerevisiae can occur in the context of little, if any, covalent histone modification. Using a SIR-regulated heat shock-inducible transgene, hsp82-2001, and a natural drug-inducible subtelomeric gene, YFR057w, as models we demonstrate that substantial transcriptional induction (>200-fold) can occur in the context of restricted histone loss and negligible levels of H3K4 trimethylation, H3K36 trimethylation and H3K79 dimethylation, modifications commonly linked to transcription initiation and elongation. Heterochromatic gene activation can also occur with minimal H3 and H4 lysine acetylation and without replacement of H2A with the transcription-linked variant H2A.Z. Importantly, absence of histone modification does not stem from reduced transcriptional output, since hsp82-ΔTATA, a euchromatic promoter mutant lacking a TATA box and with threefold lower induced transcription than heterochromatic hsp82-2001, is strongly hyperacetylated in response to heat shock. Consistent with negligible H3K79 dimethylation, dot1Δ cells lacking H3K79 methylase activity show unimpeded occupancy of RNA polymerase II within activated heterochromatic promoter and coding regions. Our results indicate that large increases in transcription can be observed in the virtual absence of histone modifications often thought necessary for gene activation. The proper regulation of gene expression is of fundamental importance in the maintenance of normal growth and development. Misregulation of genes can lead to such outcomes as cancer, diabetes and neurodegenerative disease. A key step in gene regulation occurs during the transcription of the chromosomal DNA into messenger RNA by the enzyme, RNA polymerase II. Histones are small, positively charged proteins that package genomic DNA into arrays of bead-like particles termed nucleosomes, the principal components of chromatin. Increasing evidence suggests that nucleosomal histones play an active role in regulating transcription, and that this is derived in part from reversible chemical (“covalent”) modifications that take place on their amino acids. These histone modifications create novel surfaces on nucleosomes that can serve as docking sites for other proteins that control a gene's expression state. In this study we present evidence that contrary to the general case, covalent modifications typically associated with transcription are minimally used by genes embedded in a specialized, condensed chromatin structure termed heterochromatin in the model organism baker's yeast. Our observations are significant, for they suggest that gene transcription can occur in a living cell in the virtual absence of covalent modification of the chromatin template.
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Affiliation(s)
- Hesheng Zhang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Lu Gao
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Jayamani Anandhakumar
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - David S. Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
- * E-mail:
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38
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Abstract
MYC dimerizes with MAX to bind DNA, with a preference for the E-box consensus CACGTG and several variant motifs. In cells, MYC binds DNA preferentially within transcriptionally active promoter regions. Although several thousand promoters are bound under physiological (low MYC) conditions, these represent only a fraction of all accessible, active promoters. MYC overexpression-as commonly observed in cancer cells-leads to invasion of virtually all active promoters, as well as of distal enhancer elements. We summarize here what is currently known about the mechanisms that may guide this process. We propose that binding site recognition is determined by low-affinity protein-protein interactions between MYC/MAX dimers and components of the basal transcriptional machinery, other chromatin-associated protein complexes, and/or DNA-bound transcription factors. DNA binding occurs subsequently, without an obligate requirement for sequence recognition. Local DNA scanning then leads to preferential stabilization of the MYC/MAX dimer on high-affinity DNA elements. This model is consistent with the invasion of all active promoters that occurs at elevated MYC levels, but posits that important differences in affinity persist between physiological target sites and the newly invaded elements, which may not all be bound in a productive regulatory mode. The implications of this model for transcriptional control by MYC in normal and cancer cells are discussed in the light of the latest literature.
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Affiliation(s)
- Arianna Sabò
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, 20139 Milan, Italy
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39
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Eijkelenboom A, Mokry M, Smits LM, Nieuwenhuis EE, Burgering BMT. FOXO3 selectively amplifies enhancer activity to establish target gene regulation. Cell Rep 2013; 5:1664-78. [PMID: 24360957 DOI: 10.1016/j.celrep.2013.11.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/29/2013] [Accepted: 11/15/2013] [Indexed: 12/22/2022] Open
Abstract
Forkhead box O (FOXO) transcription factors regulate diverse cellular processes, affecting tumorigenesis, metabolism, stem cell maintenance, and lifespan. We show that FOXO3 transcription regulation mainly proceeds through the most active subset of enhancers. In addition to the general distinction between "open" and "closed" chromatin, we show that the level of activity marks (H3K27ac, RNAPII, enhancer RNAs) of these open chromatin regions prior to FOXO3 activation largely determines FOXO3 DNA binding. Consequently, FOXO3 amplifies the levels of these activity marks and their absolute rather than relative changes associate best with FOXO3 target gene regulation. The importance of preexisting chromatin state in directing FOXO3 gene regulation, as shown here, provides a mechanism whereby FOXO3 can regulate cell-specific homeostasis. Genetic variation is reported to affect these chromatin signatures in a quantitative manner, and, in agreement, we observe a correlation between cancer-associated genetic variations and the amplitude of FOXO3 enhancer binding.
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Affiliation(s)
- Astrid Eijkelenboom
- Department of Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Michal Mokry
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Lydia M Smits
- Department of Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Edward E Nieuwenhuis
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Boudewijn M T Burgering
- Department of Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
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40
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Genetic selection for constitutively trimerized human HSF1 mutants identifies a role for coiled-coil motifs in DNA binding. G3-GENES GENOMES GENETICS 2013; 3:1315-24. [PMID: 23733891 PMCID: PMC3737171 DOI: 10.1534/g3.113.006692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Human heat shock transcription factor 1 (HSF1) promotes the expression of stress-responsive genes and is a critical factor for the cellular protective response to proteotoxic and other stresses. In response to stress, HSF1 undergoes a transition from a repressed cytoplasmic monomer to a homotrimer, accumulates in the nucleus, binds DNA, and activates target gene transcription. Although these steps occur as sequential and highly regulated events, our understanding of the full details of the HSF1 activation pathway remains incomplete. Here we describe a genetic screen in humanized yeast that identifies constitutively trimerized HSF1 mutants. Surprisingly, constitutively trimerized HSF1 mutants do not bind to DNA in vivo in the absence of stress and only become DNA binding competent upon stress exposure, suggesting that an additional level of regulation beyond trimerization and nuclear localization may be required for HSF1 DNA binding. Furthermore, we identified a constitutively trimerized and nuclear-localized HSF1 mutant, HSF1 L189P, located in LZ3 of the HSF1 trimerization domain, which in response to proteotoxic stress is strongly compromised for DNA binding at the Hsp70 and Hsp25 promoters but readily binds to the interleukin-6 promoter, suggesting that HSF1 DNA binding is in part regulated in a locus-dependent manner, perhaps via promoter-specific differences in chromatin architecture. Furthermore, these results implicate the LZ3 region of the HSF1 trimerization domain in a function beyond its canonical role in HSF1 trimerization.
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41
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Teves SS, Henikoff S. The heat shock response: A case study of chromatin dynamics in gene regulation. Biochem Cell Biol 2013; 91:42-8. [DOI: 10.1139/bcb-2012-0075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent studies in transcriptional regulation using the Drosophila heat shock response system have elucidated many of the dynamic regulatory processes that govern transcriptional activation and repression. The classic view that the control of gene expression occurs at the point of RNA polymerase II (Pol II) recruitment is now giving way to a more complex outlook of gene regulation. Promoter chromatin dynamics coordinate with transcription factor binding to maintain the promoters of active genes accessible. For a large number of genes, the rate-limiting step in Pol II progression occurs during its initial elongation, where Pol II transcribes 30–50 bp and pauses for further signals. These paused genes have unique genic chromatin architecture and dynamics compared with genes where Pol II recruitment is rate limiting for expression. Further elongation of Pol II along the gene causes nucleosome turnover, a continuous process of eviction and replacement, which suggests a potential mechanism for Pol II transit along a nucleosomal template. In this review, we highlight recent insights into transcription regulation of the heat shock response and discuss how the dynamic regulatory processes involved at each transcriptional stage help to generate faithful yet highly responsive gene expression.
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Affiliation(s)
- Sheila S. Teves
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
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42
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Guertin MJ, Lis JT. Mechanisms by which transcription factors gain access to target sequence elements in chromatin. Curr Opin Genet Dev 2012; 23:116-23. [PMID: 23266217 DOI: 10.1016/j.gde.2012.11.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/19/2012] [Indexed: 11/24/2022]
Abstract
Transcription factors (TF) bind DNA sequence motifs, but the presence of a consensus DNA element is not sufficient to direct TF binding to chromatin. Recent genomic data have revealed that accessibility, as measured by DNase sensitivity and the presence of active histone marks, is necessary for TF binding. DNA sequence provides the initial specification of the accessibility of DNA elements within chromatin that permits TF binding. In yeast, it is known that poly(dA-dT) tracts directly encode low-nucleosome occupancy at promoters. Recent evidence suggests that CpG islands in mammals are inherently refractory to higher-order chromatin structure and remain accessible, despite favoring nucleosome formation in vitro. Taken together, these studies support a model for how accessibility originates and then propagates throughout regulatory cascades and development.
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Affiliation(s)
- Michael J Guertin
- Department of Molecular Biology and Genetics, Cornell University, United States.
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43
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ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 2012; 13:840-52. [PMID: 23090257 DOI: 10.1038/nrg3306] [Citation(s) in RCA: 485] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP-seq protocol have motivated recent enhancements in this approach, such as reducing the number of cells that are required and increasing the resolution. Complementary experimental approaches - for example, DNaseI hypersensitive site mapping and analysis of chromatin interactions that are mediated by particular proteins - provide additional information about DNA-binding proteins and their function. These data are now being used to identify variability in the functions of DNA-binding proteins across genomes and individuals. In this Review, I describe the latest advances in methods to detect and functionally characterize DNA-bound proteins.
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Fujimoto M, Takaki E, Takii R, Tan K, Prakasam R, Hayashida N, Iemura SI, Natsume T, Nakai A. RPA Assists HSF1 Access to Nucleosomal DNA by Recruiting Histone Chaperone FACT. Mol Cell 2012; 48:182-94. [DOI: 10.1016/j.molcel.2012.07.026] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 06/22/2012] [Accepted: 07/24/2012] [Indexed: 01/10/2023]
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Welc SS, Clanton TL. The regulation of interleukin-6 implicates skeletal muscle as an integrative stress sensor and endocrine organ. Exp Physiol 2012; 98:359-71. [PMID: 22941979 DOI: 10.1113/expphysiol.2012.068189] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Skeletal muscle has been identified as an endocrine organ owing to its capacity to produce and secrete a variety of cytokines (myokines) and other proteins. To date, myokines have primarily been studied in response to exercise or metabolic challenges; however, numerous observations suggest that skeletal muscle may also release myokines in response to certain categories of internal or external stress exposure. Internal stress signals include oxidative or nitrosative stress, damaged or unfolded proteins, hyperthermia or energy imbalance. External stress signals, which act as indicators of organismal stress or injury in other cells, employ mediators such as catecholamines, endotoxin, alarmins, ATP and pro-inflammatory cytokines, such as tumour necrosis factor-α and interleukin-1β. External stress signals generally induce cellular responses through membrane receptor systems. In this review, we focus on the regulation of interleukin-6 (IL-6) as a prototypical stress response myokine and highlight evidence that IL-6 gene regulation in muscle is inherently organized to respond to a wide variety of internal and external stressors. Given that IL-6 can initiate protective, anti-inflammatory or restorative processes throughout the organism during life-threatening conditions, we present the argument that skeletal muscle has a physiological function as a sensor and responder to stress. Furthermore, we hypothesize that it may comprise a fundamental component of the organism's acute stress response.
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Affiliation(s)
- Steven S Welc
- Department of Applied Physiology & Kinesiology, University of Florida, Gainesville, FL 32611, USA
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