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Redundant and non-redundant cytokine-activated enhancers control Csn1s2b expression in the lactating mouse mammary gland. Nat Commun 2021; 12:2239. [PMID: 33854063 PMCID: PMC8047016 DOI: 10.1038/s41467-021-22500-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 03/16/2021] [Indexed: 12/27/2022] Open
Abstract
Enhancers are transcription factor platforms that synergize with promoters to control gene expression. Here, we investigate enhancers that activate gene expression several hundred-fold exclusively in the lactating mouse mammary gland. Using ChIP-seq for activating histone marks and transcription factors, we identify two candidate enhancers and one super-enhancer in the Csn1s2b locus. Through experimental mouse genetics, we dissect the lactation-specific distal enhancer bound by the mammary-enriched transcription factors STAT5 and NFIB and the glucocorticoid receptor. While deletions of canonical binding motifs for NFIB and STAT5, individually or combined, have a limited biological impact, a non-canonical STAT5 site is essential for enhancer activity during lactation. In contrast, the intronic enhancer contributes to gene expression only in late pregnancy and early lactation, possibly by interacting with the distal enhancer. A downstream super-enhancer, which physically interacts with the distal enhancer, is required for the functional establishment of the Csn1s2b promoter and gene activation. Lastly, NFIB binding in the promoter region fine-tunes Csn1s2b expression. Our study provides comprehensive insight into the anatomy and biology of regulatory elements that employ the JAK/STAT signaling pathway and preferentially activate gene expression during lactation. Enhancers and promoters work together to actively regulate gene expression affecting several biological processes. Here, the authors provide molecular insights into the regulation of enhancers and super-enhancers in the Csn1s2b locus during lactation.
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2
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Temporal dynamics of a CSF1R signaling gene regulatory network involved in epilepsy. PLoS Comput Biol 2021; 17:e1008854. [PMID: 33819288 PMCID: PMC8057615 DOI: 10.1371/journal.pcbi.1008854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 04/20/2021] [Accepted: 03/04/2021] [Indexed: 01/16/2023] Open
Abstract
Colony Stimulating Factor 1 Receptor (CSF1R) is a potential target for anti-epileptic drugs. However, inhibition of CSF1R is not well tolerated by patients, thereby prompting the need for alternative targets. To develop a framework for identification of such alternatives, we here develop a mathematical model of a pro-inflammatory gene regulatory network (GRN) involved in epilepsy and centered around CSF1R. This GRN comprises validated transcriptional and post-transcriptional regulations involving STAT1, STAT3, NFκB, IL6R, CSF3R, IRF8, PU1, C/EBPα, TNFR1, CSF1 and CSF1R. The model was calibrated on mRNA levels of all GRN components in lipopolysaccharide (LPS)-treated mouse microglial BV-2 cells, and allowed to predict that STAT1 and STAT3 have the strongest impact on the expression of the other GRN components. Microglial BV-2 cells were selected because, the modules from which the GRN was deduced are enriched for microglial marker genes. The function of STAT1 and STAT3 in the GRN was experimentally validated in BV-2 cells. Further, in silico analysis of the GRN dynamics predicted that a pro-inflammatory stimulus can induce irreversible bistability whereby the expression level of GRN components occurs as two distinct states. The irreversibility of the switch may enforce the need for chronic inhibition of the CSF1R GRN in order to achieve therapeutic benefit. The cell-to-cell heterogeneity driven by the bistability may cause variable therapeutic response. In conclusion, our modeling approach uncovered a GRN controlling CSF1R that is predominantly regulated by STAT1 and STAT3. Irreversible inflammation-induced bistability and cell-to-cell heterogeneity of the GRN provide a theoretical foundation to the need for chronic GRN control and the limited potential for disease modification via inhibition of CSF1R. Epilepsy is associated with the induction of complex molecular inflammatory processes. A better understanding of these molecular mechanisms is crucial to optimize therapeutic options. Here, we identified a gene regulatory network (GRN) involved in epilepsy that is controlled by inflammation and which regulates the expression and function of Colony Stimulating Factor 1 receptor (CSF1R), a therapeutic target for anti-epileptic drugs. Using mathematical modeling and experiments with cultured cells, we found that two of eleven components of the network, namely STAT1 and STAT3, exert a tight control on all other components. In addition, we found that inflammation can induce an irreversible switch in the expression of all components of the network, and can cause high cell-to-cell variability. Our findings provide a framework explaining why chronic, not acute, anti-inflammatory treatment is necessary to modulate the network and why drugs targeting CSF1R have limited therapeutic potential.
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3
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Hennighausen L, Lee HK. Activation of the SARS-CoV-2 Receptor Ace2 through JAK/STAT-Dependent Enhancers during Pregnancy. Cell Rep 2020; 32:108199. [PMID: 32966801 PMCID: PMC7474886 DOI: 10.1016/j.celrep.2020.108199] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/20/2020] [Accepted: 09/03/2020] [Indexed: 01/04/2023] Open
Abstract
ACE2 binds the coronavirus SARS-CoV-2 and facilitates its cellular entry. Interferons activate ACE2 expression in pneumocytes, suggesting a critical role of cytokines in SARS-CoV-2 target cells. Viral RNA was detected in breast milk in at least seven studies, raising the possibility that ACE2 is expressed in mammary tissue during lactation. Here, we show that Ace2 expression in mouse mammary tissue is induced during pregnancy and lactation, which coincides with the activation of intronic enhancers. These enhancers are occupied by the prolactin-activated transcription factor STAT5 and additional regulatory factors, including RNA polymerase II. Deletion of Stat5a results in decommissioning of the enhancers and an 83% reduction of Ace2 mRNA. We also demonstrate that Ace2 expression increases during lactation in lung, but not in kidney and intestine. JAK/STAT components are present in a range of SARS-CoV-2 target cells, opening the possibility that cytokines contribute to the viral load and extrapulmonary pathophysiology. Ace2 expression is induced in the mammary glands of pregnant and lactating mice Gene enhancers are activated by the prolactin-activated transcription factors STAT5A/B Deletion of the Stat5a gene mitigates enhancer formation and Ace2 expression Ace2 levels also increase in lung tissue during lactation
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Affiliation(s)
- Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, U.S. National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, U.S. National Institutes of Health, Bethesda, MD 20892, USA.
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4
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Zeng X, Lee HK, Wang C, Achikeh P, Liu C, Hennighausen L. The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy. Exp Mol Med 2020; 52:682-690. [PMID: 32321991 PMCID: PMC7210877 DOI: 10.1038/s12276-020-0425-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/08/2020] [Accepted: 03/16/2020] [Indexed: 11/09/2022] Open
Abstract
Lineage-specific genetic programs rely on cell-restricted super-enhancers, which are platforms for high-density transcription factor occupation. It is not known whether super-enhancers synergize specifically with their native promoters or provide autonomous and independent regulatory platforms. Here, we investigated the ability of the mammary Wap super-enhancer to activate the promoter of the juxtaposed and ubiquitously expressed Tbrg4 gene in the mouse mammary gland. The Wap super-enhancer was fused, alone or in combination with the Wap promoter, to the Tbrg4 gene. While the super-enhancer increased the expression of the Tbrg4 promoter five-fold, the combination of the super-enhancer and promoter resulted in 80-fold gene upregulation, demonstrating lineage-specific promoter-enhancer synergy. Employing ChIP-seq profiling to determine transcription factor binding and identify activating histone marks, we uncovered a chromatin platform that enables the high-level expression of the native promoter-enhancer but not the heterologous promoter. Taken together, our data reveal that lineage-specific enhancer-promoter synergy is critical for mammary gene regulation during pregnancy and lactation.
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Affiliation(s)
- Xianke Zeng
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Precious Achikeh
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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5
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Oberhuber M, Pecoraro M, Rusz M, Oberhuber G, Wieselberg M, Haslinger P, Gurnhofer E, Schlederer M, Limberger T, Lagger S, Pencik J, Kodajova P, Högler S, Stockmaier G, Grund‐Gröschke S, Aberger F, Bolis M, Theurillat J, Wiebringhaus R, Weiss T, Haitel A, Brehme M, Wadsak W, Griss J, Mohr T, Hofer A, Jäger A, Pollheimer J, Egger G, Koellensperger G, Mann M, Hantusch B, Kenner L. STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer. Mol Syst Biol 2020; 16:e9247. [PMID: 32323921 PMCID: PMC7178451 DOI: 10.15252/msb.20199247] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 01/05/2023] Open
Abstract
Prostate cancer (PCa) has a broad spectrum of clinical behavior; hence, biomarkers are urgently needed for risk stratification. Here, we aim to find potential biomarkers for risk stratification, by utilizing a gene co-expression network of transcriptomics data in addition to laser-microdissected proteomics from human and murine prostate FFPE samples. We show up-regulation of oxidative phosphorylation (OXPHOS) in PCa on the transcriptomic level and up-regulation of the TCA cycle/OXPHOS on the proteomic level, which is inversely correlated to STAT3 expression. We hereby identify gene expression of pyruvate dehydrogenase kinase 4 (PDK4), a key regulator of the TCA cycle, as a promising independent prognostic marker in PCa. PDK4 predicts disease recurrence independent of diagnostic risk factors such as grading, staging, and PSA level. Therefore, low PDK4 is a promising marker for PCa with dismal prognosis.
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6
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Lee HK, Willi M, Shin HY, Liu C, Hennighausen L. Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation. Nucleic Acids Res 2019; 46:10796-10809. [PMID: 30285185 PMCID: PMC6237736 DOI: 10.1093/nar/gky891] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/20/2018] [Indexed: 12/15/2022] Open
Abstract
The mammary luminal lineage relies on the common cytokine-sensing transcription factor STAT5 to establish super-enhancers during pregnancy and initiate a genetic program that activates milk production. As pups grow, the greatly increasing demand for milk requires progressive differentiation of mammary cells with advancing lactation. Here we investigate how persistent hormonal exposure during lactation shapes an evolving enhancer landscape and impacts the biology of mammary cells. Employing ChIP-seq, we uncover a changing transcription factor occupancy at mammary enhancers, suggesting that their activities evolve with advancing differentiation. Using mouse genetics, we demonstrate that the functions of individual enhancers within the Wap super-enhancer evolve as lactation progresses. Most profoundly, a seed enhancer, which is mandatory for the activation of the Wap super-enhancer during pregnancy, is not required during lactation, suggesting compensatory flexibility. Combinatorial deletions of structurally equivalent constituent enhancers demonstrated differentiation-specific compensatory activities during lactation. We also demonstrate that the Wap super-enhancer, which is built on STAT5 and other common transcription factors, retains its exquisite mammary specificity when placed into globally permissive chromatin, suggesting a limited role of chromatin in controlling cell specificity. Our studies unveil a previously unrecognized progressive enhancer landscape where structurally equivalent components serve unique and differentiation-specific functions.
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Affiliation(s)
- Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Michaela Willi
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Ha Youn Shin
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
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7
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Gao ST, Ma L, Zhou Z, Zhou ZK, Baumgard LH, Jiang D, Bionaz M, Bu DP. Heat stress negatively affects the transcriptome related to overall metabolism and milk protein synthesis in mammary tissue of midlactating dairy cows. Physiol Genomics 2019; 51:400-409. [PMID: 31298615 DOI: 10.1152/physiolgenomics.00039.2019] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Inadequate dry matter intake only partially accounts for the decrease in milk protein synthesis during heat stress (HS) in dairy cows. Our hypothesis is that reduced milk protein synthesis during HS in dairy cows is also caused by biological changes within the mammary gland. The objective of this study was to assess the hypothesis via RNA-Seq analysis of mammary tissue. Herein, four dairy cows were used in a crossover design where HS was induced for 9 days in environmental chambers. There was a 30-day washout between periods. Mammary tissue was collected via biopsy at the end of each environmental period (HS or pair-fed and thermal neutral) for transcriptomic analysis. RNA-Seq analysis revealed HS affected >2,777 genes (false discovery rate-adjusted P value < 0.05) in mammary tissue. Expression of main milk protein-encoding genes and several key genes related to regulation of protein synthesis and amino acid and glucose transport were downregulated by HS. Bioinformatics analysis revealed an overall decrease of mammary tissue metabolic activity by HS (especially carbohydrate and lipid metabolism) and an increase in immune activation and inflammation. Network analysis revealed a major role of TNF, IFNG, S100A8, S100A9, and IGF-1 in inducing/controlling the inflammatory response, with a central role of NF-κB in the process of immunoactivation. The same analysis indicated an overall inhibition of PPARγ. Collectively, these data suggest HS directly controls milk protein synthesis via reducing the transcription of metabolic-related genes and increasing inflammation-related genes.
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Affiliation(s)
- S T Gao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Z Zhou
- Department of Animal Science, Michigan State University, East Lansing, Michigan
| | - Z K Zhou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L H Baumgard
- Department of Animal Science, Iowa State University, Ames, Iowa
| | - D Jiang
- Statistics, Oregon State University, Corvallis, Oregon
| | - M Bionaz
- Animal and Rangeland Sciences, Oregon State University, Corvallis, Oregon
| | - D P Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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8
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Shin HY, Hennighausen L, Yoo KH. STAT5-Driven Enhancers Tightly Control Temporal Expression of Mammary-Specific Genes. J Mammary Gland Biol Neoplasia 2019; 24:61-71. [PMID: 30328555 DOI: 10.1007/s10911-018-9418-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022] Open
Abstract
The de novo formation of milk-secreting mammary epithelium during pregnancy is regulated by prolactin through activation of the transcription factor STAT5, which stimulates the expression of several hundred mammary-specific genes. In addition to its key role in activating gene expression in mammary tissue, STAT5, which is ubiquitously expressed in most cell types, implements T cell-specific programs controlled by interleukins. However, the mechanisms by which STAT5 controls cell-specific genetic programs activated by distinct cytokines remain relatively unknown. Integration of data from genome-wide surveys of chromatin markers and transcription factor binding at regulatory elements may shed light on the mechanisms that drive cell-specific programs. Here, we have illustrated how STAT5 controls cell-specific gene expression through its concentration and an auto-regulatory enhancer supporting its high levels in mammary tissue. The unique genomic features of STAT5-driven enhancers or super-enhancers that regulate mammary-specific genes and their dynamic remodeling in response to pregnancy hormone levels are described. We have further provided biological evidence supporting the in vivo function of a STAT5-driven super-enhancer with the aid of CRISPR/Cas9 genome editing. Finally, we discuss how the functions of mammary-specific super-enhancers are confined by the zinc finger protein, CTCF, to allow exclusive activation of mammary-specific genes without affecting common neighboring genes. This review comprehensively summarizes the molecular pathways underlying differential control of cell-specific gene sets by STAT5 and provides novel insights into STAT5-dependent mammary physiology.
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Affiliation(s)
- Ha Youn Shin
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- BK21 PLUS Project, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Kyung Hyun Yoo
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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9
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Yoo KH, Hennighausen L, Shin HY. Dissecting Tissue-Specific Super-Enhancers by Integrating Genome-Wide Analyses and CRISPR/Cas9 Genome Editing. J Mammary Gland Biol Neoplasia 2019; 24:47-59. [PMID: 30291498 DOI: 10.1007/s10911-018-9417-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022] Open
Abstract
Recent advances in genome-wide sequencing technologies have provided researchers with unprecedented opportunities to discover the genomic structures of gene regulatory units in living organisms. In particular, the integration of ChIP-seq, RNA-seq, and DNase-seq techniques has facilitated the mapping of a new class of regulatory elements. These elements, called super-enhancers, can regulate cell-type-specific gene sets and even fine-tune gene expression regulation in response to external stimuli, and have become a hot topic in genome biology. However, there is scant genetic evidence demonstrating their unique biological relevance and the mechanisms underlying these biological functions. In this review, we describe a robust genome-wide strategy for mapping cell-type-specific enhancers or super-enhancers in the mammary genome. In this strategy, genome-wide screening of active enhancer clusters that are co-occupied by mammary-enriched transcription factors, co-factors, and active enhancer marks is used to identify bona fide mammary tissue-specific super-enhancers. The in vivo function of these super-enhancers and their associated regulatory elements may then be investigated in various ways using the advanced CRISPR/Cas9 genome-editing technology. Based on our experience targeting various mammary genomic sites using CRISPR/Cas9 in mice, we comprehensively discuss the molecular consequences of the different targeting methods, such as the number of gRNAs and the dependence on their simultaneous or sequential injections. We also mention the considerations that are essential for obtaining accurate results and shed light on recent progress that has been made in developing modified CRISPR/Cas9 genome-editing techniques. In the future, the coupling of advanced genome-wide sequencing and genome-editing technologies could provide new insights into the complex genetic regulatory networks involved in mammary-gland development.
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Affiliation(s)
- Kyung Hyun Yoo
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- BK21 Biological Science Visiting Professor, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Ha Youn Shin
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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10
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Wang C, Nanni L, Novakovic B, Megchelenbrink W, Kuznetsova T, Stunnenberg HG, Ceri S, Logie C. Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages. Sci Rep 2019; 9:2772. [PMID: 30809020 PMCID: PMC6391480 DOI: 10.1038/s41598-019-39395-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/22/2019] [Indexed: 12/12/2022] Open
Abstract
Glucocorticoid receptor is a transcription factor that is ubiquitously expressed. Glucocorticoids are circadian steroids that regulate a wide range of bodily functions, including immunity. Here we report that synthetic glucocorticoids affect 1035 mRNAs in isolated healthy human blood monocytes but only 165 in the respective six day-old monocyte-derived macrophages. The majority of the glucocorticoid response in monocytes concerns genes that are dynamic upon monocyte to macrophage differentiation, whereby macrophage-like mRNA levels are often reached in monocytes within four hours of treatment. Concomitantly, over 5000 chromosomal H3K27ac regions undergo remodelling, of which 60% involve increased H3K27ac signal. We find that chromosomal glucocorticoid receptor binding sites correlate with positive but not with negative local epigenomic effects. To investigate further we assigned our data to topologically associating domains (TADs). This shows that about 10% of macrophage TADs harbour at least one GR binding site and that half of all the glucocorticoid-induced H3K27ac regions are confined to these TADs. Our analyses are therefore consistent with the notion that TADs naturally accommodate information from sets of distal glucocorticoid response elements.
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Affiliation(s)
- Cheng Wang
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
| | - Luca Nanni
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Boris Novakovic
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Wout Megchelenbrink
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
| | - Tatyana Kuznetsova
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
- Department of Medical Biochemistry, Academic Medical Centre of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
| | - Stefano Ceri
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Colin Logie
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands.
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11
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Agrawal P, Heimbruch KE, Rao S. Genome-Wide Maps of Transcription Regulatory Elements and Transcription Enhancers in Development and Disease. Compr Physiol 2018; 9:439-455. [PMID: 30549021 DOI: 10.1002/cphy.c180028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gene expression is regulated by numerous elements including enhancers, insulators, transcription factors, and architectural proteins. Regions of DNA distal to the transcriptional start site, called enhancers, play a central role in the temporal and tissue-specific regulation of gene expression through RNA polymerase II. The identification of enhancers and other cis regulatory elements has largely been possible due to advances in next generation sequencing technologies. Enhancers regulate gene expression through chromatin loops mediated by architectural proteins such as YY1, CTCF, the cohesin complex, and LDB1. Additionally, enhancers can be transcribed to produce noncoding RNAs termed enhancer RNAs that likely participate in transcriptional regulation. The central role of enhancers in regulating gene expression implicates them in both normal physiology but also many disease states. The importance of enhancers is evident by the suggested role of SNPs, duplications, and other alterations of enhancer function in many diseases, ranging from cancer to atherosclerosis to chronic kidney disease. Although much progress has been made in recent years, the field of enhancer biology and our knowledge of the cis regulome remains a work in progress. This review will highlight recent seminal studies which demonstrate the role of enhancers in normal physiology and disease pathogenesis. © 2019 American Physiological Society. Compr Physiol 9:439-455, 2019.
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Affiliation(s)
- Puja Agrawal
- Blood Research Institute, BloodCenter of Wisconsin, a part of Versiti, Milwaukee, Wisconsin, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Katelyn E Heimbruch
- Blood Research Institute, BloodCenter of Wisconsin, a part of Versiti, Milwaukee, Wisconsin, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Sridhar Rao
- Blood Research Institute, BloodCenter of Wisconsin, a part of Versiti, Milwaukee, Wisconsin, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Pediatrics, Division of Hematology, Oncology, and Bone Marrow Transplantation, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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12
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Lee HK, Willi M, Wang C, Yang CM, Smith HE, Liu C, Hennighausen L. Functional assessment of CTCF sites at cytokine-sensing mammary enhancers using CRISPR/Cas9 gene editing in mice. Nucleic Acids Res 2017; 45:4606-4618. [PMID: 28334928 PMCID: PMC5416830 DOI: 10.1093/nar/gkx185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/15/2017] [Indexed: 01/05/2023] Open
Abstract
The zinc finger protein CTCF has been invoked in establishing boundaries between genes, thereby controlling spatial and temporal enhancer activities. However, there is limited genetic evidence to support the concept that these boundaries restrict the search space of enhancers. We have addressed this question in the casein locus containing five mammary and two non-mammary genes under the control of at least seven putative enhancers. We have identified two CTCF binding sites flanking the locus and two associated with a super-enhancer. Individual deletion of these sites from the mouse genome did not alter expression of any of the genes. However, deletion of the border CTCF site separating the Csn1s1 mammary enhancer from neighboring genes resulted in the activation of Sult1d1 at a distance of more than 95 kb but not the more proximal and silent Sult1e1 gene. Loss of this CTCF site led to de novo interactions between the Sult1d1 promoter and several enhancers in the casein locus. Our study demonstrates that only one out of the four CTCF sites in the casein locus had a measurable in vivo activity. Studies on additional loci are needed to determine the biological role of CTCF sites associated with enhancers.
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Affiliation(s)
- Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.,Department of Cell and Developmental Biology & Dental Research Institute, Seoul National University, Seoul 110-749, Korea
| | - Michaela Willi
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.,Division of Bioinformatics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Chul Min Yang
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Harold E Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Chengyu Liu
- Transgenic Core,National Heart Lung and Blood Institute, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
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13
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Mechanisms and consequences of Jak-STAT signaling in the immune system. Nat Immunol 2017; 18:374-384. [PMID: 28323260 DOI: 10.1038/ni.3691] [Citation(s) in RCA: 744] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/23/2017] [Indexed: 12/12/2022]
Abstract
Kinases of the Jak ('Janus kinase') family and transcription factors (TFs) of the STAT ('signal transducer and activator of transcription') family constitute a rapid membrane-to-nucleus signaling module that affects every aspect of the mammalian immune system. Research on this paradigmatic pathway has experienced breakneck growth in the quarter century since its discovery and has yielded a stream of basic and clinical insights that have profoundly influenced modern understanding of human health and disease, exemplified by the bench-to-bedside success of Jak inhibitors ('jakinibs') and pathway-targeting drugs. Here we review recent advances in Jak-STAT biology, focusing on immune cell function, disease etiology and therapeutic intervention, as well as broader principles of gene regulation and signal-dependent TFs.
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14
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Shin HY, Wang C, Lee HK, Yoo KH, Zeng X, Kuhns T, Yang CM, Mohr T, Liu C, Hennighausen L. CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome. Nat Commun 2017; 8:15464. [PMID: 28561021 PMCID: PMC5460021 DOI: 10.1038/ncomms15464] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 03/31/2017] [Indexed: 12/29/2022] Open
Abstract
Although CRISPR/Cas9 genome editing has provided numerous opportunities to interrogate the functional significance of any given genomic site, there is a paucity of data on the extent of molecular scars inflicted on the mouse genome. Here we interrogate the molecular consequences of CRISPR/Cas9-mediated deletions at 17 sites in four loci of the mouse genome. We sequence targeted sites in 632 founder mice and analyse 54 established lines. While the median deletion size using single sgRNAs is 9 bp, we also obtain large deletions of up to 600 bp. Furthermore, we show unreported asymmetric deletions and large insertions of middle repetitive sequences. Simultaneous targeting of distant loci results in the removal of the intervening sequences. Reliable deletion of juxtaposed sites is only achieved through two-step targeting. Our findings also demonstrate that an extended analysis of F1 genotypes is required to obtain conclusive information on the exact molecular consequences of targeting events.
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Affiliation(s)
- Ha Youn Shin
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Cell and Developmental Biology & Dental Research Institute, Seoul National University, Seoul 110-749, Republic of Korea
| | - Kyung Hyun Yoo
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Life Systems, Sookmyung Women's University, Seoul 140-742, Republic of Korea
| | - Xianke Zeng
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tyler Kuhns
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chul Min Yang
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Teresa Mohr
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA
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15
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Connerney J, Lau-Corona D, Rampersaud A, Waxman DJ. Activation of Male Liver Chromatin Accessibility and STAT5-Dependent Gene Transcription by Plasma Growth Hormone Pulses. Endocrinology 2017; 158:1386-1405. [PMID: 28323953 PMCID: PMC6283433 DOI: 10.1210/en.2017-00060] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/10/2017] [Indexed: 02/07/2023]
Abstract
Sex differences in pituitary growth hormone (GH) secretion (pulsatile in males vs near continuous/persistent in females) impart sex-dependent expression to hundreds of genes in adult mouse liver. Signal transducer and activator of transcription (STAT) 5, a GH-activated transcription factor that is essential for liver sexual dimorphism, is dynamically activated in direct response to each male plasma GH pulse. However, the impact of GH-induced STAT5 pulses on liver chromatin accessibility and downstream transcriptional events is unknown. In this study, we investigated the impact of a single pulse of GH given to hypophysectomized mice on local liver chromatin accessibility (DNase hypersensitive site analysis), transcription rates (heterogeneous nuclear RNA analysis), and gene expression (quantitative polymerase chain reaction and RNA sequencing) determined 30, 90, or 240 minutes later. The STAT5-dependent but sex-independent early GH response genes Igf1 and Cish showed rapid, GH pulse-induced increases in chromatin accessibility and gene transcription, reversing the effects of hypophysectomy. Rapid increases in liver chromatin accessibility and transcriptional activity were also induced in hypophysectomized male mice for some (Ces2b, Ugt2b38) but not for other liver STAT5-dependent male-biased genes (Cyp7b1). Moreover, in pituitary-intact male mice, Igf1, Cish, Ces2b, and Ugt2b38 all showed remarkable cycles of chromatin opening and closing, as well as associated cycles of induced gene transcription, which closely followed each endogenous pulse of liver STAT5 activity. Thus, the endogenous rhythms of male plasma GH pulsation dynamically open and then close liver chromatin at discrete, localized regulatory sites in temporal association with transcriptional activation of Igf1, Cish, and a subset of STAT5-dependent male-biased genes.
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Affiliation(s)
- Jeannette Connerney
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
| | - Dana Lau-Corona
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
| | - Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
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16
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Ko JY, Oh S, Yoo KH. Functional Enhancers As Master Regulators of Tissue-Specific Gene Regulation and Cancer Development. Mol Cells 2017; 40:169-177. [PMID: 28359147 PMCID: PMC5386954 DOI: 10.14348/molcells.2017.0033] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 12/30/2022] Open
Abstract
Tissue-specific transcription is critical for normal development, and abnormalities causing undesirable gene expression may lead to diseases such as cancer. Such highly organized transcription is controlled by enhancers with specific DNA sequences recognized by transcription factors. Enhancers are associated with chromatin modifications that are distinct epigenetic features in a tissue-specific manner. Recently, super-enhancers comprising enhancer clusters co-occupied by lineage-specific factors have been identified in diverse cell types such as adipocytes, hair follicle stem cells, and mammary epithelial cells. In addition, noncoding RNAs, named eRNAs, are synthesized at super-enhancer regions before their target genes are transcribed. Many functional studies revealed that super-enhancers and eRNAs are essential for the regulation of tissue-specific gene expression. In this review, we summarize recent findings concerning enhancer function in tissue-specific gene regulation and cancer development.
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Affiliation(s)
- Je Yeong Ko
- Molecular Medicine Laboratory, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310,
Korea
| | - Sumin Oh
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310,
Korea
| | - Kyung Hyun Yoo
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310,
Korea
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