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Kaestner K, Zhu G, Lahori D, Schug J. Villification of the intestinal epithelium is driven by Foxl1. RESEARCH SQUARE 2024:rs.3.rs-4882679. [PMID: 39184090 PMCID: PMC11343282 DOI: 10.21203/rs.3.rs-4882679/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
The primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation a dramatic transformation occurs in which the epithelium is both restructured into its final cuboidal form and simultaneously folded and refolded to create intestinal villi and intervillus regions, the incipient crypts. Here we show that the mesenchymal winged helix transcription factor Foxl1, itself induced by epithelial hedgehog signaling, controls villification by activating BMP and PDGFRa as well as planar cell polarity genes in epithelial-adjacent telocyte progenitors, both directly and in a feed- forward loop with Foxo3. In the absence of Foxl1-dependent mesenchymal signaling, villus formation is delayed, the separation of epithelial cells into mitotic intervillus and postmitotic villus cells impaired, and the differentiation of secretory progenitors blocked. Thus, Foxl1 orchestrates key events during the epithelial transition of the fetal mammalian gut.
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2
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Saito M, Atsumi GI. [Mechanisms of bone formation by primary cilia]. Nihon Yakurigaku Zasshi 2024; 159:198-202. [PMID: 38684398 DOI: 10.1254/fpj.23113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Primary cilia are immotile cilia assembled from the centriole-derived basal body, and they protrude on the cell surface in almost all cell types during the cell cycle G0 phase. Due to the diffusion barrier at the ciliary base, cilia harbor selective G protein-coupled receptors, growth factor receptors, and ion channels on their membrane. Thus, cilia act as sensory organelles, regulating the proliferation and differentiation of the cells and promoting the formation and maturation of various organs including bone, brain, and kidney. It has been unveiled that malformation and dysregulation of cilia cause organ dysplasia, so-called ciliopathy, thus research on primary cilia has become active during the past 20 years. Research on the roles of cilia in bone formation and its regulatory mechanisms have also progressed. It is widely recognized that cilia of preosteoblasts receive hedgehog and promote differentiation of the cells to osteoblasts, resulting in the formation of skulls and long bones. Recently, it has been shown that a membrane-associated protein 4.1G is important in ciliogenesis, hedgehog signaling, and osteoblast differentiation in neonatal bone formation. In this review, we would like to summarize the roles of primary cilia in bone formation and their regulatory mechanisms including the contribution of 4.1G.
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Affiliation(s)
- Masaki Saito
- Department of Molecular Physiology and Pathology, Faculty of Pharmaceutical Sciences, Teikyo University
| | - Gen-Ichi Atsumi
- Department of Molecular Physiology and Pathology, Faculty of Pharmaceutical Sciences, Teikyo University
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3
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Chang TY, Waxman DJ. HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo. RESEARCH SQUARE 2024:rs.3.rs-4559581. [PMID: 38978599 PMCID: PMC11230509 DOI: 10.21203/rs.3.rs-4559581/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues. Results Here, we describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed. Comparisons of HDI-STARR-seq activity between male and female mouse livers and in livers from males treated with an activating ligand of the transcription factor CAR (Nr1i3) identified many condition-dependent enhancers linked to condition-specific gene expression. Further, thousands of active liver enhancers were identified using a high complexity STARR-seq library comprised of ~ 50,000 genomic regions released by DNase-I digestion of mouse liver nuclei. When compared to stringently inactive library sequences, the active enhancer sequences identified were highly enriched for liver open chromatin regions with activating histone marks (H3K27ac, H3K4me1, H3K4me3), were significantly closer to gene transcriptional start sites, and were significantly depleted of repressive (H3K27me3, H3K9me3) and transcribed region histone marks (H3K36me3). Conclusions HDI-STARR-seq offers substantial improvements over current methodologies for large scale, functional profiling of enhancers, including condition-dependent enhancers, in liver tissue in vivo, and can be adapted to characterize enhancer activities in a variety of species and tissues by selecting suitable tissue- and species-specific promoter sequences.
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4
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Chang TY, Waxman DJ. HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598329. [PMID: 38915578 PMCID: PMC11195054 DOI: 10.1101/2024.06.10.598329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues. Here, we describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed. Comparisons of HDI-STARR-seq activity between male and female mouse livers and in livers from males treated with an activating ligand of the transcription factor CAR (Nr1i3) identified many condition-dependent enhancers linked to condition-specific gene expression. Further, thousands of active liver enhancers were identified using a high complexity STARR-seq library comprised of ~50,000 genomic regions released by DNase-I digestion of mouse liver nuclei. When compared to stringently inactive library sequences, the active enhancer sequences identified were highly enriched for liver open chromatin regions with activating histone marks (H3K27ac, H3K4me1, H3K4me3), were significantly closer to gene transcriptional start sites, and were significantly depleted of repressive (H3K27me3, H3K9me3) and transcribed region histone marks (H3K36me3). HDI-STARR-seq offers substantial improvements over current methodologies for large scale, functional profiling of enhancers, including condition-dependent enhancers, in liver tissue in vivo, and can be adapted to characterize enhancer activities in a variety of species and tissues by selecting suitable tissue- and species-specific promoter sequences.
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Affiliation(s)
- Ting-Ya Chang
- Departments of Biology and Biomedical Engineering, and Bioinformatics program, Boston University, Boston, MA 02215
| | - David J Waxman
- Departments of Biology and Biomedical Engineering, and Bioinformatics program, Boston University, Boston, MA 02215
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5
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Wei GH, Dong D, Zhang P, Liu M, Wei Y, Wang Z, Xu W, Zhang Q, Zhu Y, Zhang Q, Yang X, Zhu J, Wang L. Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus. RESEARCH SQUARE 2024:rs.3.rs-3943095. [PMID: 38645058 PMCID: PMC11030545 DOI: 10.21203/rs.3.rs-3943095/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Genome wide association studies (GWASs) have identified numerous risk loci associated with prostate cancer, yet unraveling their functional significance remains elusive. Leveraging our high-throughput SNPs-seq method, we pinpointed rs4519489 within the multi-ancestry GWAS-discovered 2p25 locus as a potential functional SNP due to its significant allelic differences in protein binding. Here, we conduct a comprehensive analysis of rs4519489 and its associated gene, NOL10, employing diverse cohort data and experimental models. Clinical findings reveal a synergistic effect between rs4519489 genotype and NOL10 expression on prostate cancer prognosis and severity. Through unbiased proteomics screening, we reveal that the risk allele A of rs4519489 exhibits enhanced binding to USF1, a novel oncogenic transcription factor (TF) implicated in prostate cancer progression and prognosis, resulting in elevated NOL10 expression. Furthermore, we elucidate that NOL10 regulates cell cycle pathways, fostering prostate cancer progression. The concurrent expression of NOL10 and USF1 correlates with aggressive prostate cancer characteristics and poorer prognosis. Collectively, our study offers a robust strategy for functional SNP screening and TF identification through high-throughput SNPs-seq and unbiased proteomics, highlighting the rs4519489-USF1-NOL10 regulatory axis as a promising biomarker or therapeutic target for clinical diagnosis and treatment of prostate cancer.
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Affiliation(s)
- Gong-Hong Wei
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School Basic Medical Sciences, Shanghai Medi
| | - Dandan Dong
- Shanghai Medical College of Fudan University
| | - Peng Zhang
- Shanghai Medical College of Fudan University
| | - Mengqi Liu
- Shanghai Medical College of Fudan University
| | - Yu Wei
- Fudan Unversity Shanghai Cancer Center
| | - Zixian Wang
- Shanghai Medical College of Fudan University
| | - Wenjie Xu
- Shanghai Medical College of Fudan University
| | | | - Yao Zhu
- Fudan University Shanghai Cancer Center
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6
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Zhu G, Lahori D, Schug J, Kaestner KH. Villification of the intestinal epithelium is driven by Foxl1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582300. [PMID: 38464137 PMCID: PMC10925215 DOI: 10.1101/2024.02.27.582300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation a dramatic transformation occurs in which the epithelium is both restructured into its final cuboidal form and simultaneously folded and refolded to create intestinal villi and intervillus regions, the incipient crypts. Here we show that the mesenchymal winged helix transcription factor Foxl1, itself induced by epithelial hedgehog signaling, controls villification by activating BMP and PDGFRα as well as planar cell polarity genes in epithelial-adjacent telocyte progenitors, both directly and in a feed-forward loop with Foxo3.
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Affiliation(s)
- Guoli Zhu
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA, 19104-5156, USA
| | - Deeksha Lahori
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA, 19104-5156, USA
| | - Jonathan Schug
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA, 19104-5156, USA
| | - Klaus H Kaestner
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA, 19104-5156, USA
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7
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Pfotenhauer AC, Reuter DN, Clark M, Harbison SA, Schimel TM, Stewart CN, Lenaghan SC. Development of new binary expression systems for plant synthetic biology. PLANT CELL REPORTS 2023; 43:22. [PMID: 38150091 DOI: 10.1007/s00299-023-03100-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/10/2023] [Indexed: 12/28/2023]
Abstract
KEY MESSAGE A novel plant binary expression system was developed from the compactin biosynthetic pathway 27 of Penicillium citrinum ML-236B. The system achieved >fivefold activation of gene expression in 28 transgenic tobacco. A diverse and well-characterized genetic toolset is fundamental to achieve the overall goals of plant synthetic biology. To properly coordinate expression of a multigene pathway, this toolset should include binary systems that control gene expression at the level of transcription. In plants, few highly functional, orthogonal transcriptional regulators have been identified. Here, we describe the process of developing synthetic plant transcription factors using regulatory elements from the Penicillium citrinum ML-236B (compactin) pathway. This pathway contains several genes including mlcA and mlcC that are transcriptionally regulated in a dose-dependent manner by the activator mlcR. In Nicotiana benthamiana, we first expressed mlcR with several cognate synthetic promoters driving expression of GFP. Synthetic promoters contained operator sequences from the compactin gene cluster. Following identification of the most active synthetic promoter, the DNA-binding domain from mlcR was used to generate chimeric transcription factors containing variable activation domains, including QF from the Neurospora crassa Q-system. Activity was measured at both protein and RNA levels which correlated with an R2 value of 0.94. A synthetic transcription factor with a QF activation domain increased gene expression from its synthetic promoter up to sixfold in N. benthamiana. Two systems were characterized in transgenic tobacco plants. The QF-based plants maintained high expression in tobacco, increasing expression from the cognate synthetic promoter by fivefold. Transgenic plants and non-transgenic plants were morphologically indistinguishable. The framework of this study can easily be adopted for other putative transcription factors to continue improvement of the plant synthetic biology toolbox.
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Affiliation(s)
- Alexander C Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - D Nikki Reuter
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Mikayla Clark
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Stacee A Harbison
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tayler M Schimel
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA.
- Department of Food Science, The University of Tennessee, Knoxville, Knoxville, TN, USA.
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Li S, Luo Y, Wei G, Zong W, Zeng W, Xiao D, Zhang H, Song Y, Hao Y, Sun K, Lei C, Guo X, Xu B, Li W, Wu Z, Liu Y, Xie X, Guo J. Improving yield-related traits by editing the promoter of the heading date gene Ehd1 in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:239. [PMID: 37930441 DOI: 10.1007/s00122-023-04489-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE We developed an efficient promoter editing method to create different weak Ehd1 alleles in elite japonica rice variety ZJ8 with slightly delayed heading and improved yield for use in breeding. Heading date is an important agronomic trait of rice (Oryza sativa) that determines the planting areas and cultivation seasons of different varieties, thus affecting final yield. Early heading date 1 (Ehd1) is a major rice integrator gene in the regulatory network of heading date whose expression level is negatively correlated with heading date and grain yield. Some elite japonica varieties such as Zhongjia 8 (ZJ8) show very early heading with poor agronomic traits when planted in South China. This problem can be addressed by downregulating the expression of Ehd1. In this study, we analyzed the cis-regulatory elements in the Ehd1 promoter region. We then used CRISPR/Cas9-mediated editing to modify the Ehd1 promoter at multiple target sites in ZJ8. We rapidly identified homozygous allelic mutations in the T2 generation via long-read sequencing. We obtained several Ehd1 promoter mutants with different degrees of lower Ehd1 expression, delayed heading date, and improved yield-related traits. We developed an efficient promoter editing method to create different weak Ehd1 alleles for breeding selection. Using this method, a series of heading date materials from elite varieties can be created to expand the planting area of rice and improve grain yields.
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Affiliation(s)
- Shengting Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanqiu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China
| | - Guangliang Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wanyong Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dongdong Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Han Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingang Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Kangli Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chen Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaotong Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Bingqun Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Weitao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zeqiang Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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9
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Saito M, Otsu W, Miyadera K, Nishimura Y. Recent advances in the understanding of cilia mechanisms and their applications as therapeutic targets. Front Mol Biosci 2023; 10:1232188. [PMID: 37780208 PMCID: PMC10538646 DOI: 10.3389/fmolb.2023.1232188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
The primary cilium is a single immotile microtubule-based organelle that protrudes into the extracellular space. Malformations and dysfunctions of the cilia have been associated with various forms of syndromic and non-syndromic diseases, termed ciliopathies. The primary cilium is therefore gaining attention due to its potential as a therapeutic target. In this review, we examine ciliary receptors, ciliogenesis, and ciliary trafficking as possible therapeutic targets. We first discuss the mechanisms of selective distribution, signal transduction, and physiological roles of ciliary receptors. Next, pathways that regulate ciliogenesis, specifically the Aurora A kinase, mammalian target of rapamycin, and ubiquitin-proteasome pathways are examined as therapeutic targets to regulate ciliogenesis. Then, in the photoreceptors, the mechanism of ciliary trafficking which takes place at the transition zone involving the ciliary membrane proteins is reviewed. Finally, some of the current therapeutic advancements highlighting the role of large animal models of photoreceptor ciliopathy are discussed.
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Affiliation(s)
- Masaki Saito
- Department of Molecular Physiology and Pathology, School of Pharma-Sciences, Teikyo University, Tokyo, Japan
| | - Wataru Otsu
- Department of Biomedical Research Laboratory, Gifu Pharmaceutical University, Gifu, Japan
| | - Keiko Miyadera
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
- Mie University Research Center for Cilia and Diseases, Tsu, Mie, Japan
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10
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Zhang Y, Beachy PA. Cellular and molecular mechanisms of Hedgehog signalling. Nat Rev Mol Cell Biol 2023; 24:668-687. [PMID: 36932157 DOI: 10.1038/s41580-023-00591-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 03/19/2023]
Abstract
The Hedgehog signalling pathway has crucial roles in embryonic tissue patterning, postembryonic tissue regeneration, and cancer, yet aspects of Hedgehog signal transmission and reception have until recently remained unclear. Biochemical and structural studies surprisingly reveal a central role for lipids in Hedgehog signalling. The signal - Hedgehog protein - is modified by cholesterol and palmitate during its biogenesis, thereby necessitating specialized proteins such as the transporter Dispatched and several lipid-binding carriers for cellular export and receptor engagement. Additional lipid transactions mediate response to the Hedgehog signal, including sterol activation of the transducer Smoothened. Access of sterols to Smoothened is regulated by the apparent sterol transporter and Hedgehog receptor Patched, whose activity is blocked by Hedgehog binding. Alongside these lipid-centric mechanisms and their relevance to pharmacological pathway modulation, we discuss emerging roles of Hedgehog pathway activity in stem cells or their cellular niches, with translational implications for regeneration and restoration of injured or diseased tissues.
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Affiliation(s)
- Yunxiao Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute and Neuroscience Department, The Scripps Research Institute, La Jolla, CA, USA
| | - Philip A Beachy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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11
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Smith GD, Ching WH, Cornejo-Páramo P, Wong ES. Decoding enhancer complexity with machine learning and high-throughput discovery. Genome Biol 2023; 24:116. [PMID: 37173718 PMCID: PMC10176946 DOI: 10.1186/s13059-023-02955-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their flexible organization and functional redundancies make deciphering their sequence-function relationships challenging. This article provides an overview of the current understanding of enhancer organization and evolution, with an emphasis on factors that influence these relationships. Technological advancements, particularly in machine learning and synthetic biology, are discussed in light of how they provide new ways to understand this complexity. Exciting opportunities lie ahead as we continue to unravel the intricacies of enhancer function.
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Affiliation(s)
- Gabrielle D Smith
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Wan Hern Ching
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
| | - Paola Cornejo-Páramo
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Emily S Wong
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia.
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12
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Di Giorgio E, Benetti R, Kerschbamer E, Xodo L, Brancolini C. Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:97-148. [PMID: 37657861 DOI: 10.1016/bs.ircmb.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Super-enhancers evolve as elements at the top of the hierarchical control of gene expression. They are important end-gatherers of signaling pathways that control stemness, differentiation or adaptive responses. Many epigenetic regulations focus on these regions, and not surprisingly, during the process of tumorigenesis, various alterations can account for their dysfunction. Super-enhancers are emerging as key drivers of the aberrant gene expression landscape that sustain the aggressiveness of cancer cells. In this review, we will describe and discuss about the structure of super-enhancers, their epigenetic regulation, and the major changes affecting their functionality in cancer.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Roberta Benetti
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Emanuela Kerschbamer
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Luigi Xodo
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy.
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13
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Preissl S, Gaulton KJ, Ren B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet 2023; 24:21-43. [PMID: 35840754 PMCID: PMC9771884 DOI: 10.1038/s41576-022-00509-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
Abstract
Cell type-specific gene expression patterns and dynamics during development or in disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. Distinct classes of CREs can be characterized by their epigenomic features, including DNA methylation, chromatin accessibility, combinations of histone modifications and conformation of local chromatin. Tremendous progress has been made in cataloguing CREs in the human genome using bulk transcriptomic and epigenomic methods. However, single-cell epigenomic and multi-omic technologies have the potential to provide deeper insight into cell type-specific gene regulatory programmes as well as into how they change during development, in response to environmental cues and through disease pathogenesis. Here, we highlight recent advances in single-cell epigenomic methods and analytical tools and discuss their readiness for human tissue profiling.
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Affiliation(s)
- Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Kyle J Gaulton
- Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
| | - Bing Ren
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
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14
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Giannareas N, Zhang Q, Yang X, Na R, Tian Y, Yang Y, Ruan X, Huang D, Yang X, Wang C, Zhang P, Manninen A, Wang L, Wei GH. Extensive germline-somatic interplay contributes to prostate cancer progression through HNF1B co-option of TMPRSS2-ERG. Nat Commun 2022; 13:7320. [PMID: 36443337 PMCID: PMC9705428 DOI: 10.1038/s41467-022-34994-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Genome-wide association studies have identified 270 loci conferring risk for prostate cancer (PCa), yet the underlying biology and clinical impact remain to be investigated. Here we observe an enrichment of transcription factor genes including HNF1B within PCa risk-associated regions. While focused on the 17q12/HNF1B locus, we find a strong eQTL for HNF1B and multiple potential causal variants involved in the regulation of HNF1B expression in PCa. An unbiased genome-wide co-expression analysis reveals PCa-specific somatic TMPRSS2-ERG fusion as a transcriptional mediator of this locus and the HNF1B eQTL signal is ERG fusion status dependent. We investigate the role of HNF1B and find its involvement in several pathways related to cell cycle progression and PCa severity. Furthermore, HNF1B interacts with TMPRSS2-ERG to co-occupy large proportion of genomic regions with a remarkable enrichment of additional PCa risk alleles. We finally show that HNF1B co-opts ERG fusion to mediate mechanistic and biological effects of the PCa risk-associated locus 17p13.3/VPS53/FAM57A/GEMIN4. Taken together, we report an extensive germline-somatic interaction between TMPRSS2-ERG fusion and genetic variations underpinning PCa risk association and progression.
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Affiliation(s)
- Nikolaos Giannareas
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Qin Zhang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Xiayun Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Rong Na
- Division of Urology, Department of Surgery, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong, China
| | - Yijun Tian
- Department of Tumour Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Yuehong Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Xiaohao Ruan
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Da Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoqun Yang
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Peng Zhang
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Aki Manninen
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Liang Wang
- Department of Tumour Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
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15
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Jiang J. Hedgehog signaling mechanism and role in cancer. Semin Cancer Biol 2022; 85:107-122. [PMID: 33836254 PMCID: PMC8492792 DOI: 10.1016/j.semcancer.2021.04.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022]
Abstract
Cell-cell communication through evolutionarily conserved signaling pathways governs embryonic development and adult tissue homeostasis. Deregulation of these signaling pathways has been implicated in a wide range of human diseases including cancer. One such pathway is the Hedgehog (Hh) pathway, which was originally discovered in Drosophila and later found to play a fundamental role in human development and diseases. Abnormal Hh pathway activation is a major driver of basal cell carcinomas (BCC) and medulloblastoma. Hh exerts it biological influence through a largely conserved signal transduction pathway from the activation of the GPCR family transmembrane protein Smoothened (Smo) to the conversion of latent Zn-finger transcription factors Gli/Ci proteins from their repressor (GliR/CiR) to activator (GliA/CiA) forms. Studies from model organisms and human patients have provided deep insight into the Hh signal transduction mechanisms, revealed roles of Hh signaling in a wide range of human cancers, and suggested multiple strategies for targeting this pathway in cancer treatment.
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Affiliation(s)
- Jin Jiang
- Department of Molecular Biology and Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA.
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16
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Lu C, Wang HJ, Song JY, Wang S, Li XY, Huang T, Wang H. Fine Mapping of the MAP2K5 Region Identified rs7175517 as a Causal Variant Related to BMI in China and the United Kingdom Populations. Front Genet 2022; 13:838685. [PMID: 35368675 PMCID: PMC8967323 DOI: 10.3389/fgene.2022.838685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/10/2022] [Indexed: 12/04/2022] Open
Abstract
Background: Genome-wide association studies (GWASs) have consistently identified MAP2K5 as an obesity susceptibility gene. To deepen our understanding of the potential causal genetic variants of this region, a fine-mapping study of MAP2K5 was conducted. Methods and Results: SNPs rs7175517 (G > A) and rs4776970 (T > A) were identified as the leading SNPs associated with BMI in both Chinese and the United Kingdom populations. Second, colocalization of GWAS and expression quantitative trait loci (eQTL) analyses and bioinformatic analyses indicated that rs7175517 is the functionally leading variant in the MAP2K5 gene region. Dual-luciferase assays indicated that the G allele of rs7175517 reduced the mRNA expression of MAP2K5 in HEK293T cells. The possible mechanism was that the G allele interacted with more RNA repressors from nuclei extracts, which was evidenced by electrophoretic mobility shift assays (EMSAs). Furthermore, the pathway enrichment analyses of the products from DNA pull-down and protein mass spectrometry demonstrated that the G allele of rs7175517 might interact with RNA catabolic or splicing transcription factors, which consequentially increased adiposity deposition. Conclusion: SNP rs7175517 of the MAP2K5 gene was the putative causal variant associated with BMI. More precisely designed in vitro or animal experiments are warranted to further delineate the function of MAP2K5 in adipogenesis.
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Affiliation(s)
- Ce Lu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hai-Jun Wang
- Department of Maternal and Child Health, School of Public Health, Peking University, Beijing, China
| | - Jie-Yun Song
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China
| | - Shuo Wang
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China
| | - Xue-Ying Li
- Department of Maternal and Child Health, School of Public Health, Peking University, Beijing, China
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hui Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Maternal and Child Health, School of Public Health, Peking University, Beijing, China
- *Correspondence: Hui Wang,
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17
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Özturan D, Morova T, Lack NA. Androgen Receptor-Mediated Transcription in Prostate Cancer. Cells 2022; 11:898. [PMID: 35269520 PMCID: PMC8909478 DOI: 10.3390/cells11050898] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
Androgen receptor (AR)-mediated transcription is critical in almost all stages of prostate cancer (PCa) growth and differentiation. This process involves a complex interplay of coregulatory proteins, chromatin remodeling complexes, and other transcription factors that work with AR at cis-regulatory enhancer regions to induce the spatiotemporal transcription of target genes. This enhancer-driven mechanism is remarkably dynamic and undergoes significant alterations during PCa progression. In this review, we discuss the AR mechanism of action in PCa with a focus on how cis-regulatory elements modulate gene expression. We explore emerging evidence of genetic variants that can impact AR regulatory regions and alter gene transcription in PCa. Finally, we highlight several outstanding questions and discuss potential mechanisms of this critical transcription factor.
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Affiliation(s)
- Doğancan Özturan
- School of Medicine, Koç University, Istanbul 34450, Turkey;
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Tunç Morova
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
| | - Nathan A. Lack
- School of Medicine, Koç University, Istanbul 34450, Turkey;
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
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18
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Zhang L, Fu X, Ni L, Liu C, Zheng Y, You H, Li M, Xiu C, Zhang L, Gong T, Luo N, Zhang Z, He G, Hu S, Yang H, Chen D, Chen J. Hedgehog Signaling Controls Bone Homeostasis by Regulating Osteogenic/Adipogenic Fate of Skeletal Stem/Progenitor Cells in Mice. J Bone Miner Res 2022; 37:559-576. [PMID: 34870341 DOI: 10.1002/jbmr.4485] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/22/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022]
Abstract
Skeletal stem/progenitor cells (SSPCs) can differentiate into osteogenic or adipogenic lineage. The mechanism governing lineage allocation of SSPCs is still not completely understood. Hedgehog (Hh) signaling plays an essential role in specifying osteogenic fate of mesenchymal progenitors during embryogenesis. However, it is still unclear whether Hh signaling is required for lineage allocation of SSPCs in postnatal skeleton, and whether its dysregulation is related to age-related osteoporosis. Here, we demonstrated that Hh signaling was activated in metaphyseal SSPCs during osteogenic differentiation in the adult skeleton, and its activity decreased with aging. Inactivation of Hh signaling by genetic ablation of Smo, a key molecule in Hh signaling, in Osx-Cre-targeted SSPCs and hypertrophic chondrocytes led to decreased bone formation and increased bone marrow adiposity, two key pathological features of age-related osteoporosis. Moreover, we found that the bone-fat imbalance phenotype caused by Smo deletion mainly resulted from aberrant allocation of SSPCs toward adipogenic lineage at the expense of osteogenic differentiation, but not due to accelerated transdifferentiation of chondrocytes into adipocytes. Mechanistically, we found that Hh signaling regulated osteoblast versus adipocyte fate of SSPCs partly through upregulating Wnt signaling. Thus, our results indicate that Hh signaling regulates bone homeostasis and age-related osteoporosis by acting as a critical switch of cell fate decisions of Osx-Cre-targeted SSPCs in mice and suggest that Hh signaling may serve as a potential therapeutic target for the treatment of osteoporosis and other metabolic bone diseases. © 2021 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Liwei Zhang
- Orthopedic Department, Taizhou Hospital Affiliated to Wenzhou Medical University, Zhejiang, China.,Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Xuejie Fu
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Li Ni
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Cunchang Liu
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Yixin Zheng
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Hongji You
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Meng Li
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Chunmei Xiu
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Lei Zhang
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Tingting Gong
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Na Luo
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China
| | - Zunyi Zhang
- Key Laboratory of Mammalian Organogenesis and Regeneration, Hangzhou Normal University, Zhejiang, China
| | - Guangxu He
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Shijun Hu
- Institute for Cardiovascular Science, Medical College, Soochow University, Suzhou, China
| | - Huilin Yang
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China.,Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Di Chen
- Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jianquan Chen
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China.,Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
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19
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Jiang Y, Peng J, Song J, He J, Jiang M, Wang J, Ma L, Wang Y, Lin M, Wu H, Zhang Z, Gao D, Zhao Y. Loss of Hilnc prevents diet-induced hepatic steatosis through binding of IGF2BP2. Nat Metab 2021; 3:1569-1584. [PMID: 34750570 PMCID: PMC9235319 DOI: 10.1038/s42255-021-00488-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/05/2021] [Indexed: 12/26/2022]
Abstract
The Hedgehog (Hh) signalling pathway plays a critical role in regulating liver lipid metabolism and related diseases. However, the underlying mechanisms are poorly understood. Here, we show that the Hh signalling pathway induces a previously undefined long non-coding RNA (Hilnc, Hedgehog signalling-induced long non-coding RNA), which controls hepatic lipid metabolism. Mutation of the Gli-binding sites in the Hilnc promoter region (HilncBM/BM) decreases the expression of Hilnc in vitro and in vivo. HilncBM/BM and Hilnc-knockout mice are resistant to diet-induced obesity and hepatic steatosis through attenuation of the peroxisome proliferator-activated receptor signalling pathway, as Hilnc directly interacts with IGF2BP2 to enhance Pparγ mRNA stability. Furthermore, we identify a potential functional human homologue of Hilnc, h-Hilnc, which has a similar function in regulating cellular lipid metabolism. These findings uncover a critical role of the Hh-Hilnc-IGF2BP2 signalling axis in lipid metabolism and suggest a potential therapeutic target for the treatment of diet-induced hepatic steatosis.
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Affiliation(s)
- Yiao Jiang
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiayin Peng
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiawen Song
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan He
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Man Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jia Wang
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liya Ma
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuang Wang
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Moubin Lin
- Department of General Surgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Hailong Wu
- Shanghai Key Laboratory for Molecular Imaging, Collaborative Research Center, Shanghai University of Medicine and Health Science, Shanghai, P. R. China
| | - Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dong Gao
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shangha, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yun Zhao
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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20
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No Need to Stick Together to Be Connected: Multiple Types of Enhancers' Networking. Cancers (Basel) 2021; 13:cancers13205201. [PMID: 34680347 PMCID: PMC8533737 DOI: 10.3390/cancers13205201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Transcription regulation programs require the functional interaction of distal and proximal regulatory regions, interacting by specific 3D chromatin configurations. Enhancers are cis-acting regulatory elements able to promote gene expression regardless their orientation and distance from the transcription starting site. Their systematic mapping by genome-wide chromatin profiling and chromosome conformation analysis, combined with the development of gene-editing approaches to modulate their function, revealed that many enhancers work together to fine-tune the expression of their target genes. This review aim to describe the functions of different types of enhancers and the modalities of enhancers’ interaction, focusing on their role in the regulation of complex biological processes like cancer development. Abstract The control of gene expression at a transcriptional level requires a widespread landscape of regulatory elements. Central to these regulatory circuits are enhancers (ENHs), which are defined as cis-acting DNA elements able to increase the transcription of a target gene in a distance- and orientation-independent manner. ENHs are not independent functional elements but work in a complex and dynamic cooperative network, constituting the building blocks of multimodular domains of gene expression regulation. The information from each of these elements converges on the target promoter, contributing to improving the precision and sharpness of gene modulation. ENHs’ interplay varies in its nature and extent, ranging from an additive to redundant effect depending on contexts. Moving from super-enhancers that drive the high expression levels of identity genes, to shadow-enhancers, whose redundant functions contribute to buffering the variation in gene expression, this review aims to describe the different modalities of ENHs’ interaction and their role in the regulation of complex biological processes like cancer development.
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21
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den Hoed J, Devaraju K, Fisher SE. Molecular networks of the FOXP2 transcription factor in the brain. EMBO Rep 2021; 22:e52803. [PMID: 34260143 PMCID: PMC8339667 DOI: 10.15252/embr.202152803] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/19/2021] [Accepted: 06/23/2021] [Indexed: 01/06/2023] Open
Abstract
The discovery of the FOXP2 transcription factor, and its implication in a rare severe human speech and language disorder, has led to two decades of empirical studies focused on uncovering its roles in the brain using a range of in vitro and in vivo methods. Here, we discuss what we have learned about the regulation of FOXP2, its downstream effectors, and its modes of action as a transcription factor in brain development and function, providing an integrated overview of what is currently known about the critical molecular networks.
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Affiliation(s)
- Joery den Hoed
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- International Max Planck Research School for Language SciencesMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Karthikeyan Devaraju
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Simon E Fisher
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- Donders Institute for Brain, Cognition and BehaviourRadboud UniversityNijmegenThe Netherlands
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22
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Williams K, Carrasquilla GD, Ingerslev LR, Hochreuter MY, Hansson S, Pillon NJ, Donkin I, Versteyhe S, Zierath JR, Kilpeläinen TO, Barrès R. Epigenetic rewiring of skeletal muscle enhancers after exercise training supports a role in whole-body function and human health. Mol Metab 2021; 53:101290. [PMID: 34252634 PMCID: PMC8355925 DOI: 10.1016/j.molmet.2021.101290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022] Open
Abstract
Objectives Regular physical exercise improves health by reducing the risk of a plethora of chronic disorders. We hypothesized that endurance exercise training remodels the activity of gene enhancers in skeletal muscle and that this remodeling contributes to the beneficial effects of exercise on human health. Methods and results By studying changes in histone modifications, we mapped the genome-wide positions and activities of enhancers in skeletal muscle biopsies collected from young sedentary men before and after 6 weeks of endurance exercise. We identified extensive remodeling of enhancer activities after exercise training, with a large subset of the remodeled enhancers located in the proximity of genes transcriptionally regulated after exercise. By overlapping the position of enhancers with genetic variants, we identified an enrichment of disease-associated genetic variants within the exercise-remodeled enhancers. Conclusion Our data provide evidence of a functional link between epigenetic rewiring of enhancers to control their activity after exercise training and the modulation of disease risk in humans. Exercise training changes in skeletal muscle gene expression is enriched for secreted factors. The activity of skeletal muscle enhancers undergoes substantial remodeling after exercise training. Skeletal muscle enhancer activity and gene transcription are strongly associated. Exercise training-remodeled enhancer regions are enriched for GWAS SNPs associated with human traits and diseases.
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Affiliation(s)
- Kristine Williams
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Germán D Carrasquilla
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Lars Roed Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Mette Yde Hochreuter
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Svenja Hansson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Nicolas J Pillon
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Ida Donkin
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Soetkin Versteyhe
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark; Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark.
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23
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Duan B, Fu D, Zhang C, Ding P, Dong X, Xia B. Selective Nonmethylated CpG DNA Recognition Mechanism of Cysteine Clamp Domains. J Am Chem Soc 2021; 143:7688-7697. [PMID: 33983734 DOI: 10.1021/jacs.1c00599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Methylation of DNA at CpG sites is a major mark for epigenetic regulation, but how transcription factors are influenced by CpG methylation is not well understood. Here, we report the molecular mechanisms of how the TCF (T-cell factor) and GEF (glucose transporter 4 enhancer factor) families of proteins selectively target unmethylated DNA sequences with a C-clamp type zinc finger domain. The structure of the C-clamp domain from human GEF family protein HDBP1 (C-clampHDBP1) in complex with DNA was determined using NMR spectroscopy, which adopts a unique zinc finger fold and selectively binds RCCGG (R = A/G) DNA sequences with an "Arg···Trp-Lys-Lys" DNA recognition motif inserted in the major groove. The CpG base pairs are central to the binding due to multiple hydrogen bonds formed with the backbone carbonyl groups of Trp378 and Lys379, as well as the side chain ε-amino groups of Lys379 and Lys380 from C-clampHDBP1. Consequently, methylation of the CpG dinucleotide almost abolishes the binding. Homology modeling reveals that the C-clamp domain from human TCF1E (C-clampTCF1E) binds DNA through essentially the same mechanism, with a similar "Arg···Arg-Lys-Lys" DNA recognition motif. The substitution of tryptophan by arginine makes C-clampHDBP1 prefer RCCGC DNA sequences. The two signature DNA recognition motifs are invariant in the GEF and TCF families of proteins, respectively, from fly to human. The recognition of the CpG dinucleotide through two consecutive backbone carbonyl groups is the same as that of the CXXC type unmethylated CpG DNA binding domains, suggesting a common mechanism shared by unmethylated CpG binding proteins.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dihong Fu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Chaoqun Zhang
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianzhi Dong
- Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
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24
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Hong J, Gao R, Yang Y. CrepHAN: Cross-species prediction of enhancers by using hierarchical attention networks. Bioinformatics 2021; 37:3436-3443. [PMID: 33978703 DOI: 10.1093/bioinformatics/btab349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 01/17/2023] Open
Abstract
MOTIVATION Enhancers are important functional elements in genome sequences. The identification of enhancers is a very challenging task due to the great diversity of enhancer sequences and the flexible localization on genomes. Till now, the interactions between enhancers and genes have not been fully understood yet. To speed up the studies of the regulatory roles of enhancers, computational tools for the prediction of enhancers have emerged in recent years. Especially, thanks to the ENCODE project and the advances of high-throughput experimental techniques, a large amount of experimentally verified enhancers have been annotated on the human genome, which allows large-scale predictions of unknown enhancers using data-driven methods. However, except for human and some model organisms, the validated enhancer annotations are scarce for most species, leading to more difficulties in the computational identification of enhancers for their genomes. RESULTS In this study, we propose a deep learning-based predictor for enhancers, named CrepHAN, which is featured by a hierarchical attention neural network and word embedding-based representations for DNA sequences. We use the experimentally-supported data of the human genome to train the model, and perform experiments on human and other mammals, including mouse, cow, and dog. The experimental results show that CrepHAN has more advantages on cross-species predictions, and outperforms the existing models by a large margin. Especially, for human-mouse cross-predictions, the AUC score of ROC curve is increased by 0.033∼0.145 on the combined tissue dataset and 0.032∼0.109 on tissue-specific datasets. AVAILABILITY bcmi.sjtu.edu.cn/~yangyang/CrepHAN.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jianwei Hong
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Rd., Shanghai 200240, China.,School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruitian Gao
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Yang
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Rd., Shanghai 200240, China.,Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, 200240, China
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25
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Parisi C, Vashisht S, Winata CL. Fish-Ing for Enhancers in the Heart. Int J Mol Sci 2021; 22:3914. [PMID: 33920121 PMCID: PMC8069060 DOI: 10.3390/ijms22083914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precise control of gene expression is crucial to ensure proper development and biological functioning of an organism. Enhancers are non-coding DNA elements which play an essential role in regulating gene expression. They contain specific sequence motifs serving as binding sites for transcription factors which interact with the basal transcription machinery at their target genes. Heart development is regulated by intricate gene regulatory network ensuring precise spatiotemporal gene expression program. Mutations affecting enhancers have been shown to result in devastating forms of congenital heart defect. Therefore, identifying enhancers implicated in heart biology and understanding their mechanism is key to improve diagnosis and therapeutic options. Despite their crucial role, enhancers are poorly studied, mainly due to a lack of reliable way to identify them and determine their function. Nevertheless, recent technological advances have allowed rapid progress in enhancer discovery. Model organisms such as the zebrafish have contributed significant insights into the genetics of heart development through enabling functional analyses of genes and their regulatory elements in vivo. Here, we summarize the current state of knowledge on heart enhancers gained through studies in model organisms, discuss various approaches to discover and study their function, and finally suggest methods that could further advance research in this field.
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Affiliation(s)
- Costantino Parisi
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Shikha Vashisht
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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26
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GLI1/GLI2 functional interplay is required to control Hedgehog/GLI targets gene expression. Biochem J 2021; 477:3131-3145. [PMID: 32766732 DOI: 10.1042/bcj20200335] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/05/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023]
Abstract
The Hedgehog-regulated transcription factors GLI1 and GLI2 play overlapping roles in development and disease; however, the mechanisms underlying their interplay remain elusive. We report for the first time that GLI1 and GLI2 physically and functionally interact in cancer cells. GLI1 and GLI2 were shown to co-immunoprecipitate in PANC1 pancreatic cancer cells and RMS13 rhabdomyosarcoma cells. Mapping analysis demonstrated that the zinc finger domains of both proteins are required for their heteromerization. RNAi knockdown of either GLI1 or GLI2 inhibited expression of many well-characterized GLI target genes (BCL2, MYCN, PTCH2, IL7 and CCND1) in PANC1 cells, whereas PTCH1 expression was only inhibited by GLI1 depletion. qPCR screening of a large set of putative canonical and non-canonical Hedgehog/GLI targets identified further genes (e.g. E2F1, BMP1, CDK2) strongly down-regulated by GLI1 and/or GLI2 depletion in PANC1 cells, and demonstrated that ANO1, AQP1 and SOCS1 are up-regulated by knockdown of either GLI1 or GLI2. Chromatin immunoprecipitation showed that GLI1 and GLI2 occupied the same regions at the BCL2, MYCN and CCND1 promoters. Furthermore, depletion of GLI1 inhibited GLI2 occupancy at these promoters, suggesting that GLI1/GLI2 interaction is required for the recruitment of GLI2 to these sites. Together, these findings indicate that GLI1 and GLI2 co-ordinately regulate the transcription of some genes, and provide mechanistic insight into the roles of GLI proteins in carcinogenesis.
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27
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Geyer N, Gerling M. Hedgehog Signaling in Colorectal Cancer: All in the Stroma? Int J Mol Sci 2021; 22:ijms22031025. [PMID: 33498528 PMCID: PMC7864206 DOI: 10.3390/ijms22031025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Hedgehog (Hh) signaling regulates intestinal development and homeostasis. The role of Hh signaling in cancer has been studied for many years; however, its role in colorectal cancer (CRC) remains controversial. It has become increasingly clear that the “canonical” Hh pathway, in which ligand binding to the receptor PTCH1 initiates a signaling cascade that culminates in the activation of the GLI transcription factors, is mainly organized in a paracrine manner, both in the healthy colon and in CRC. Such canonical Hh signals largely act as tumor suppressors. In addition, stromal Hh signaling has complex immunomodulatory effects in the intestine with a potential impact on carcinogenesis. In contrast, non-canonical Hh activation may have tumor-promoting roles in a subset of CRC tumor cells. In this review, we attempt to summarize the current knowledge of the Hh pathway in CRC, with a focus on the tumor-suppressive role of canonical Hh signaling in the stroma. Despite discouraging results from clinical trials using Hh inhibitors in CRC and other solid cancers, we argue that a more granular understanding of Hh signaling might allow the exploitation of this key morphogenic pathway for cancer therapy in the future.
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Affiliation(s)
- Natalie Geyer
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden;
| | - Marco Gerling
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden;
- Theme Cancer, Oncology, Karolinska University Hospital, 17176 Solna, Sweden
- Correspondence:
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28
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Minnoye L, Taskiran II, Mauduit D, Fazio M, Van Aerschot L, Hulselmans G, Christiaens V, Makhzami S, Seltenhammer M, Karras P, Primot A, Cadieu E, van Rooijen E, Marine JC, Egidy G, Ghanem GE, Zon L, Wouters J, Aerts S. Cross-species analysis of enhancer logic using deep learning. Genome Res 2020; 30:1815-1834. [PMID: 32732264 PMCID: PMC7706731 DOI: 10.1101/gr.260844.120] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/15/2020] [Indexed: 12/23/2022]
Abstract
Deciphering the genomic regulatory code of enhancers is a key challenge in biology because this code underlies cellular identity. A better understanding of how enhancers work will improve the interpretation of noncoding genome variation and empower the generation of cell type-specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable enhancer models. We apply this strategy to decipher the enhancer code in melanoma, a relevant case study owing to the presence of distinct melanoma cell states. We trained and validated a deep learning model, called DeepMEL, using chromatin accessibility data of 26 melanoma samples across six different species. We show the accuracy of DeepMEL predictions on the CAGI5 challenge, where it significantly outperforms existing models on the melanoma enhancer of IRF4 Next, we exploit DeepMEL to analyze enhancer architectures and identify accurate transcription factor binding sites for the core regulatory complexes in the two different melanoma states, with distinct roles for each transcription factor, in terms of nucleosome displacement or enhancer activation. Finally, DeepMEL identifies orthologous enhancers across distantly related species, where sequence alignment fails, and the model highlights specific nucleotide substitutions that underlie enhancer turnover. DeepMEL can be used from the Kipoi database to predict and optimize candidate enhancers and to prioritize enhancer mutations. In addition, our computational strategy can be applied to other cancer or normal cell types.
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Affiliation(s)
- Liesbeth Minnoye
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - David Mauduit
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Maurizio Fazio
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Linde Van Aerschot
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
- Laboratory for Disease Mechanisms in Cancer, KU Leuven, 3000 Leuven, Belgium
| | - Gert Hulselmans
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Valerie Christiaens
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Samira Makhzami
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Monika Seltenhammer
- Center for Forensic Medicine, Medical University of Vienna, 1090 Vienna, Austria
- Division of Livestock Sciences (NUWI) - BOKU University of Natural Resources and Life Sciences, 1180 Vienna, Austria
| | - Panagiotis Karras
- VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- KU Leuven, Department of Oncology KU Leuven, 3000 Leuven, Belgium
| | - Aline Primot
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, 35000 Rennes, France
| | - Edouard Cadieu
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, 35000 Rennes, France
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Jean-Christophe Marine
- VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- KU Leuven, Department of Oncology KU Leuven, 3000 Leuven, Belgium
| | - Giorgia Egidy
- Université Paris-Saclay, INRA, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Ghanem-Elias Ghanem
- Institut Jules Bordet, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Leonard Zon
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Jasper Wouters
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Stein Aerts
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
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29
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Zhang Y, Wang F, Wu F, Wang Y, Wang X, Gui Y, Li Q. Tnni1b-ECR183-d2, an 87 bp cardiac enhancer of zebrafish. PeerJ 2020; 8:e10289. [PMID: 33194440 PMCID: PMC7648457 DOI: 10.7717/peerj.10289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
Background Several heart malformations are associated with mutations in the regulatory regions of cardiac genes. Troponin I type 1b (tnni1b) is important for the formation of the atrioventricular canal in zebrafish hearts; however, the regulation of tnni1b is poorly understand. We aimed to identify a small but functional enhancer that is distal to tnni1b. Methods Evolutionary Conserved Region (ECR) Browser was used to analyze the 219 kb zebrafish and human genomes covering the tnni1b gene as well as the 100 kb regions upstream and downstream of tnni1b. Putative transcription factor binding sites (TFBSs) were analyzed using JASPAR and PROMO, and the enhancer activity was identified using zebrafish embryos and the luciferase reporter assay. A correlation analysis between the enhancer and transcription factors (TFs) was performed via TF overexpression and TFBS mutation experiments and the electrophoretic mobility shift assay (EMSA). To analyze the conservation between zebrafish and human enhancers, human DNA fragments were functionally verified. Images were captured and analyzed by fluorescence microscopy or confocal microscopy. Results Combined with comparative analysis and functional validation, we identified a 183 bp ECR (termed tnni1b-ECR183) that was located approximately 84 kb upstream of tnni1b that had the heart-specific enhancer activity in zebrafish. TFBS analysis and the enhancer activity detection assay data showed that the 87 bp core region (termed tnni1b-ECR183-d2) was capable of driving specific GFP expression near the atrioventricular junction and increased luciferase expression in HEK293 and HL1 cell lines. The GFP pattern in zebrafish embryos was similar to the expression profiles of tnni1b. A correlation analysis showed that the enhancer activity of tnni1b-ECR183-d2 was increased when NKX2.5 (p = 0.0006) or JUN (p < 0.0001) was overexpressed and was decreased when the TFBSs of NKX2.5 (p < 0.0001) or JUN (p = 0.0018) were mutated. In addition, DNA-protein interactions were not observed between these TFs and tnni1b-ECR183-d2 in the EMSA experiment. The conservation analysis showed that tnni1b-ECR183-h179 (aligned from tnni1b-ECR183) drove GFP expression in the heart and skeletal muscles and increased the luciferase expression after NKX2.5 (p < 0.0001), JUN (p < 0.0001) or ETS1 (p < 0.0001) was overexpressed. Interestingly, the truncated fragment tnni1b-ECR183-h84 mainly drove GFP expression in the skeletal muscles of zebrafish and the enhancer activity decreased when NKX2.5 (p = 0.0028), ETS1 (p = 0.0001) or GATA4 (p < 0.0001) was overexpressed. Conclusions An 87 bp cardiac-specific enhancer located 84 kb upstream of tnni1b in zebrafish was positively correlated with NKX2.5 or JUN. The zebrafish and human enhancers in this study target different tissues. The GFP expression mediated by tnni1b-ECR183-d2 is a valuable tool for marking the domain around the atrioventricular junction.
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Affiliation(s)
- Yawen Zhang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Feng Wang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Fang Wu
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Youhua Wang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xu Wang
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yonghao Gui
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Qiang Li
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
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30
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Elliott KH, Chen X, Salomone J, Chaturvedi P, Schultz PA, Balchand SK, Servetas JD, Zuniga A, Zeller R, Gebelein B, Weirauch MT, Peterson KA, Brugmann SA. Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks. eLife 2020; 9:e56450. [PMID: 33006313 PMCID: PMC7556880 DOI: 10.7554/elife.56450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022] Open
Abstract
Despite a common understanding that Gli TFs are utilized to convey a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. Using the mouse model (Mus musculus), we demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the basic helix-loop-helix TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, 'divergent' Gli-binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.
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Affiliation(s)
- Kelsey H Elliott
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research FoundationCincinnatiUnited States
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Joseph Salomone
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research FoundationCincinnatiUnited States
- Medical-Scientist Training Program, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Preston A Schultz
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Sai K Balchand
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | | | - Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Matthew T Weirauch
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | | | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Shriners Children’s HospitalCincinnatiUnited States
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31
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Yan C, Zhu M, Ding Y, Yang M, Wang M, Li G, Ren C, Huang T, Yang W, He B, Wang M, Yu F, Wang J, Zhang R, Wang T, Ni J, Chen J, Jiang Y, Dai J, Zhang E, Ma H, Wang Y, Xu D, Wang S, Chen Y, Xu Z, Zhou J, Ji G, Wang Z, Zhang Z, Hu Z, Wei Q, Shen H, Jin G. Meta-analysis of genome-wide association studies and functional assays decipher susceptibility genes for gastric cancer in Chinese populations. Gut 2020; 69:641-651. [PMID: 31383772 DOI: 10.1136/gutjnl-2019-318760] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/24/2019] [Accepted: 07/12/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Although a subset of genetic loci have been associated with gastric cancer (GC) risk, the underlying mechanisms are largely unknown. We aimed to identify new susceptibility genes and elucidate their mechanisms in GC development. DESIGN We conducted a meta-analysis of four genome-wide association studies (GWASs) encompassing 3771 cases and 5426 controls. After targeted sequencing and functional annotation, we performed in vitro and in vivo experiments to confirm the functions of genetic variants and candidate genes. Moreover, we selected 33 promising variants for two-stage replication in 7035 cases and 8323 controls from other five studies. RESULTS The meta-analysis of GWASs identified three loci at 1q22, 5p13.1 and 10q23.33 associated with GC risk at p<5×10-8 and replicated seven known loci at p<0.05. At 5p13.1, the risk rs59133000[C] allele enhanced the binding affinity of NF-κB1 (nuclear factor kappa B subunit 1) to the promoter of PRKAA1, resulting in a reduced promoter activity and lower expression. The knockout of PRKAA1 promoted both GC cell proliferation and xenograft tumour growth in nude mice. At 10q23.33, the rs3781266[C] and rs3740365[T] risk alleles in complete linkage disequilibrium disrupted and created, respectively, the binding motifs of POU2F1 and PAX3, resulting in an increased enhancer activity and expression of NOC3L, while the NOC3L knockdown suppressed GC cell growth. Moreover, two new loci at 3q11.2 (OR=1.21, p=4.56×10-9) and 4q28.1 (OR=1.14, p=3.33×10-11) were associated with GC risk. CONCLUSION We identified 12 loci to be associated with GC risk in Chinese populations and deciphered the mechanisms of PRKAA1 at 5p13.1 and NOC3L at 10q23.33 in gastric tumourigenesis.
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Affiliation(s)
- Caiwang Yan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yanbing Ding
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, China
| | - Mengyun Wang
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gang Li
- Department of General Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Chuanli Ren
- Department of Laboratory Medicine, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Tongtong Huang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wenjun Yang
- Key Laboratory of Fertility Preservation and Maintenance, The General Hospital, Ningxia Medical University, Yinchuan, China
| | - Bangshun He
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nangjing, China
| | - Meilin Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Fei Yu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jinchen Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ruoxin Zhang
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tianpei Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jing Ni
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jiaping Chen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yue Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yanong Wang
- Department of Gastric Cancer and Soft Tissue Sarcomas, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Dazhi Xu
- Department of Gastric Cancer and Soft Tissue Sarcomas, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Shukui Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nangjing, China
| | - Yun Chen
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Zekuan Xu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianwei Zhou
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guozhong Ji
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zhengdong Zhang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
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32
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Mahmud AKMF, Yang D, Stenberg P, Ioshikhes I, Nandi S. Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules. J Comput Biol 2019; 27:1313-1328. [PMID: 31855461 DOI: 10.1089/cmb.2018.0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple transcription factors (TFs) bind to specific sites in the genome and interact among themselves to form the cis-regulatory modules (CRMs). They are essential in modulating the expression of genes, and it is important to study this interplay to understand gene regulation. In the present study, we integrated experimentally identified TF binding sites collected from published studies with computationally predicted TF binding sites to identify Drosophila CRMs. Along with the detection of the previously known CRMs, this approach identified novel protein combinations. We determined high-occupancy target sites, where a large number of TFs bind. Investigating these sites revealed that Giant, Dichaete, and Knirp are highly enriched in these locations. A common TAG team motif was observed at these sites, which might play a role in recruiting other TFs. While comparing the binding sites at distal and proximal promoters, we found that certain regulatory TFs, such as Zelda, were highly enriched in enhancers. Our study has shown that, from the information available concerning the TF binding sites, the real CRMs could be predicted accurately and efficiently. Although we only may claim co-occurrence of these proteins in this study, it may actually point to their interaction (as known interaction proteins typically co-occur together). Such an integrative approach can, therefore, help us to provide a better understanding of the interplay among the factors, even though further experimental verification is required.
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Affiliation(s)
| | - Doo Yang
- Ottawa Institute of Computational Biology and Bioinformatics (OICBB) and Ottawa Institute of Systems Biology (OISB) and Department of Biochemistry, Microbiology and Immunology (BMI), Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Ilya Ioshikhes
- Ottawa Institute of Computational Biology and Bioinformatics (OICBB) and Ottawa Institute of Systems Biology (OISB) and Department of Biochemistry, Microbiology and Immunology (BMI), Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Soumyadeep Nandi
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Guwahati, India; Amity University Haryana, Gurugram, India
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33
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Lenzini L, Di Patti F, Livi R, Fondi M, Fani R, Mengoni A. A Method for the Structure-Based, Genome-Wide Analysis of Bacterial Intergenic Sequences Identifies Shared Compositional and Functional Features. Genes (Basel) 2019; 10:genes10100834. [PMID: 31652625 PMCID: PMC6826451 DOI: 10.3390/genes10100834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/07/2019] [Accepted: 10/16/2019] [Indexed: 11/16/2022] Open
Abstract
In this paper, we propose a computational strategy for performing genome-wide analyses of intergenic sequences in bacterial genomes. Following similar directions of a previous paper, where a method for genome-wide analysis of eucaryotic Intergenic sequences was proposed, here we developed a tool for implementing similar concepts in bacteria genomes. This allows us to (i) classify intergenic sequences into clusters, characterized by specific global structural features and (ii) draw possible relations with their functional features.
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Affiliation(s)
- Leonardo Lenzini
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
- Istituto Nazionale di Fisica Nucleare, Sesto Fiorentino, 50019, Italy.
| | - Francesca Di Patti
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse, Sesto Fiorentino, 50019, Italy.
| | - Roberto Livi
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
- Istituto Nazionale di Fisica Nucleare, Sesto Fiorentino, 50019, Italy.
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse, Sesto Fiorentino, 50019, Italy.
- Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, 50019, Italy.
| | - Marco Fondi
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
| | - Renato Fani
- Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, 50019, Italy.
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
| | - Alessio Mengoni
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
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34
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Zamudio AV, Dall'Agnese A, Henninger JE, Manteiga JC, Afeyan LK, Hannett NM, Coffey EL, Li CH, Oksuz O, Sabari BR, Boija A, Klein IA, Hawken SW, Spille JH, Decker TM, Cisse II, Abraham BJ, Lee TI, Taatjes DJ, Schuijers J, Young RA. Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes. Mol Cell 2019; 76:753-766.e6. [PMID: 31563432 DOI: 10.1016/j.molcel.2019.08.016] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/14/2019] [Accepted: 08/16/2019] [Indexed: 01/09/2023]
Abstract
The gene expression programs that define the identity of each cell are controlled by master transcription factors (TFs) that bind cell-type-specific enhancers, as well as signaling factors, which bring extracellular stimuli to these enhancers. Recent studies have revealed that master TFs form phase-separated condensates with the Mediator coactivator at super-enhancers. Here, we present evidence that signaling factors for the WNT, TGF-β, and JAK/STAT pathways use their intrinsically disordered regions (IDRs) to enter and concentrate in Mediator condensates at super-enhancers. We show that the WNT coactivator β-catenin interacts both with components of condensates and DNA-binding factors to selectively occupy super-enhancer-associated genes. We propose that the cell-type specificity of the response to signaling is mediated in part by the IDRs of the signaling factors, which cause these factors to partition into condensates established by the master TFs and Mediator at genes with prominent roles in cell identity.
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Affiliation(s)
- Alicia V Zamudio
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - John C Manteiga
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ozgur Oksuz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Benjamin R Sabari
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Susana W Hawken
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jan-Hendrik Spille
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tim-Michael Decker
- Department of Biochemistry, University of Colorado, Boulder, Boulder, CO 80303, USA
| | - Ibrahim I Cisse
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tong I Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, Boulder, CO 80303, USA
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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35
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Liu W, Yue S, Zheng X, Hu M, Cao J, Zheng Y. aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq. Epigenetics 2019; 14:877-893. [PMID: 31169445 PMCID: PMC6691993 DOI: 10.1080/15592294.2019.1621139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 05/04/2019] [Accepted: 05/14/2019] [Indexed: 10/26/2022] Open
Abstract
Much effort has been devoted to understand how chromatin modification regulates development and disease. Despite recent progress, however, it remains difficult to obtain high-quality epigenomic maps using chromatin-immunoprecipitation-coupled deep sequencing (ChIP-seq) in samples with low-cell numbers. Here, we present an Atlantis dsDNase-based technology, aFARP-ChIP-seq, that provides accurate profiling of genome-wide histone modifications in as few as 100 cells. By mapping histone lysine trimethylation (H3K4me3) and acetylation (H3K27Ac) in group I innate lymphoid cells (ILC1) sorted from different tissues in parallel, aFARP-ChIP-seq uncovers putative active promoter and enhancer landscapes of several tissue-specific Natural Killer cells (NK) and ILC1. aFARP-ChIP-seq is also highly effective in mapping transcription factor binding sites in small number of cells. Thus, aFARP-ChIP-seq offers multiplexing mapping of both epigenome and transcription factor binding sites using a small number of cells.
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Affiliation(s)
- Wenbin Liu
- Department of Embryology, Carnegie Institution for Science Baltimore, Baltimore, MD, USA
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Sibiao Yue
- Department of Embryology, Carnegie Institution for Science Baltimore, Baltimore, MD, USA
| | - Xiaobin Zheng
- Department of Embryology, Carnegie Institution for Science Baltimore, Baltimore, MD, USA
| | - Minjie Hu
- Department of Embryology, Carnegie Institution for Science Baltimore, Baltimore, MD, USA
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science Baltimore, Baltimore, MD, USA
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36
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Torres-Ruiz R, Benítez-Burraco A, Martínez-Lage M, Rodríguez-Perales S, García-Bellido P. Functional characterization of two enhancers located downstream FOXP2. BMC MEDICAL GENETICS 2019; 20:65. [PMID: 31046704 PMCID: PMC6498672 DOI: 10.1186/s12881-019-0810-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND Mutations in the coding region of FOXP2 are known to cause speech and language impairment. However, it is not clear how dysregulation of the gene contributes to language deficit. Interestingly, microdeletions of the region downstream the gene have been associated with cognitive deficits. METHODS Here, we investigate changes in FOXP2 expression in the SK-N-MC neuroblastoma human cell line after deletion by CRISPR-Cas9 of two enhancers located downstream of the gene. RESULTS Deletion of any of these two functional enhancers downregulates FOXP2, but also upregulates the closest 3' gene MDFIC. Because this effect is not statistically significant in a HEK 293 cell line, derived from the human kidney, both enhancers might confer a tissue specific regulation to both genes. We have also found that the deletion of any of these enhancers downregulates six well-known FOXP2 target genes in the SK-N-MC cell line. CONCLUSIONS We expect these findings contribute to a deeper understanding of how FOXP2 and MDFIC are regulated to pace neuronal development supporting cognition, speech and language.
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Affiliation(s)
- Raúl Torres-Ruiz
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), University of Seville, Seville, Spain.
| | - Marta Martínez-Lage
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, Spain
| | | | - Paloma García-Bellido
- Faculty of Modern Languages, University of Oxford, Oxford, UK.,Faculty of Linguistics, Philology and Phonetics, University of Oxford, Oxford, UK
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37
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Dikicioglu D, Nightingale DJH, Wood V, Lilley KS, Oliver SG. Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae. FEMS Yeast Res 2019; 19:5315759. [PMID: 30753445 DOI: 10.1093/femsyr/foz014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/08/2019] [Indexed: 12/17/2022] Open
Abstract
Topological analysis of large networks, which focus on a specific biological process or on related biological processes, where functional coherence exists among the interacting members, may provide a wealth of insight into cellular functionality. This work presents an unbiased systems approach to analyze genetic, transcriptional regulatory and physical interaction networks of yeast genes possessing such functional coherence to gain novel biological insight. The present analysis identified only a few transcriptional regulators amongst a large gene cohort associated with the protein metabolism and processing in yeast. These transcription factors are not functionally required for the maintenance of these tasks in growing cells. Rather, they are involved in rewiring gene transcription in response to such major challenges as starvation, hypoxia, DNA damage, heat shock or the accumulation of unfolded proteins. Indeed, only a subset of these proteins were captured empirically in the nuclear-enriched fraction of non-stressed yeast cells, suggesting that the transcriptional regulation of protein metabolism and processing in yeast is primarily concerned with maintaining cellular robustness in the face of threat by either internal or external stressors.
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Affiliation(s)
- Duygu Dikicioglu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.,Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Daniel J H Nightingale
- Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.,Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.,Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Valerie Wood
- Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.,Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Kathryn S Lilley
- Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.,Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.,Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.,Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
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38
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Wei M, Ma R, Huang S, Liao Y, Ding Y, Li Z, Guo Q, Tan R, Zhang L, Zhao L. Oroxylin A increases the sensitivity of temozolomide on glioma cells by hypoxia-inducible factor 1α/hedgehog pathway under hypoxia. J Cell Physiol 2019; 234:17392-17404. [PMID: 30790292 DOI: 10.1002/jcp.28361] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022]
Abstract
Microenvironmental hypoxia-mediated drug resistance is responsible for the failure of cancer therapy. To date, the role of the hedgehog pathway in resistance to temozolomide (TMZ) under hypoxia has not been investigated. In this study, we discovered that the increasing hypoxia-inducible factor 1α (HIF-1α) activated the hedgehog pathway in hypoxic microenvironment by promoting autocrine secretion of sonic hedgehog protein (Shh), and then upregulating transfer of Gli1 to the nucleus, finally contributed to TMZ resistance in glioma cells. Oroxylin A (C16H12O5), a bioactive flavonoid, could induce HIF-1α degradation via prolyl-hydroxylases-VHL signaling pathway, resulting in the inactivation of the hedgehog. Besides, oroxylin A increased the expression of Sufu, which is a negative regulator of Gli1. By this mechanism, oroxylin A sensitized TMZ on glioma cells. U251 intracranial transplantation model and GL261 xenograft model were used to confirm the reversal effects of oroxylin A in vivo. In conclusion, our results demonstrated that HIF-1α/hedgehog pathway conferred TMZ resistance under hypoxia, and oroxylin A was capable of increasing the sensitivity of TMZ on glioma cells in vitro and in vivo by inhibiting HIF-1α/hedgehog pathway and depressing the activation of Gli1 directly.
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Affiliation(s)
- Mian Wei
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Rong Ma
- Department of Anesthesiology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Shaoliang Huang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Yan Liao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Youxiang Ding
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Zhaohe Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Qinglong Guo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Renxiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Xianlin, Nanjing, China
| | - Lulu Zhang
- The Key Laboratory of Modern Toxicology of Ministry of Education, Department of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Zhao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
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39
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Nikkanen J, Landoni JC, Balboa D, Haugas M, Partanen J, Paetau A, Isohanni P, Brilhante V, Suomalainen A. A complex genomic locus drives mtDNA replicase POLG expression to its disease-related nervous system regions. EMBO Mol Med 2019; 10:13-21. [PMID: 29109127 PMCID: PMC5760859 DOI: 10.15252/emmm.201707993] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
DNA polymerase gamma (POLG), the mtDNA replicase, is a common cause of mitochondrial neurodegeneration. Why POLG defects especially cause central nervous system (CNS) diseases is unknown. We discovered a complex genomic regulatory locus for POLG, containing three functional CNS‐specific enhancers that drive expression specifically in oculomotor complex and sensory interneurons of the spinal cord, completely overlapping with the regions showing neuronal death in POLG patients. The regulatory locus also expresses two functional RNAs, LINC00925‐RNA and MIR9‐3, which are coexpressed with POLG. The MIR9‐3 targets include NR2E1, a transcription factor maintaining neural stem cells in undifferentiated state, and MTHFD2, the regulatory enzyme of mitochondrial folate cycle, linking POLG expression to stem cell differentiation and folate metabolism. Our evidence suggests that distant genomic non‐coding regions contribute to regulation of genes encoding mitochondrial proteins. Such genomic arrangement of POLG locus, driving expression to CNS regions affected in POLG patients, presents a potential mechanism for CNS‐specific manifestations in POLG disease.
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Affiliation(s)
- Joni Nikkanen
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Juan Cruz Landoni
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Diego Balboa
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland
| | - Maarja Haugas
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Juha Partanen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Anders Paetau
- HUSLAB and Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pirjo Isohanni
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Department of Pediatric Neurology, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Virginia Brilhante
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Anu Suomalainen
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland .,Department of Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Neuroscience Center, University of Helsinki, Helsinki, Finland
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Sox13 is a novel early marker for hair follicle development. Biochem Biophys Res Commun 2019; 509:862-868. [PMID: 30638933 DOI: 10.1016/j.bbrc.2018.12.163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 12/25/2018] [Indexed: 12/16/2022]
Abstract
Sox13, a group D member of the Sry-related high-mobility group box (Sox) transcription factor family, is expressed in various tissues including the hair follicle. However, its spatiotemporal expression patterns in the hair follicle and its role in hair development remain to be elucidated. To address these questions, we generated Sox13-LacZ-knock-in mice (Sox13LacZ/+), in which the LacZ reporter gene was inserted in-frame into exon 2, which contains the translation initiation codon. X-gal staining in Sox13LacZ/+ embryos revealed that Sox13 is initially expressed in the epithelial portion of the placode, and subsequently in the hair germ and the hair peg during early hair follicle development. In postnatal catagen and anagen, Sox13 was detected in the epithelial sheath, whereas in telogen, Sox13 was localized in the bulge region, where hair follicle stem cells reside. Immunohistochemistry with an anti-β-galactosidase antibody and anti-hair keratin antibodies that specifically mark the different layers of the hair follicle revealed that Sox13 was predominantly expressed in the outer root sheath in anagen. However, the integumentary structures of Sox13LacZ/LacZ mice were grossly and histologically indistinguishable from those of wild type mice. These results suggest that although Sox13 is dispensable for epidermal and adnexal development, Sox13 is a useful marker for early hair follicle development.
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Analysis of the transcriptional logic governing differential spatial expression in Hh target genes. PLoS One 2019; 14:e0209349. [PMID: 30615641 PMCID: PMC6322776 DOI: 10.1371/journal.pone.0209349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 12/04/2018] [Indexed: 11/19/2022] Open
Abstract
This work provides theoretical tools to analyse the transcriptional effects of certain biochemical mechanisms (i.e. affinity and cooperativity) that have been proposed in previous literature to explain the proper spatial expression of Hedgehog target genes involved in Drosophila development. Specifically we have focused on the expression of decapentaplegic, wingless, stripe and patched. The transcription of these genes is believed to be controlled by enhancer modules able to interpret opposing gradients of the activator and repressor forms of the transcription factor Cubitus interruptus (Ci). This study is based on a thermodynamic approach, which provides expression rates for these genes. These expression rates are controlled by transcription factors which are competing and cooperating for common binding sites. We have made mathematical representations of the different expression rates which depend on multiple factors and variables. The expressions obtained with the model have been refined to produce simpler equivalent formulae which allow for their mathematical analysis. Thanks to this, we can evaluate the correlation between the different interactions involved in transcription and the biological features observed at tissular level. These mathematical models can be applied to other morphogenes to help understand the complex transcriptional logic of opposing activator and repressor gradients.
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Wang J, Dai X, Berry LD, Cogan JD, Liu Q, Shyr Y. HACER: an atlas of human active enhancers to interpret regulatory variants. Nucleic Acids Res 2019; 47:D106-D112. [PMID: 30247654 PMCID: PMC6323890 DOI: 10.1093/nar/gky864] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 12/19/2022] Open
Abstract
Recent studies have shown that disease-susceptibility variants frequently lie in cell-type-specific enhancer elements. To identify, interpret, and prioritize such risk variants, we must identify the enhancers active in disease-relevant cell types, their upstream transcription factor (TF) binding, and their downstream target genes. To address this need, we built HACER (http://bioinfo.vanderbilt.edu/AE/HACER/), an atlas of Human ACtive Enhancers to interpret Regulatory variants. The HACER atlas catalogues and annotates in-vivo transcribed cell-type-specific enhancers, as well as placing enhancers within transcriptional regulatory networks by integrating ENCODE TF ChIP-Seq and predicted/validated chromatin interaction data. We demonstrate the utility of HACER in (i) offering a mechanistic hypothesis to explain the association of SNP rs614367 with ER-positive breast cancer risk, (ii) exploring tumor-specific enhancers in selective MYC dysregulation and (iii) prioritizing/annotating non-coding regulatory regions targeting CCND1. HACER provides a valuable resource for studies of GWAS, non-coding variants, and enhancer-mediated regulation.
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Affiliation(s)
- Jing Wang
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xizhen Dai
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lynne D Berry
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
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Wu HH, Li YL, Liu NJ, Yang Z, Tao XM, Du YP, Wang XC, Lu B, Zhang ZY, Hu RM, Wen J. TCF7L2 regulates pancreatic β-cell function through PI3K/AKT signal pathway. Diabetol Metab Syndr 2019; 11:55. [PMID: 31312258 PMCID: PMC6612183 DOI: 10.1186/s13098-019-0449-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 06/24/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Transcription factor 7-like 2 (TCF7L2), which previously known as TCF-4, is a major form of transcription factor involved in the downstream WNT signaling and exhibits the strongest association to diabetes susceptibility. Although we still do not know mechanistically how TCF7L2 exerts its physiological functions on pancreatic endocrine cells, it had been suggested that TCF7L2 may directly affect β-cell function by regulating the activation of PI3K/AKT signaling pathway. METHODS MIN6 cells were transfected with TCF7L2 knockdown virus or lenti-TCF7L2 virus for 48 h to evaluate the contribution of TCF7L2 to the PI3K/AKT signaling pathway and pancreatic β-cell function. This was confirmed by measuring the expression of PI3K p85 and p-Akt by western blotting and insulin secretion by enzyme-linked immunosorbent assay (ELISA), respectively. Chromatin immunoprecipitation (ChIP) and polymerase chain reaction (PCR) experiments were performed to explore the genomic distribution of TCF7L2-binding sites in the promoter of PIK3R1, the affinity between which was analyzed by the luciferase reporter assay. RESULTS In the present study, we strikingly identified that TCF7L2 could profoundly inhibit the expression of PIK3R1 gene and its encoding protein PI3K p85, which then could lead to the activation of PI3K/AKT signaling and stimulate insulin secretion in pancreatic β-cells. However, the integrity and stability of evolutionarily conserved TCF7L2-binding motif plays a very crucial role in the binding events between transcription factor TCF7L2 and its candidate target genes. We also found that the affinity of TCF7L2 to the promoter region of PIK3R1 alters upon the specific binding sites, which further provides statistical validation to the necessity of TCF7L2-binding motif. CONCLUSIONS This study demonstrated that TCF7L2 is closely bound to the specific binding regions of PIK3R1 promoter and prominently controls the transcription of its encoding protein p85, which further affects the activation of PI3K/AKT signaling pathway and insulin secretion.
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Affiliation(s)
- Hui-Hui Wu
- Department of Endocrinology and Metabolism, Jing’an District Center Hospital of Shanghai, Shanghai, 200040 China
| | - Yan-Liang Li
- Department of Endocrinology and Metabolism, Huashan Hospital of Fudan University, NO. 12 Wulumuqi Mid Road, Building 0#, Jing’an District, Shanghai, 200040 China
| | - Nai-Jia Liu
- Department of Endocrinology and Metabolism, Huashan Hospital of Fudan University, NO. 12 Wulumuqi Mid Road, Building 0#, Jing’an District, Shanghai, 200040 China
| | - Zhen Yang
- Department of Endocrinology and Metabolism, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, 200020 China
| | - Xiao-Ming Tao
- Department of Endocrinology and Metabolism, Hua Dong Hospital, Fudan University, Shanghai, 200040 China
| | - Yan-Ping Du
- Department of Endocrinology and Metabolism, Hua Dong Hospital, Fudan University, Shanghai, 200040 China
| | - Xuan-Chun Wang
- Department of Endocrinology and Metabolism, Huashan Hospital of Fudan University, NO. 12 Wulumuqi Mid Road, Building 0#, Jing’an District, Shanghai, 200040 China
| | - Bin Lu
- Department of Endocrinology and Metabolism, Huashan Hospital of Fudan University, NO. 12 Wulumuqi Mid Road, Building 0#, Jing’an District, Shanghai, 200040 China
| | - Zhao-Yun Zhang
- Department of Endocrinology and Metabolism, Huashan Hospital of Fudan University, NO. 12 Wulumuqi Mid Road, Building 0#, Jing’an District, Shanghai, 200040 China
| | - Ren-Ming Hu
- Department of Endocrinology and Metabolism, Huashan Hospital of Fudan University, NO. 12 Wulumuqi Mid Road, Building 0#, Jing’an District, Shanghai, 200040 China
| | - Jie Wen
- Department of Endocrinology and Metabolism, Jing’an District Center Hospital of Shanghai, Shanghai, 200040 China
- Department of Endocrinology and Metabolism, Huashan Hospital of Fudan University, NO. 12 Wulumuqi Mid Road, Building 0#, Jing’an District, Shanghai, 200040 China
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Diao Y, Rahman MFU, Vyatkin Y, Azatyan A, St Laurent G, Kapranov P, Zaphiropoulos PG. Identification of novel GLI1 target genes and regulatory circuits in human cancer cells. Mol Oncol 2018; 12:1718-1734. [PMID: 30098229 PMCID: PMC6166001 DOI: 10.1002/1878-0261.12366] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/03/2018] [Accepted: 07/26/2018] [Indexed: 01/12/2023] Open
Abstract
Hedgehog (HH) signaling is involved in many physiological processes, and pathway deregulation can result in a wide range of malignancies. Glioma‐associated oncogene 1 (GLI1) is a transcription factor and a terminal effector of the HH cascade. Despite its crucial role in tumorigenesis, our understanding of the GLI1 cellular targets is quite limited. In this study, we identified multiple new GLI1 target genes using a combination of different genomic surveys and then subjected them to in‐depth validation in human cancer cell lines. We were able to validate >90% of the new targets, which were enriched in functions involved in neurogenesis and regulation of transcription, in at least one type of follow‐up experiment. Strikingly, we found that RNA editing of GLI1 can modulate effects on the targets. Furthermore, one of the top targets, FOXS1, a gene encoding a transcription factor previously implicated in nervous system development, was shown to act in a negative feedback loop limiting the cellular effects of GLI1 in medulloblastoma and rhabdomyosarcoma cells. Moreover, FOXS1 is both highly expressed and positively correlated with GLI1 in medulloblastoma samples of the Sonic HH subgroup, further arguing for the existence of FOXS1/GLI1 interplay in human tumors. Consistently, high FOXS1 expression predicts longer relapse‐free survival in breast cancer. Overall, our findings open multiple new avenues in HH signaling pathway research and have potential for translational implications.
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Affiliation(s)
- Yumei Diao
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Yuri Vyatkin
- St. Laurent Institute, Cambridge, MA, USA.,AcademGene LLC, Novosibirsk, Russia
| | - Ani Azatyan
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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Skarp S, Kämäräinen OP, Wei GH, Jakkula E, Kiviranta I, Kröger H, Auvinen J, Lehenkari P, Ala-Kokko L, Männikkö M. Whole exome sequencing in Finnish families identifies new candidate genes for osteoarthritis. PLoS One 2018; 13:e0203313. [PMID: 30157244 PMCID: PMC6114922 DOI: 10.1371/journal.pone.0203313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/18/2018] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Osteoarthritis (OA) is the most common degenerative joint disease and one of the major causes of disability worldwide. It is a multifactorial disorder with a significant genetic component. The heritability of OA has been estimated to be 60% for hip OA and 39% for knee OA. Genetic factors behind OA are still largely unknown. Studying families with strong history of OA, facilitates examining the co-segregation of genetic variation and OA. The aim of this study was to identify new, rare genetic factors and novel candidate genes for OA. METHODS Eight patients from three Finnish families with hip and knee OA were studied using whole exome sequencing. We focused on rare exonic variants with predicted pathogenicity and variants located in active promoter or strong enhancer regions. Expression of identified candidate genes were studied in bone and cartilage tissues and the observed variants were investigated using bioinformatic analyses. RESULTS Two rare variants co-segregated with OA in two families. In Family 8 a missense variant (c.628C>G, p.Arg210Gly) was observed in the OLIG3 gene that encodes a transcription factor known to be associated with rheumatoid arthritis and inflammatory polyarthritis. The Arg210Gly variant was estimated to be pathogenic by Polyphen-2 and Mutation taster and the locus is conserved among mammals. In Family 12 the observed variant (c.-127G>T) was located in the transcription start site of the FIP1L1 gene. FIP1L1 participates in the regulation of polyadenylation. The c.-127G>T is located in the transcription start site and may alter the DNA-binding of transcription factors. Both, OLIG3 and FIP1L1 were observed in human bone and cartilage. CONCLUSION The identified variants revealed novel candidate genes for OA. OLIG3 and FIP1L1 have specific roles in transcription and may effect expression of other genes. Identified variants in these genes may thus have a role in the regulatory events leading to OA.
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Affiliation(s)
- Sini Skarp
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- * E-mail:
| | | | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Eveliina Jakkula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ilkka Kiviranta
- Department of Orthopaedics and Traumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Orthopaedics and Traumatology, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Heikki Kröger
- Department of Orthopaedics and Traumatology, Kuopio University Hospital and Kuopio Musculoskeletal Research Unit, University of Eastern Finland, Kuopio, Finland
| | - Juha Auvinen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Petri Lehenkari
- Department of Anatomy and Cell biology and Surgery Clinic, Medical Research Center, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Leena Ala-Kokko
- Connective Tissue Gene Tests, Allentown, PA, United States of America
| | - Minna Männikkö
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Northern Finland Birth Cohort, Faculty of Medicine, University of Oulu, Oulu, Finland
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Wang J, Zhao Y, Zhou X, Hiebert SW, Liu Q, Shyr Y. Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation. BMC Genomics 2018; 19:633. [PMID: 30139328 PMCID: PMC6107967 DOI: 10.1186/s12864-018-5016-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 08/14/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Enhancers are distal cis-regulatory elements that control gene expression. Despite an increasing appreciation of the importance of enhancers in cellular function and disease, our knowledge of enhancer-regulated transcription is very limited. Nascent RNA sequencing technologies, such as global nuclear run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq), not only provide a direct and reliable measurement of enhancer activity, but also allow for quantifying transcription of enhancers and target genes simultaneously, making these technologies extremely useful for exploring enhancer-mediated regulation. RESULTS Nascent RNA sequencing analysis (NRSA) provides a comprehensive view of enhancer-mediated gene regulation. NRSA not only outperforms existing methods for enhancer identification, but also enables annotation and quantification of active enhancers, and prediction of their target genes. Furthermore, NRSA identifies functionally important enhancers by integrating 1) nascent transcriptional changes in enhancers and their target genes and 2) binding profiles from regulator(s) of interest. Applied to wildtype and histone deacetylase 3 (Hdac3) knockout mouse livers, NRSA showed that HDAC3 regulates RNA polymerase recruitment through both proximal (promoter) and distal (enhancer) regulatory elements. Integrating ChIP-seq with PRO-seq data, NRSA prioritized enhancers based on their potential contribution to mediating HDAC3 regulation. CONCLUSIONS NRSA will greatly facilitate the usage of nascent RNA sequencing techniques and accelerate the study of enhancer-mediated regulation.
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Affiliation(s)
- Jing Wang
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN USA
| | - Yue Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Xiaofan Zhou
- Department of Biological Science, Vanderbilt University, Nashville, TN USA
| | - Scott W. Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN USA
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Gao P, Xia JH, Sipeky C, Dong XM, Zhang Q, Yang Y, Zhang P, Cruz SP, Zhang K, Zhu J, Lee HM, Suleman S, Giannareas N, Liu S, Tammela TLJ, Auvinen A, Wang X, Huang Q, Wang L, Manninen A, Vaarala MH, Wang L, Schleutker J, Wei GH. Biology and Clinical Implications of the 19q13 Aggressive Prostate Cancer Susceptibility Locus. Cell 2018; 174:576-589.e18. [PMID: 30033361 PMCID: PMC6091222 DOI: 10.1016/j.cell.2018.06.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/28/2018] [Accepted: 05/31/2018] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies (GWAS) have identified rs11672691 at 19q13 associated with aggressive prostate cancer (PCa). Here, we independently confirmed the finding in a cohort of 2,738 PCa patients and discovered the biological mechanism underlying this association. We found an association of the aggressive PCa-associated allele G of rs11672691 with elevated transcript levels of two biologically plausible candidate genes, PCAT19 and CEACAM21, implicated in PCa cell growth and tumor progression. Mechanistically, rs11672691 resides in an enhancer element and alters the binding site of HOXA2, a novel oncogenic transcription factor with prognostic potential in PCa. Remarkably, CRISPR/Cas9-mediated single-nucleotide editing showed the direct effect of rs11672691 on PCAT19 and CEACAM21 expression and PCa cellular aggressive phenotype. Clinical data demonstrated synergistic effects of rs11672691 genotype and PCAT19/CEACAM21 gene expression on PCa prognosis. These results provide a plausible mechanism for rs11672691 associated with aggressive PCa and thus lay the ground work for translating this finding to the clinic.
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Affiliation(s)
- Ping Gao
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Ji-Han Xia
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, 20014 Turku, Finland
| | - Xiao-Ming Dong
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Qin Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Yuehong Yang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Peng Zhang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sara Pereira Cruz
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Kai Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Jing Zhu
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hang-Mao Lee
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Sufyan Suleman
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Nikolaos Giannareas
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Song Liu
- State Key Laboratory of Medical Molecular Biology, Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, 100005 Beijing, China
| | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, 33521 Tampere, Finland
| | - Anssi Auvinen
- University of Tampere, School of Health Sciences, 33520 Tampere, Finland
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, 100005 Beijing, China
| | - Qilai Huang
- School of Life Science, Shandong University, 250012 Jinan, China
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Aki Manninen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Markku H Vaarala
- Oulu University Hospital, 90014 Oulu, Finland; Medical Research Center Oulu, University of Oulu and Oulu University Hospital, 90014 Oulu, Finland
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, 20014 Turku, Finland; Medical Genetics, Division of Laboratory, Turku University Hospital, 20521 Turku, Finland
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland.
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Gao L, Bao W, Zhang H, Yuan CA, Huang DS. Fast sequence analysis based on diamond sampling. PLoS One 2018; 13:e0198922. [PMID: 29953448 PMCID: PMC6023231 DOI: 10.1371/journal.pone.0198922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/29/2018] [Indexed: 12/02/2022] Open
Abstract
Both in DNA and protein contexts, an important method for modelling motifs is to utilize position weight matrix (PWM) in biological sequences. With the development of genome sequencing technology, the quantity of the sequence data is increasing explosively, so the faster searching algorithms which have the ability to meet the increasingly need are desired to develop. In this paper, we proposed a method for speeding up the searching process of candidate transcription factor binding sites (TFBS), and the users can be allowed to specify p threshold to get the desired trade-off between speed and sensitivity for a particular sequence analysis. Moreover, the proposed method can also be generalized to large-scale annotation and sequence projects.
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Affiliation(s)
- Liangxin Gao
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China
| | - Wenzhen Bao
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China
| | - Hongbo Zhang
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China
| | - Chang-An Yuan
- Science Computing and Intelligent Information Processing of GuangXi Higher Education Key Laboratory, Guangxi Teachers Education University, Nanning, Guangxi, China
| | - De-Shuang Huang
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China
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Lochmann TL, Powell KM, Ham J, Floros KV, Heisey DAR, Kurupi RIJ, Calbert ML, Ghotra MS, Greninger P, Dozmorov M, Gowda M, Souers AJ, Reynolds CP, Benes CH, Faber AC. Targeted inhibition of histone H3K27 demethylation is effective in high-risk neuroblastoma. Sci Transl Med 2018; 10:eaao4680. [PMID: 29769286 PMCID: PMC6200133 DOI: 10.1126/scitranslmed.aao4680] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/18/2018] [Accepted: 04/20/2018] [Indexed: 12/17/2022]
Abstract
High-risk neuroblastoma is often distinguished by amplification of MYCN and loss of differentiation potential. We performed high-throughput drug screening of epigenetic-targeted therapies across a large and diverse tumor cell line panel and uncovered the hypersensitivity of neuroblastoma cells to GSK-J4, a small-molecule dual inhibitor of lysine 27 of histone 3 (H3K27) demethylases ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX), and histone demethylase Jumonji D3 (JMJD3). Mechanistically, GSK-J4 induced neuroblastoma differentiation and endoplasmic reticulum (ER) stress, with accompanying up-regulation of p53 up-regulated modulator of apoptosis (PUMA) and induction of cell death. Retinoic acid (RA)-resistant neuroblastoma cells were sensitive to GSK-J4. In addition, GSK-J4 was effective at blocking the growth of chemorefractory and patient-derived xenograft models of high-risk neuroblastoma in vivo. Furthermore, GSK-J4 and RA combination increased differentiation and ER stress over GSK-J4 effects and limited the growth of neuroblastomas resistant to either drug alone. In MYCN-amplified neuroblastoma, PUMA induction by GSK-J4 sensitized tumors to the B cell lymphoma 2 (BCL-2) inhibitor venetoclax, demonstrating that epigenetic-targeted therapies and BCL-2 homology domain 3 mimetics can be rationally combined to treat this high-risk subset of neuroblastoma. Therefore, H3K27 demethylation inhibition is a promising therapeutic target to treat high-risk neuroblastoma, and H3K27 demethylation can be part of rational combination therapies to induce robust antineuroblastoma activity.
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Affiliation(s)
- Timothy L Lochmann
- Virginia Commonwealth University Philips Institute, School of Dentistry and Massey Cancer Center, Richmond, VA 23298, USA
| | - Krista M Powell
- Virginia Commonwealth University Philips Institute, School of Dentistry and Massey Cancer Center, Richmond, VA 23298, USA
| | - Jungoh Ham
- Virginia Commonwealth University Philips Institute, School of Dentistry and Massey Cancer Center, Richmond, VA 23298, USA
| | - Konstantinos V Floros
- Virginia Commonwealth University Philips Institute, School of Dentistry and Massey Cancer Center, Richmond, VA 23298, USA
| | - Daniel A R Heisey
- Virginia Commonwealth University Philips Institute, School of Dentistry and Massey Cancer Center, Richmond, VA 23298, USA
| | - Richard I J Kurupi
- Virginia Commonwealth University Philips Institute, School of Dentistry and Massey Cancer Center, Richmond, VA 23298, USA
| | - Marissa L Calbert
- Virginia Commonwealth University Philips Institute, School of Dentistry and Massey Cancer Center, Richmond, VA 23298, USA
| | - Maninderjit S Ghotra
- Virginia Commonwealth University Philips Institute, School of Dentistry and Massey Cancer Center, Richmond, VA 23298, USA
| | - Patricia Greninger
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Mikhail Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Madhu Gowda
- Division of Pediatric Hematology, Oncology, and Stem Cell Transplantation, Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, VA 23298, USA
| | | | - C Patrick Reynolds
- Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, TX 79430, USA
| | - Cyril H Benes
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Anthony C Faber
- Virginia Commonwealth University Philips Institute, School of Dentistry and Massey Cancer Center, Richmond, VA 23298, USA.
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Meers MP, Adelman K, Duronio RJ, Strahl BD, McKay DJ, Matera AG. Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. BMC Genomics 2018; 19:157. [PMID: 29466941 PMCID: PMC5822475 DOI: 10.1186/s12864-018-4510-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/30/2018] [Indexed: 12/15/2022] Open
Abstract
Background High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis. Results The data recapitulate major regulatory classes of TSSs, based on peak width, promoter-proximal polymerase pausing, and cis-regulatory element density. We confirm the paucity of divergent transcription units in D. melanogaster, but also identify notable exceptions. Furthermore, we identify thousands of novel initiation events occurring at unannotated TSSs that can be classified into functional categories by their local density of histone modifications. Interestingly, a sub-class of these unannotated TSSs overlaps with functionally validated enhancer elements, consistent with a regulatory role for “enhancer RNAs” (eRNAs) in defining developmental transcription programs. Conclusions High-depth TSS mapping is a powerful strategy for identifying and characterizing low-abundance and/or low-stability RNAs. Global analysis of transcription initiation patterns in a developing organism reveals a vast number of novel initiation events that identify potential eRNAs as well as other non-coding transcripts critical for animal development. Electronic supplementary material The online version of this article (10.1186/s12864-018-4510-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael P Meers
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA.,Departments of Biology and Genetics, University of North Carolina, Chapel Hill, 27599, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA.,Departments of Biology and Genetics, University of North Carolina, Chapel Hill, 27599, USA
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA.,Departments of Biology and Genetics, University of North Carolina, Chapel Hill, 27599, USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, 27599, USA. .,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA. .,Departments of Biology and Genetics, University of North Carolina, Chapel Hill, 27599, USA.
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