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Trimbour R, Deutschmann IM, Cantini L. Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS. Bioinformatics 2024; 40:btae143. [PMID: 38460192 PMCID: PMC11065476 DOI: 10.1093/bioinformatics/btae143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/20/2023] [Accepted: 03/07/2024] [Indexed: 03/11/2024] Open
Abstract
MOTIVATION The molecular identity of a cell results from a complex interplay between heterogeneous molecular layers. Recent advances in single-cell sequencing technologies have opened the possibility to measure such molecular layers of regulation. RESULTS Here, we present HuMMuS, a new method for inferring regulatory mechanisms from single-cell multi-omics data. Differently from the state-of-the-art, HuMMuS captures cooperation between biological macromolecules and can easily include additional layers of molecular regulation. We benchmarked HuMMuS with respect to the state-of-the-art on both paired and unpaired multi-omics datasets. Our results proved the improvements provided by HuMMuS in terms of transcription factor (TF) targets, TF binding motifs and regulatory regions prediction. Finally, once applied to snmC-seq, scATAC-seq and scRNA-seq data from mouse brain cortex, HuMMuS enabled to accurately cluster scRNA profiles and to identify potential driver TFs. AVAILABILITY AND IMPLEMENTATION HuMMuS is available at https://github.com/cantinilab/HuMMuS.
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Affiliation(s)
- Remi Trimbour
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015 Paris, France
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
| | - Ina Maria Deutschmann
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
| | - Laura Cantini
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015 Paris, France
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
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2
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Wang Y, Gu Z, Dong J, Zhu J, Liu C, Li G, Lu M, Han J, Cao S, Chen L, Wang W. Green synthesis of chlorella-derived carbon dots and their fluorescence imaging in zebrafish. RSC Adv 2024; 14:1459-1463. [PMID: 38188260 PMCID: PMC10768801 DOI: 10.1039/d3ra07623g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024] Open
Abstract
Recently, carbon dots (CDs) have been shown to exhibit exceptional water solubility, low toxicity, favorable biocompatibility, stable fluorescence properties with a wide and continuous excitation spectrum, and an adjustable emission spectrum. Their remarkable characteristics make them highly promising for applications in the field of bioimaging. Zebrafish is currently extensively studied because of its high genetic homology with humans and the applicability of disease research findings from zebrafish to humans. Therefore, spirulina, a commonly used feed additive in aquaculture, was chosen as the raw material for synthesizing fluorescent CDs using a hydrothermal method. On the one hand, CDs can modulate dopamine receptors in the brain of zebrafish, leading to an increase in dopamine production and subsequently promoting their locomotor activity. On the other hand, CDs have been shown to enhance the intestinal anti-inflammatory capacity of zebrafish. This study aimed to explore the chronic toxicity and genotoxicity of CDs in zebrafish while providing valuable insights for their future application in biological and medical fields.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
| | - Zhihi Gu
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
| | - Jingyi Dong
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
| | - Jie Zhu
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
| | - Cunguang Liu
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
| | - Guohan Li
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
| | - Meichen Lu
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
| | - Jian Han
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
| | - Shengnan Cao
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
| | - Liyong Chen
- Department of Pharmaceutical Engineering, Bengbu Medical College Bengbu 233030 China
| | - Wei Wang
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University Dalian 116023 China
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3
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Umarov R, Hon CC. Enhancer target prediction: state-of-the-art approaches and future prospects. Biochem Soc Trans 2023; 51:1975-1988. [PMID: 37830459 DOI: 10.1042/bst20230917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023]
Abstract
Enhancers are genomic regions that regulate gene transcription and are located far away from the transcription start sites of their target genes. Enhancers are highly enriched in disease-associated variants and thus deciphering the interactions between enhancers and genes is crucial to understanding the molecular basis of genetic predispositions to diseases. Experimental validations of enhancer targets can be laborious. Computational methods have thus emerged as a valuable alternative for studying enhancer-gene interactions. A variety of computational methods have been developed to predict enhancer targets by incorporating genomic features (e.g. conservation, distance, and sequence), epigenomic features (e.g. histone marks and chromatin contacts) and activity measurements (e.g. covariations of enhancer activity and gene expression). With the recent advances in genome perturbation and chromatin conformation capture technologies, data on experimentally validated enhancer targets are becoming available for supervised training of these methods and evaluation of their performance. In this review, we categorize enhancer target prediction methods based on their rationales and approaches. Then we discuss their merits and limitations and highlight the future directions for enhancer targets prediction.
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Affiliation(s)
- Ramzan Umarov
- RIKEN Centre for Integrative Medical Sciences, Yokohama RIKEN Institute, Yokohama, Japan
| | - Chung-Chau Hon
- RIKEN Centre for Integrative Medical Sciences, Yokohama RIKEN Institute, Yokohama, Japan
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Jimenez Gonzalez A, Baranasic D, Müller F. Zebrafish regulatory genomic resources for disease modelling and regeneration. Dis Model Mech 2023; 16:dmm050280. [PMID: 37529920 PMCID: PMC10417509 DOI: 10.1242/dmm.050280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
In the past decades, the zebrafish has become a disease model with increasing popularity owing to its advantages that include fast development, easy genetic manipulation, simplicity for imaging, and sharing conserved disease-associated genes and pathways with those of human. In parallel, studies of disease mechanisms are increasingly focusing on non-coding mutations, which require genome annotation maps of regulatory elements, such as enhancers and promoters. In line with this, genomic resources for zebrafish research are expanding, producing a variety of genomic data that help in defining regulatory elements and their conservation between zebrafish and humans. Here, we discuss recent developments in generating functional annotation maps for regulatory elements of the zebrafish genome and how this can be applied to human diseases. We highlight community-driven developments, such as DANIO-CODE, in generating a centralised and standardised catalogue of zebrafish genomics data and functional annotations; consider the advantages and limitations of current annotation maps; and offer considerations for interpreting and integrating existing maps with comparative genomics tools. We also discuss the need for developing standardised genomics protocols and bioinformatic pipelines and provide suggestions for the development of analysis and visualisation tools that will integrate various multiomic bulk sequencing data together with fast-expanding data on single-cell methods, such as single-cell assay for transposase-accessible chromatin with sequencing. Such integration tools are essential to exploit the multiomic chromatin characterisation offered by bulk genomics together with the cell-type resolution offered by emerging single-cell methods. Together, these advances will build an expansive toolkit for interrogating the mechanisms of human disease in zebrafish.
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Affiliation(s)
- Ada Jimenez Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London SW7 2AZ, UK
- MRC London Institute of Medical Sciences, London W12 0NN, UK
- Division of Electronics, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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Tesfaye RA, Lavaud M, Charrier C, Brounais-Le Royer B, Cartron PF, Verrecchia F, Baud'huin M, Lamoureux F, Georges S, Ory B. Tracking Targets of Dynamic Super-Enhancers in Vitro to Better Characterize Osteoclastogenesis and to Evaluate the Effect of Diuron on the Maturation of Human Bone Cells. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:67007. [PMID: 37307168 DOI: 10.1289/ehp11690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Osteoclasts are major actors in the maintenance of bone homeostasis. The full functional maturation of osteoclasts from monocyte lineage cells is essential for the degradation of old/damaged bone matrix. Diuron is one of the most frequently encountered herbicides, particularly in water sources. However, despite a reported delayed ossification in vivo, its impact on bone cells remains largely unknown. OBJECTIVES The objectives of this study were to first better characterize osteoclastogenesis by identifying genes that drive the differentiation of CD14+ monocyte progenitors into osteoclasts and to evaluate the toxicity of diuron on osteoblastic and osteoclastic differentiation in vitro. METHODS We performed chromatin immunoprecipitation (ChIP) against H3K27ac followed by ChIP-sequencing (ChIP-Seq) and RNA-sequencing (RNA-Seq) at different stages of differentiation of CD14+ monocytes into active osteoclasts. Differentially activated super-enhancers and their potential target genes were identified. Then to evaluate the toxicity of diuron on osteoblasts and osteoclasts, we performed RNA-Seq and functional tests during in vitro osteoblastic and osteoclastic differentiation by exposing cells to different concentrations of diuron. RESULTS The combinatorial study of the epigenetic and transcriptional remodeling taking place during differentiation has revealed a very dynamic epigenetic profile that supports the expression of genes vital for osteoclast differentiation and function. In total, we identified 122 genes induced by dynamic super-enhancers at late days. Our data suggest that high concentration of diuron (50μM) affects viability of mesenchymal stem cells (MSCs) in vitro associated with a decrease of bone mineralization. At a lower concentration (1μM), an inhibitory effect was observed in vitro on the number of osteoclasts derived from CD14+ monocytes without affecting cell viability. Among the diuron-affected genes, our analysis suggests a significant enrichment of genes targeted by pro-differentiation super-enhancers, with an odds ratio of 5.12 (ρ=2.59×10-5). DISCUSSION Exposure to high concentrations of diuron decreased the viability of MSCs and could therefore affect osteoblastic differentiation and bone mineralization. This pesticide also disrupted osteoclasts maturation by impairing the expression of cell-identity determining genes. Indeed, at sublethal concentrations, differences in the expression of these key genes were mild during the course of in vitro osteoclast differentiation. Taken together our results suggest that high exposure levels of diuron could have an effect on bone homeostasis. https://doi.org/10.1289/EHP11690.
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Affiliation(s)
- Robel A Tesfaye
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
- Cancéropole Grand-Ouest, réseau Epigénétique, Nantes, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Melanie Lavaud
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Céline Charrier
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | | | - Pierre-François Cartron
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
- LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Cancéropole Grand-Ouest, réseau Epigénétique, Nantes, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Franck Verrecchia
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Marc Baud'huin
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - François Lamoureux
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Steven Georges
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Benjamin Ory
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
- Cancéropole Grand-Ouest, réseau Epigénétique, Nantes, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
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Lei P, Zhang W, Ma J, Xia Y, Yu H, Du J, Fang Y, Wang L, Zhang K, Jin L, Sun D, Zhong J. Advances in the Utilization of Zebrafish for Assessing and Understanding the Mechanisms of Nano-/Microparticles Toxicity in Water. TOXICS 2023; 11:380. [PMID: 37112607 PMCID: PMC10142380 DOI: 10.3390/toxics11040380] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 06/19/2023]
Abstract
A large amount of nano-/microparticles (MNPs) are released into water, not only causing severe water pollution, but also negatively affecting organisms. Therefore, it is crucial to evaluate MNP toxicity and mechanisms in water. There is a significant degree of similarity between the genes, the central nervous system, the liver, the kidney, and the intestines of zebrafish and the human body. It has been shown that zebrafish are exceptionally suitable for evaluating the toxicity and action mechanisms of MNPs in water on reproduction, the central nervous system, and metabolism. Providing ideas and methods for studying MNP toxicity, this article discusses the toxicity and mechanisms of MNPs from zebrafish.
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Affiliation(s)
- Pengyu Lei
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China (L.J.)
| | - Wenxia Zhang
- Department of Burn and Plastic Surgery, Zigong Fourth People’s Hospital, Zigong 643099, China
| | - Jiahui Ma
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China (L.J.)
| | - Yuping Xia
- Department of Burn and Plastic Surgery, Zigong Fourth People’s Hospital, Zigong 643099, China
| | - Haiyang Yu
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China (L.J.)
| | - Jiao Du
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China (L.J.)
| | - Yimeng Fang
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China (L.J.)
| | - Lei Wang
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China (L.J.)
| | - Kun Zhang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, China
| | - Libo Jin
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China (L.J.)
| | - Da Sun
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China (L.J.)
| | - Junbo Zhong
- Department of Burn and Plastic Surgery, Zigong Fourth People’s Hospital, Zigong 643099, China
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7
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McManus JN, Lovelett RJ, Lowengrub D, Christensen S. A unifying statistical framework to discover disease genes from GWASs. CELL GENOMICS 2023; 3:100264. [PMID: 36950381 PMCID: PMC10025450 DOI: 10.1016/j.xgen.2023.100264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/07/2022] [Accepted: 01/19/2023] [Indexed: 03/10/2023]
Abstract
Genome-wide association studies (GWASs) identify genomic loci associated with complex traits, but it remains a challenge to identify the genes affected by causal genetic variants in these loci. Attempts to solve this challenge are frustrated by a number of compounding problems. Here, we show how to combine solutions to these problems into a unified mathematical framework. From this synthesis, it becomes possible to compute the probability that each gene in the genome is affected by a causal variant, given a particular trait, without making assumptions about the relevant cell types or tissues. We validate each component of the framework individually and in combination. When applied to large GWASs of human disease, the resulting paradigm can rediscover the majority of well-known disease genes. Moreover, it establishes human genetics support for many genes previously implicated only by clinical or preclinical evidence, and it uncovers a plethora of novel disease genes with compelling biological rationale.
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Affiliation(s)
- Justin N.J. McManus
- Kallyope, Inc., 430 East 29th Street, New York, NY 10016, USA
- Corresponding author
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8
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Xiao Q, Xiao Y, Li LY, Chen MK, Wu M. Multifaceted regulation of enhancers in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194839. [PMID: 35750313 DOI: 10.1016/j.bbagrm.2022.194839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022]
Abstract
Enhancer is one kind of cis-elements regulating gene transcription, whose activity is tightly controlled by epigenetic enzymes and histone modifications. Active enhancers are classified into typical enhancers, super-enhancers and over-active enhancers, according to the enrichment and location of histone modifications. Epigenetic factors control the level of histone modifications on enhancers to determine their activity, such as histone methyltransferases and acetylases. Transcription factors, cofactors and mediators co-operate together and are required for enhancer functions. In turn, abnormalities in these trans-acting factors affect enhancer activity. Recent studies have revealed enhancer dysregulation as one of the important features for cancer. Variations in enhancer regions and mutations of enhancer regulatory genes are frequently observed in cancer cells, and altering the activity of onco-enhancers is able to repress oncogene expression, and suppress tumorigenesis and metastasis. Here we summarize the recent discoveries about enhancer regulation in cancer and discuss their potential application in diagnosis and treatment.
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Affiliation(s)
- Qiong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Yong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Ming-Kai Chen
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
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9
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Song C, Li W, Wang Z. The Landscape of Liver Chromatin Accessibility and Conserved Non-coding Elements in Larimichthys crocea, Nibea albiflora, and Lateolabrax maculatus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:763-775. [PMID: 35895229 DOI: 10.1007/s10126-022-10142-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Large yellow croaker (Larimichthys crocea), yellow drum (Nibea albiflora), and Chinese seabass (Lateolabrax maculatus) are important economic marine fishes in China. The conserved non-coding elements (CNEs) in the liver tissues of the three kinds of fish are directly or indirectly involved in the regulation of gene expression and affect liver functions. However, the fishes' CNEs and even chromatin accessibility landscape have not been effectively investigated. Hence, this study established the landscapes of the fishes' genome-wide chromatin accessibility and CNEs by detecting regions of the open chromatin in their livers using an assay for transposase-accessible chromatin by high-throughput sequencing (ATAC-seq) and comparative genomics approach. The results showed that Smad1, Sp1, and Foxl1 transcription factor binding motifs were considerably enriched in the chromatin accessibility landscape in the liver of the three species, and the three transcription factors (TFs) had a wide range of common targets. The hypothetical gene set was targeted by one, two, or all three TFs, which was much higher than would be expected for an accidental outcome. The gene sets near the CNEs were mainly enriched through processes such as a macromolecule metabolic process and ribonucleoprotein complex biogenesis. The active CNEs were found in the promoter regions of genes such as ap1g1, hax1, and ndufs2. And 5 CNEs were predicted to be highly conserved active enhancers. These results demonstrated that Smad1, Sp1, and Foxl1 might be related to the liver function in the three fishes. In addition, we found a series of ATAC-seq-labeled CNEs located in the gene promoter regions, and highly conserved H3k27ac + -labeled CNEs located in the liver function genes. The highly conserved nature of these regulatory elements suggests that they play important roles in the liver in fish. This study mined the landscape of chromatin accessibility and CNEs of three important economic fishes to fill the knowledge gaps in this field. Moreover, the work provides useful data for the industrial application and theoretical research of these three fish species.
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Affiliation(s)
- Chaowei Song
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao, China.
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10
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Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat Genet 2022; 54:1037-1050. [PMID: 35789323 PMCID: PMC9279159 DOI: 10.1038/s41588-022-01089-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
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Affiliation(s)
- Damir Baranasic
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Piotr J Balwierz
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tobias Zehnder
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Abdul Kadir Mukarram
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Chirag Nepal
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Csilla Várnai
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Ada Jimenez-Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nan Li
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joseph Wragg
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Fabio M D'Orazio
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Dorde Relic
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mikhail Pachkov
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Institute of Marine Sciences, Barcelona, Spain
| | | | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Marcus Stoiber
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michaël Dong
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Irene Stevens
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Samuel E Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Anne Eagle
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Ryan Martin
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Oluwapelumi Obasaju
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alison C McGarvey
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Wolfgang Kopp
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Emily Chambers
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Dennis Wang
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Hyejeong R Kim
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Vanessa Chong
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Liège, Belgium
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Fondazione Human Technopole, Milano, Italy
| | - Uwe Ohler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Scott Allen Lacadie
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Shawn M Burgess
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Freek van Eeden
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Daria Onichtchouk
- Department of Developmental Biology, Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ben James Brown
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Fiona C Wardle
- Randall Centre for Cell & Molecular Biophysics, Guy's Campus, King's College London, London, UK
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.
- Science for Life Laboratory, Solna, Sweden.
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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11
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Classification of non-coding variants with high pathogenic impact. PLoS Genet 2022; 18:e1010191. [PMID: 35486646 PMCID: PMC9094564 DOI: 10.1371/journal.pgen.1010191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 05/11/2022] [Accepted: 04/05/2022] [Indexed: 01/22/2023] Open
Abstract
Whole genome sequencing is increasingly used to diagnose medical conditions of genetic origin. While both coding and non-coding DNA variants contribute to a wide range of diseases, most patients who receive a WGS-based diagnosis today harbour a protein-coding mutation. Functional interpretation and prioritization of non-coding variants represents a persistent challenge, and disease-causing non-coding variants remain largely unidentified. Depending on the disease, WGS fails to identify a candidate variant in 20–80% of patients, severely limiting the usefulness of sequencing for personalised medicine. Here we present FINSURF, a machine-learning approach to predict the functional impact of non-coding variants in regulatory regions. FINSURF outperforms state-of-the-art methods, owing in particular to optimized control variants selection during training. In addition to ranking candidate variants, FINSURF breaks down the score for each variant into contributions from individual annotations, facilitating the evaluation of their functional relevance. We applied FINSURF to a diverse set of 30 diseases with described causative non-coding mutations, and correctly identified the disease-causative non-coding variant within the ten top hits in 22 cases. FINSURF is implemented as an online server to as well as custom browser tracks, and provides a quick and efficient solution to prioritize candidate non-coding variants in realistic clinical settings.
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12
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Qin T, Lee C, Li S, Cavalcante RG, Orchard P, Yao H, Zhang H, Wang S, Patil S, Boyle AP, Sartor MA. Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data. Genome Biol 2022; 23:105. [PMID: 35473573 PMCID: PMC9044877 DOI: 10.1186/s13059-022-02668-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Revealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cell types, while the accuracy of genome-wide approaches remains elusive due to the lack of a systematic evaluation. We combined multiple spatial and in silico approaches for defining enhancer locations and linking them to their target genes aggregated across >500 cell types, generating 1860 human genome-wide distal enhancer-to-target gene definitions (EnTDefs). To evaluate performance, we used gene set enrichment (GSE) testing on 87 independent ENCODE ChIP-seq datasets of 34 transcription factors (TFs) and assessed concordance of results with known TF Gene Ontology annotations, and other benchmarks. RESULTS The top ranked 741 (40%) EnTDefs significantly outperform the common, naïve approach of linking distal regions to the nearest genes, and the top 10 EnTDefs perform well when applied to ChIP-seq data of other cell types. The GSE-based ranking of EnTDefs is highly concordant with ranking based on overlap with curated benchmarks of enhancer-gene interactions. Both our top general EnTDef and cell-type-specific EnTDefs significantly outperform seven independent computational and experiment-based enhancer-gene pair datasets. We show that using our top EnTDefs for GSE with either genome-wide DNA methylation or ATAC-seq data is able to better recapitulate the biological processes changed in gene expression data performed in parallel for the same experiment than our lower-ranked EnTDefs. CONCLUSIONS Our findings illustrate the power of our approach to provide genome-wide interpretation regardless of cell type.
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Affiliation(s)
- Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Christopher Lee
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shiting Li
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Raymond G Cavalcante
- Biomedical Research Core Facilities, Epigenomics Core, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Heming Yao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hanrui Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shuze Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Snehal Patil
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alan P Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Biostatistics, School of Public Health, University of Michigan Medical School, Ann Arbor, MI, USA.
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13
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Sepehri Z, Banerjee A, Vizeacoumar FS, Freywald A, Vizeacoumar FJ, Dolinsky VW, Davie JR. Differential expression of
HNF1A
and
HNF1A‐AS1
in colon cancer cells. IUBMB Life 2022; 74:496-507. [DOI: 10.1002/iub.2609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Zahra Sepehri
- Department of Biochemistry and Medical Genetics University of Manitoba Winnipeg Manitoba Canada
- Department of Internal Medicine Zabol University of Medical Sciences Zabol Iran
| | - Archana Banerjee
- Division of Oncology, College of Medicine University of Saskatchewan Saskatoon SK Canada
- Cancer Research Department, Saskatchewan Cancer Agency, 107 Wiggins Road Saskatoon SK Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive Saskatoon SK Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine College of Medicine, University of Saskatchewan, Room 2841, Royal University Hospital, 103 Hospital Drive Saskatoon SK Canada
| | - Franco J. Vizeacoumar
- Division of Oncology, College of Medicine University of Saskatchewan Saskatoon SK Canada
- Cancer Research Department, Saskatchewan Cancer Agency, 107 Wiggins Road Saskatoon SK Canada
| | - Vernon W. Dolinsky
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba Winnipeg MB Canada
- Department of Pharmacology and Therapeutics University of Manitoba Winnipeg MB Canada
| | - James R. Davie
- Department of Biochemistry and Medical Genetics University of Manitoba Winnipeg Manitoba Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba Winnipeg Manitoba Canada
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14
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Functional Validation of Osteoporosis Genetic Findings Using Small Fish Models. Genes (Basel) 2022; 13:genes13020279. [PMID: 35205324 PMCID: PMC8872034 DOI: 10.3390/genes13020279] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022] Open
Abstract
The advancement of human genomics has revolutionized our understanding of the genetic architecture of many skeletal diseases, including osteoporosis. However, interpreting results from human association studies remains a challenge, since index variants often reside in non-coding regions of the genome and do not possess an obvious regulatory function. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary, such as the one offered by animal models. These models enable us to identify causal mechanisms, clarify the underlying biology, and apply interventions. Over the past several decades, small teleost fishes, mostly zebrafish and medaka, have emerged as powerful systems for modeling the genetics of human diseases. Due to their amenability to genetic intervention and the highly conserved genetic and physiological features, fish have become indispensable for skeletal genomic studies. The goal of this review is to summarize the evidence supporting the utility of Zebrafish (Danio rerio) for accelerating our understanding of human skeletal genomics and outlining the remaining gaps in knowledge. We provide an overview of zebrafish skeletal morphophysiology and gene homology, shedding light on the advantages of human skeletal genomic exploration and validation. Knowledge of the biology underlying osteoporosis through animal models will lead to the translation into new, better and more effective therapeutic approaches.
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15
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Laverre A, Tannier E, Necsulea A. Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness. Genome Res 2021; 32:280-296. [PMID: 34930799 PMCID: PMC8805723 DOI: 10.1101/gr.275901.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022]
Abstract
Gene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements are rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Here, we address these questions by comparing genome-wide maps of promoter-centered chromatin contacts in mouse and human. We show that there is significant evolutionary conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter–enhancer contacts, illustrating how the structure of regulatory landscapes constrains large-scale genome evolution. We show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny, or contacts with target genes, is significantly associated with gene expression evolution.
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Affiliation(s)
- Alexandre Laverre
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive
| | - Eric Tannier
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Centre de recherche Inria de Lyon
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16
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Role of Non-Coding Regulatory Elements in the Control of GR-Dependent Gene Expression. Int J Mol Sci 2021; 22:ijms22084258. [PMID: 33923915 PMCID: PMC8073421 DOI: 10.3390/ijms22084258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 11/17/2022] Open
Abstract
The glucocorticoid receptor (GR, also known as NR3C1) coordinates molecular responses to stress. It is a potent transcription activator and repressor that influences hundreds of genes. Enhancers are non-coding DNA regions outside of the core promoters that increase transcriptional activity via long-distance interactions. Active GR binds to pre-existing enhancer sites and recruits further factors, including EP300, a known transcriptional coactivator. However, it is not known how the timing of GR-binding-induced enhancer remodeling relates to transcriptional changes. Here we analyze data from the ENCODE project that provides ChIP-Seq and RNA-Seq data at distinct time points after dexamethasone exposure of human A549 epithelial-like cell line. This study aimed to investigate the temporal interplay between GR binding, enhancer remodeling, and gene expression. By investigating a single distal GR-binding site for each differentially upregulated gene, we show that transcriptional changes follow GR binding, and that the largest enhancer remodeling coincides in time with the highest gene expression changes. A detailed analysis of the time course showed that for upregulated genes, enhancer activation persists after gene expression changes settle. Moreover, genes with the largest change in EP300 binding showed the highest expression dynamics before the peak of EP300 recruitment. Overall, our results show that enhancer remodeling may not directly be driving gene expression dynamics but rather be a consequence of expression activation.
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17
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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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18
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Giudicelli F, Roest Crollius H. On the importance of evolutionary constraint for regulatory sequence identification. Brief Funct Genomics 2021:elab015. [PMID: 33754633 DOI: 10.1093/bfgp/elab015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/15/2021] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression relies on the activity of specialized genomic elements, enhancers or silencers, distributed over sometimes large distance from their target gene promoters. A significant part of vertebrate genomes consists in such regulatory elements, but their identification and that of their target genes remains challenging, due to the lack of clear signature at the nucleotide level. For many years the main hallmark used for identifying functional elements has been their sequence conservation between genomes of distant species, indicative of purifying selection. More recently, genome-wide biochemical assays have opened new avenues for detecting regulatory regions, shifting attention away from evolutionary constraints. Here, we review the respective contributions of comparative genomics and biochemical assays for the definition of regulatory elements and their targets and advocate that both sequence conservation and preserved synteny, taken as signature of functional constraint, remain essential tools in this task.
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19
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Yuan X, Scott IC, Wilson MD. Heart Enhancers: Development and Disease Control at a Distance. Front Genet 2021; 12:642975. [PMID: 33777110 PMCID: PMC7987942 DOI: 10.3389/fgene.2021.642975] [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] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bound by lineage-determining transcription factors and signaling effectors, enhancers play essential roles in controlling spatiotemporal gene expression profiles during development, homeostasis and disease. Recent synergistic advances in functional genomic technologies, combined with the developmental biology toolbox, have resulted in unprecedented genome-wide annotation of heart enhancers and their target genes. Starting with early studies of vertebrate heart enhancers and ending with state-of-the-art genome-wide enhancer discovery and testing, we will review how studying heart enhancers in metazoan species has helped inform our understanding of cardiac development and disease.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian C. Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D. Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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20
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Powell DL, Payne C, Banerjee SM, Keegan M, Bashkirova E, Cui R, Andolfatto P, Rosenthal GG, Schumer M. The Genetic Architecture of Variation in the Sexually Selected Sword Ornament and Its Evolution in Hybrid Populations. Curr Biol 2021; 31:923-935.e11. [PMID: 33513352 DOI: 10.1016/j.cub.2020.12.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
Biologists since Darwin have been fascinated by the evolution of sexually selected ornaments, particularly those that reduce viability. Uncovering the genetic architecture of these traits is key to understanding how they evolve and are maintained. Here, we investigate the genetic architecture and evolutionary loss of a sexually selected ornament, the "sword" fin extension that characterizes many species of swordtail fish (Xiphophorus). Using sworded and swordless sister species of Xiphophorus, we generated a mapping population and show that the sword ornament is polygenic-with ancestry across the genome explaining substantial variation in the trait. After accounting for the impacts of genome-wide ancestry, we identify one major-effect quantitative trait locus (QTL) that explains ~5% of the overall variation in the trait. Using a series of approaches, we narrow this large QTL interval to several likely candidate genes, including genes involved in fin regeneration and growth. Furthermore, we find evidence of selection on ancestry at one of these candidates in four natural hybrid populations, consistent with selection against the sword in these populations.
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Affiliation(s)
- Daniel L Powell
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA.
| | - Cheyenne Payne
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Shreya M Banerjee
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Mackenzie Keegan
- Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Elizaveta Bashkirova
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, New York, NY 10032, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY 10032, USA
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA; Max Planck Institute for the Biology of Aging, Postfach 41 06 23, 50931 Cologne, Germany; School of Ecology, Sun Yat-sen University, 135 Xingang West Road, Binjiang Road, Haizhu District, Guangdong Province, China
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA
| | - Molly Schumer
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Howard Hughes Medical Institute, 327 Campus Drive, Stanford, CA 94305, USA.
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21
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Zrimec J, Börlin CS, Buric F, Muhammad AS, Chen R, Siewers V, Verendel V, Nielsen J, Töpel M, Zelezniak A. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nat Commun 2020; 11:6141. [PMID: 33262328 PMCID: PMC7708451 DOI: 10.1038/s41467-020-19921-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression levels remains unclear. Here we apply deep learning on over 20,000 mRNA datasets to examine the genetic regulatory code controlling mRNA abundance in 7 model organisms ranging from bacteria to Human. In all organisms, we can predict mRNA abundance directly from DNA sequence, with up to 82% of the variation of transcript levels encoded in the gene regulatory structure. By searching for DNA regulatory motifs across the gene regulatory structure, we discover that motif interactions could explain the whole dynamic range of mRNA levels. Co-evolution across coding and non-coding regions suggests that it is not single motifs or regions, but the entire gene regulatory structure and specific combination of regulatory elements that define gene expression levels.
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Affiliation(s)
- Jan Zrimec
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Christoph S Börlin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Filip Buric
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Azam Sheikh Muhammad
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Rhongzen Chen
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Vilhelm Verendel
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center (GGBC), Box 461, 40530, Gothenburg, Sweden
| | - Aleksej Zelezniak
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23a, SE-171 65, Stockholm, Sweden.
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22
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Beacon TH, Delcuve GP, Davie JR. Epigenetic regulation of ACE2, the receptor of the SARS-CoV-2 virus 1. Genome 2020; 64:386-399. [PMID: 33086021 DOI: 10.1139/gen-2020-0124] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The angiotensin-converting enzyme 2 (ACE2) is the receptor for the three coronaviruses HCoV-NL63, SARS-CoV, and SARS-CoV-2. ACE2 is involved in the regulation of the renin-angiotensin system and blood pressure. ACE2 is also involved in the regulation of several signaling pathways, including integrin signaling. ACE2 expression is regulated transcriptionally and post-transcriptionally. The expression of the gene is regulated by two promoters, with usage varying among tissues. ACE2 expression is greatest in the small intestine, kidney, and heart and detectable in a variety of tissues and cell types. Herein we review the chemical and mechanical signal transduction pathways regulating the expression of the ACE2 gene and the epigenetic/chromatin features of the expressed gene.
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Affiliation(s)
- Tasnim H Beacon
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Geneviève P Delcuve
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
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23
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Abstract
Sarcopenia – the accelerated age-related loss of muscle mass and function – is an under-diagnosed condition, and is central to deteriorating mobility, disability and frailty in older age. There is a lack of treatment options for older adults at risk of sarcopenia. Although sarcopenia's pathogenesis is multifactorial, its major phenotypes – muscle mass and muscle strength – are highly heritable. Several genome-wide association studies of muscle-related traits were published recently, providing dozens of candidate genes, many with unknown function. Therefore, animal models are required not only to identify causal mechanisms, but also to clarify the underlying biology and translate this knowledge into new interventions. Over the past several decades, small teleost fishes had emerged as powerful systems for modeling the genetics of human diseases. Owing to their amenability to rapid genetic intervention and the large number of conserved genetic and physiological features, small teleosts – such as zebrafish, medaka and killifish – have become indispensable for skeletal muscle genomic studies. The goal of this Review is to summarize evidence supporting the utility of small fish models for accelerating our understanding of human skeletal muscle in health and disease. We do this by providing a basic foundation of the (zebra)fish skeletal muscle morphology and physiology, and evidence of muscle-related gene homology. We also outline challenges in interpreting zebrafish mutant phenotypes and in translating them to human disease. Finally, we conclude with recommendations on future directions to leverage the large body of tools developed in small fish for the needs of genomic exploration in sarcopenia. Summary: Zebrafish and other small fish have become powerful disease models. Here, we summarize the evidence for the utility of small teleost models for genetic research in sarcopenia – the age-related loss of muscle mass and function.
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Affiliation(s)
- Alon Daya
- The Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel
| | - Rajashekar Donaka
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 130010, Israel
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 130010, Israel .,Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA 02131, USA
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24
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Xu H, Zhang S, Yi X, Plewczynski D, Li MJ. Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction. Comput Struct Biotechnol J 2020; 18:558-570. [PMID: 32226593 PMCID: PMC7090358 DOI: 10.1016/j.csbj.2020.02.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 12/12/2022] Open
Abstract
Mechanisms underlying gene regulation are key to understand how multicellular organisms with various cell types develop from the same genetic blueprint. Dynamic interactions between enhancers and genes are revealed to play central roles in controlling gene transcription, but the determinants to link functional enhancer-promoter pairs remain elusive. A major challenge is the lack of reliable approach to detect and verify functional enhancer-promoter interactions (EPIs). In this review, we summarized the current methods for detecting EPIs and described how developing techniques facilitate the identification of EPI through assessing the merits and drawbacks of these methods. We also reviewed recent state-of-art EPI prediction methods in terms of their rationale, data usage and characterization. Furthermore, we briefly discussed the evolved strategies for validating functional EPIs.
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Affiliation(s)
- Hang Xu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Shijie Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
| | - Mulin Jun Li
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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