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Stojak J, Rocha D, Mörke C, Kühn C, Blanquet V, Taniguchi H. Establishment of a cloning-free CRISPR/Cas9 protocol to generate large deletions in the bovine MDBK cell line. J Appl Genet 2024; 65:399-402. [PMID: 38418802 PMCID: PMC11003909 DOI: 10.1007/s13353-024-00846-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/11/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
The CRISPR/Cas9 technique applied to modify the cattle genome has value in increasing animal health and welfare. Here, we established a simple, fast, and efficient cloning-free CRISPR/Cas9 protocol for large deletions of genomic loci in the frequently used model bovine MDBK cell line. The main advantages of our protocol are as follows: (i) pre-screening of the sgRNA efficiency with a fast and simple cleavage assay, (ii) reliable detection of genomic edits primarily by PCR and confirmed by DNA sequencing, and (iii) single cell sorting with FACS providing specific genetic information from modified cells of interest. Therefore, our method could be successfully applied in different studies, including functional validation of any genetic or regulatory elements.
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Affiliation(s)
- Joanna Stojak
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, Poland.
| | - Dominique Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Caroline Mörke
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Christa Kühn
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Agricultural and Environmental Faculty, University Rostock, 18059, Rostock, Germany
- Friedrich-Loeffler-Institut (FLI), 17493, Greifswald, Insel Riems, Germany
| | - Veronique Blanquet
- Faculté Des Sciences Et Techniques, University of Limoges, 123 Avenue Albert Thomas, 87060, Limoges, France
| | - Hiroaki Taniguchi
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, Poland.
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, 43150, Ben Guerir, Morocco.
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2
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Li X, Liu Q, Fu C, Li M, Li C, Li X, Zhao S, Zheng Z. Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption. J Genet Genomics 2024; 51:394-406. [PMID: 38056526 DOI: 10.1016/j.jgg.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Structural variants (SVs), such as deletions (DELs) and insertions (INSs), contribute substantially to pig genetic diversity and phenotypic variation. Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes, we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes. Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation. Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements. We identify that the genotypes of two DELs (296-bp DEL, chr7: 52,172,101-52,172,397; 278-bp DEL, chr18: 23,840,143-23,840,421) located in muscle-specific enhancers are associated with the expression of target genes related to meat quality (FSD2) and muscle fiber hypertrophy (LMOD2 and WASL) in pigs. Our results highlight the role of SVs in domestic porcine evolution, and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.
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Affiliation(s)
- Xin Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Quan Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Chong Fu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mengxun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Changchun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
| | - Zhuqing Zheng
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Agricultural Biotechnology, Jingchu University of Technology, Jingmen, Hubei 448000, China.
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Mebrahtu A, Aniander G, Mega A, Moradi Barzadd M, Berndt Thalén N, Gudmundsdotter L, Backström Rydin E, Sandegren A, Frejd FY, Rockberg J. Co-culture platform for tuning of cancer receptor density allows for evaluation of bispecific immune cell engagers. N Biotechnol 2024; 79:120-126. [PMID: 38159596 DOI: 10.1016/j.nbt.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Cancer immunotherapy, where a patient's immune system is harnessed to eradicate cancer cells selectively, is a leading strategy for cancer treatment. However, successes with immune checkpoint inhibitors (ICI) are hampered by reported systemic and organ-specific toxicities and by two-thirds of the patients being non-responders or subsequently acquiring resistance to approved ICIs. Hence substantial efforts are invested in discovering novel targeted immunotherapies aimed at reduced side-effects and improved potency. One way is utilizing the dual targeting feature of bispecific antibodies, which have made them increasingly popular for cancer immunotherapy. Easy and predictive screening methods for activation ranking of candidate drugs in tumor contra non-tumor environments are however lacking. Herein, we present a cell-based assay mimicking the tumor microenvironment by co-culturing B cells with engineered human embryonic kidney 293 T cells (HEK293T), presenting a controllable density of platelet-derived growth factor receptor β (PDGFRβ). A target density panel with three different surface protein levels on HEK293T cells was established by genetic constructs carrying regulatory elements limiting RNA translation of PDGFRβ. We employed a bispecific antibody-affibody construct called an AffiMab capable of binding PDGFRβ on cancer cells and CD40 expressed by B cells as a model. Specific activation of CD40-mediated signaling of immune cells was demonstrated with the two highest receptor-expressing cell lines, Level 2/3 and Level 4, while low-to-none in the low-expressing cell lines. The concept of receptor tuning and the presented co-culture protocol may be of general utility for assessing and developing novel bi-specific antibodies for immuno-oncology applications.
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Affiliation(s)
- Aman Mebrahtu
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden
| | - Gustav Aniander
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden
| | - Alessandro Mega
- Affibody Medical AB, Scheeles väg 2, SE-171 65 Solna, Sweden
| | - Mona Moradi Barzadd
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden
| | - Niklas Berndt Thalén
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden
| | | | | | - Anna Sandegren
- Affibody Medical AB, Scheeles väg 2, SE-171 65 Solna, Sweden
| | - Fredrik Y Frejd
- Affibody Medical AB, Scheeles väg 2, SE-171 65 Solna, Sweden
| | - Johan Rockberg
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Dept. of Protein Science, SE-106 91 Stockholm, Sweden.
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Breeze CE, Haugen E, Gutierrez-Arcelus M, Yao X, Teschendorff A, Beck S, Dunham I, Stamatoyannopoulos J, Franceschini N, Machiela MJ, Berndt SI. FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome Biol 2024; 25:3. [PMID: 38167104 PMCID: PMC10763681 DOI: 10.1186/s13059-023-03126-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mechanisms for further functional experiments can be challenging. To address this challenge, we developed FORGEdb ( https://forgedb.cancer.gov/ ; https://forge2.altiusinstitute.org/files/forgedb.html ; and https://doi.org/10.5281/zenodo.10067458 ), a standalone and web-based tool that integrates multiple datasets, delivering information on associated regulatory elements, transcription factor binding sites, and target genes for over 37 million variants. FORGEdb scores provide researchers with a quantitative assessment of the relative importance of each variant for targeted functional experiments.
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Affiliation(s)
- Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue 98121, Seattle, USA.
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue 98121, Seattle, USA
| | - María Gutierrez-Arcelus
- Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaozheng Yao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew Teschendorff
- CAS Key Lab of Computational Biology, Shanghai Institute for Biological Sciences, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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Muley VY. Prediction and Analysis of Transcription Factor Binding Sites: Practical Examples and Case Studies Using R Programming. Methods Mol Biol 2024; 2719:199-225. [PMID: 37803120 DOI: 10.1007/978-1-0716-3461-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Transcription factors (TFs) bind to specific regions of DNA known as transcription factor binding sites (TFBSs) and modulate gene expression by interacting with the transcriptional machinery. TFBSs are typically located upstream of target genes, within a few thousand base pairs of the transcription start site. The binding of TFs to TFBSs influences the recruitment of the transcriptional machinery, thereby regulating gene transcription in a precise and specific manner. This chapter provides practical examples and case studies demonstrating the extraction of upstream gene regions from the genome, identification of TFBSs using PWMEnrich R/Bioconductor package, interpretation of results, and preparation of publication-ready figures and tables. The EOMES promoter is used as a case study for single DNA sequence analysis, revealing potential regulation by the LHX9-FOXP1 complex during embryonic development. Additionally, an example is presented on how to investigate TFBSs in the upstream regions of a group of genes, using a case study of differentially expressed genes in response to human parainfluenza virus type 1 (HPIV1) infection and interferon-beta. Key regulators identified in this context include the STAT1:STAT2 heterodimer and interferon regulatory factor family proteins. The presented protocol is designed to be accessible to individuals with basic computer literacy. Understanding the interactions between TFs and TFBSs provides insights into the complex transcriptional regulatory networks that govern gene expression, with broad implications for several fields such as developmental biology, immunology, and disease research.
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Affiliation(s)
- Vijaykumar Yogesh Muley
- Independent Researcher, Hingoli, India
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
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Wang W, Sun Y, Xu P, Liang H, Wang Y, Deng D, Cao J, Yu M. Epigenomic analysis of the myometrium during late implantation revealed regulatory elements in genes related to the cellular zinc homeostasis pathway in pigs. Genomics 2024; 116:110768. [PMID: 38128703 DOI: 10.1016/j.ygeno.2023.110768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/31/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
The myometrium, composed of the inner circular muscle (CM) and outer longitudinal muscle (LM), is crucial in establishing and maintaining early pregnancy. However, the molecular mechanisms involved are not well understood. In this study, we identified the transcriptomic features of the CM and LM collected from the mesometrial (M) and anti-mesometrial (AM) sides of the pig uterus on day 18 of pregnancy during the placentation initiation phase. Some genes in the cellular zinc ion level regulatory pathways (MT-1A, MT-1D, MT-2B, SLC30A2, and SLC39A2) were spatially and highly enriched in uterine CM at the mesometrial side. In addition, the histone modification profiles of H3K27ac and H3K4me3 in uterine CM and LM collected from the mesometrial side were characterized. Genomic regions associated with the expression of genes regulating the cellular zinc ion level were detected. Moreover, six highly linked variants in the H3K27ac-enriched region of the pig SLC30A2 gene were identified and found to be significantly associated with the total number born at the second parity (P < 0.05). In conclusion, the genes in the pathways of cellular zinc homeostasis and their regulatory elements identified have implications for pig reproduction trait improvement and warrant further investigations.
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Affiliation(s)
- Weiwei Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yan Sun
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Pengfei Xu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hao Liang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yue Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dadong Deng
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jianhua Cao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Mei Yu
- Frontiers Science Center for Animal Breeding and Sustainable Production (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China.
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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Hoolehan W, Kulpa AM, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. Epigenetics Chromatin 2023; 16:45. [PMID: 37953264 PMCID: PMC10642035 DOI: 10.1186/s13072-023-00522-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation, DNA modifications in particular, of gene expression between neurons and glia. RESULTS After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT-whole genome oxidative bisulfite sequencing (WGoxBS) to assess the neuronal translatome and epigenome in the hippocampus of young mice (4 months old). WGoxBS findings were validated with enzymatic methyl-Seq (EM-Seq) and nanopore sequencing. Comparing neuronal data to microglial and astrocytic data from NuTRAP models, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, rather than proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of gene body mCG and a positive relationship between distal promoter and gene body hmCG with gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. CONCLUSIONS Neurons, astrocytes, and microglia demonstrate different genome-wide levels of mCG, hmCG, and mCH that are reproducible across analytical methods. However, modification-gene expression relationships are conserved across cell types. Enrichment of differential modifications across cell types in gene bodies and distal regulatory elements, but not proximal promoters, highlights epigenomic patterning in these regions as potentially greater determinants of cell identity. These findings also demonstrate the importance of differentiating between mC and hmC in neuroepigenomic analyses, as up to 30% of what is conventionally interpreted as mCG can be hmCG, which often has a different relationship to gene expression than mCG.
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Affiliation(s)
- Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Ana J Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adeline H Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Kevin D Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Walker Hoolehan
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adam M Kulpa
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Willard M Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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Li Y, Chen J, Zheng Y, Chen Z, Wang T, Sun Q, Wan X, Liu H, Sun X. A novel microdeletion of 517 kb downstream of the PAX6 gene in a Chinese family with congenital aniridia. BMC Ophthalmol 2023; 23:393. [PMID: 37752489 PMCID: PMC10523764 DOI: 10.1186/s12886-023-03147-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND To identify the disease-causing gene in a Chinese family affected with congenital aniridia. METHODS Patients underwent systematic ophthalmic examinations such as anterior segment photography, fundus photography, optical coherence tomography, and fundus fluorescein angiography. The proband was screened for pathogenic variants by whole exome sequencing (WES) and copy number variant (CNV) analysis. Real-time quantitative PCR (RT-qPCR) was applied to confirm the CNV results. Breakpoints were identified by long-range PCR followed by Sanger sequencing. RESULTS All seven members of this Chinese family, including four patients and three normal individuals, were recruited for this study. All patients showed bilateral congenital aniridia with nystagmus, except the son of the proband, who presented with bilateral partial coloboma of the iris. A novel heterozygous deletion (chr11:31,139,019-31,655,997) containing the 3' regulatory enhancers of the PAX6 gene was detected in this family. We also reviewed the reported microdeletions downstream of PAX6 in patients with aniridia. CONCLUSIONS We identified a novel microdeletion, 517 kb in size located about 133 kb downstream of the PAX6 gene, responsible for congenital aniridia in this Chinese family, which expands the spectrum of aniridia-associated mutations in PAX6.
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Affiliation(s)
- Yinwen Li
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Jieqiong Chen
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Ying Zheng
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Zhixuan Chen
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Tao Wang
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Qian Sun
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xiaoling Wan
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
- National Clinical Research Center for Eye Diseases, Shanghai, China.
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China.
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.
| | - Haiyun Liu
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
- National Clinical Research Center for Eye Diseases, Shanghai, China.
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China.
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.
| | - Xiaodong Sun
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
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São José C, Garcia-Pelaez J, Ferreira M, Arrieta O, André A, Martins N, Solís S, Martínez-Benítez B, Ordóñez-Sánchez ML, Rodríguez-Torres M, Sommer AK, Te Paske IBAW, Caldas C, Tischkowitz M, Tusié MT, Hoogerbrugge N, Demidov G, de Voer RM, Laurie S, Oliveira C. Combined loss of CDH1 and downstream regulatory sequences drive early-onset diffuse gastric cancer and increase penetrance of hereditary diffuse gastric cancer. Gastric Cancer 2023; 26:653-666. [PMID: 37249750 PMCID: PMC10361908 DOI: 10.1007/s10120-023-01395-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/30/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND Germline CDH1 pathogenic or likely pathogenic variants cause hereditary diffuse gastric cancer (HDGC). Once a genetic cause is identified, stomachs' and breasts' surveillance and/or prophylactic surgery is offered to asymptomatic CDH1 carriers, which is life-saving. Herein, we characterized an inherited mechanism responsible for extremely early-onset gastric cancer and atypical HDGC high penetrance. METHODS Whole-exome sequencing (WES) re-analysis was performed in an unsolved HDGC family. Accessible chromatin and CDH1 promoter interactors were evaluated in normal stomach by ATAC-seq and 4C-seq, and functional analysis was performed using CRISPR-Cas9, RNA-seq and pathway analysis. RESULTS We identified a germline heterozygous 23 Kb CDH1-TANGO6 deletion in a family with eight diffuse gastric cancers, six before age 30. Atypical HDGC high penetrance and young cancer-onset argued towards a role for the deleted region downstream of CDH1, which we proved to present accessible chromatin, and CDH1 promoter interactors in normal stomach. CRISPR-Cas9 edited cells mimicking the CDH1-TANGO6 deletion display the strongest CDH1 mRNA downregulation, more impacted adhesion-associated, type-I interferon immune-associated and oncogenic signalling pathways, compared to wild-type or CDH1-deleted cells. This finding solved an 18-year family odyssey and engaged carrier family members in a cancer prevention pathway of care. CONCLUSION In this work, we demonstrated that regulatory elements lying down-stream of CDH1 are part of a chromatin network that control CDH1 expression and influence cell transcriptome and associated signalling pathways, likely explaining high disease penetrance and very young cancer-onset. This study highlights the importance of incorporating scientific-technological updates and clinical guidelines in routine diagnosis, given their impact in timely genetic diagnosis and disease prevention.
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Affiliation(s)
- Celina São José
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - José Garcia-Pelaez
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Marta Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Department Computer Science Faculty of Science, University of Porto, Porto, Portugal
| | - Oscar Arrieta
- Thoracic Oncology Unit, Department of Thoracic Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Ana André
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Nelson Martins
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
- Master Programme in Molecular Medicine and Oncology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Samantha Solís
- INCMNSZ/Instituto de Investigaciones Biomédicas, Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, UNAM Mexico City, Mexico
| | - Braulio Martínez-Benítez
- Pathology Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, INCMNSZ Mexico City, Mexico
| | - María Luisa Ordóñez-Sánchez
- INCMNSZ/Instituto de Investigaciones Biomédicas, Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, UNAM Mexico City, Mexico
| | - Maribel Rodríguez-Torres
- INCMNSZ/Instituto de Investigaciones Biomédicas, Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, UNAM Mexico City, Mexico
| | - Anna K Sommer
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Iris B A W Te Paske
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre (ECMC), CRUK Cambridge Centre, NIHR Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Maria Teresa Tusié
- INCMNSZ/Instituto de Investigaciones Biomédicas, Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, UNAM Mexico City, Mexico
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, Tübingen, Germany
| | - Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Steve Laurie
- The Barcelona Institute of Science and Technology, CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Carla Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
- FMUP-Faculty of Medicine of the University of Porto, Porto, Portugal.
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10
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Berres S, Gromoll J, Wöste M, Sandmann S, Laurentino S. OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations. BMC Bioinformatics 2023; 24:300. [PMID: 37496002 PMCID: PMC10369718 DOI: 10.1186/s12859-023-05422-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/18/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Modern genome sequencing leads to an ever-growing collection of genomic annotations. Combining these elements with a set of input regions (e.g. genes) would yield new insights in genomic associations, such as those involved in gene regulation. The required data are scattered across different databases making a manual approach tiresome, unpractical, and prone to error. Semi-automatic approaches require programming skills in data parsing, processing, overlap calculation, and visualization, which most biomedical researchers lack. Our aim was to develop an automated tool providing all necessary algorithms, benefiting both bioinformaticians and researchers without bioinformatic training. RESULTS We developed overlapping annotated genomic regions (OGRE) as a comprehensive tool to associate and visualize input regions with genomic annotations. It does so by parsing regions of interest, mining publicly available annotations, and calculating possible overlaps between them. The user can thus identify location, type, and number of associated regulatory elements. Results are presented as easy to understand visualizations and result tables. We applied OGRE to recent studies and could show high reproducibility and potential new insights. To demonstrate OGRE's performance in terms of running time and output, we have conducted a benchmark and compared its features with similar tools. CONCLUSIONS OGRE's functions and built-in annotations can be applied as a downstream overlap association step, which is compatible with most genomic sequencing outputs, and can thus enrich pre-existing analyses pipelines. Compared to similar tools, OGRE shows competitive performance, offers additional features, and has been successfully applied to two recent studies. Overall, OGRE addresses the lack of tools for automatic analysis, local genomic overlap calculation, and visualization by providing an easy to use, end-to-end solution for both biologists and computational scientists.
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Affiliation(s)
- Sven Berres
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany
| | - Jörg Gromoll
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1 Building A11, 48149, Munster, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1 Building A11, 48149, Munster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany.
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11
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Zhou LY, Zhang S, Li LY, Yang GY, Zeng L. Optimization of mammalian expression vector by cis-regulatory element combinations. Mol Genet Genomics 2023:10.1007/s00438-023-02042-0. [PMID: 37318628 DOI: 10.1007/s00438-023-02042-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
The regulation of gene expression in mammalian cells by combining various cis-regulatory features has rarely been discussed. In this study, we constructed expression vectors containing various combinations of regulatory elements to examine the regulation of gene expression by different combinations of cis-regulatory elements. The effects of four promoters (CMV promoter, PGK promoter, Polr2a promoter, and EF-1α core promoter), two enhancers (CMV enhancer and SV40 enhancer), two introns (EF-1α intron A and hybrid intron), two terminators (CYC1 terminator and TEF terminator), and their different combinations on downstream gene expression were compared in various mammalian cells using fluorescence microscopy to observe fluorescence, quantitative real-time PCR (qRT-PCR), and western blot. The receptor binding domain (RBD) sequence from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein was used to replace the eGFP sequence in the expression vector and the RBD expression was detected by qRT-PCR and western blot. The results showed that protein expression can be regulated by optimizing the combination of cis-acting elements. The vector with the CMV enhancer, EF-1α core promoter, and TEF terminator was found to express approximately threefold higher eGFP than the unmodified vector in different animal cells, as well as 2.63-fold higher recombinant RBD protein than the original vector in HEK-293T cells. Moreover, we suggest that combinations of multiple regulatory elements capable of regulating gene expression do not necessarily exhibit synergistic effects to enhance expression further. Overall, our findings provide insights into biological applications that require the regulation of gene expression and will help to optimize expression vectors for biosynthesis and other fields. Additionally, we provide valuable insights into the production of RBD proteins, which may aid in developing reagents for diagnosis and treatment during the COVID-19 pandemic.
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Affiliation(s)
- Lu-Yu Zhou
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China
| | - Shuang Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China
| | - Li-Yun Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China
| | - Guo-Yu Yang
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China
| | - Lei Zeng
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China.
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China.
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China.
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12
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Abulfaraj AA. Relationships between some transcription factors and concordantly expressed drought stress-related genes in bread wheat. Saudi J Biol Sci 2023; 30:103652. [PMID: 37206446 PMCID: PMC10189290 DOI: 10.1016/j.sjbs.2023.103652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/18/2023] [Accepted: 04/09/2023] [Indexed: 05/21/2023] Open
Abstract
The challenge of climate change makes it mandatory to improve tolerance to drought stress in bread wheat (Triticum aestivum) via biotechnological approaches. Drought stress experiment was conducted followed by RNA-Seq analysis for leaves of two wheat cultivars namely Giza 168 and Gemmiza 10 with contrasting genotypes. Expression patterns of the regulated stress-related genes and concordantly expressed TFs were detected, then, validated via qPCR for two loss-of-function mutants in Arabidopsis background harboring mutated genes analogue to those in wheat. Drought-stress related genes were searched for concordantly expressed TFs and a total of eight TFs were shown to coexpress with 14 stress-related genes. Among these genes, one TF belongs to the zinc finger protein CONSTANS family and proved via qPCR to drive expression of a gene encoding a speculative TF namely zinc transporter 3-like and two other stress related genes encoding tryptophan synthase alpha chain and asparagine synthetase. Known functions of the two TFs under drought stress complement those of the two concordantly expressed stress-related genes, thus, it is likely that they are related. This study highlights the possibility to utilize metabolic engineering approaches to decipher and incorporate existing regulatory frameworks under drought stress in future breeding programs of bread wheat.
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13
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Kühlwein JK, Ruf WP, Kandler K, Witzel S, Lang C, Mulaw MA, Ekici AB, Weishaupt JH, Ludolph AC, Grozdanov V, Danzer KM. ALS is imprinted in the chromatin accessibility of blood cells. Cell Mol Life Sci 2023; 80:131. [PMID: 37095391 PMCID: PMC10126052 DOI: 10.1007/s00018-023-04769-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 04/26/2023]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a complex and incurable neurodegenerative disorder in which genetic and epigenetic factors contribute to the pathogenesis of all forms of ALS. The interplay of genetic predisposition and environmental footprints generates epigenetic signatures in the cells of affected tissues, which then alter transcriptional programs. Epigenetic modifications that arise from genetic predisposition and systemic environmental footprints should in theory be detectable not only in affected CNS tissue but also in the periphery. Here, we identify an ALS-associated epigenetic signature ('epiChromALS') by chromatin accessibility analysis of blood cells of ALS patients. In contrast to the blood transcriptome signature, epiChromALS includes also genes that are not expressed in blood cells; it is enriched in CNS neuronal pathways and it is present in the ALS motor cortex. By combining simultaneous ATAC-seq and RNA-seq with single-cell sequencing in PBMCs and motor cortex from ALS patients, we demonstrate that epigenetic changes associated with the neurodegenerative disease can be found in the periphery, thus strongly suggesting a mechanistic link between the epigenetic regulation and disease pathogenesis.
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Affiliation(s)
- Julia K Kühlwein
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Wolfgang P Ruf
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Katharina Kandler
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Simon Witzel
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Christina Lang
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Medhanie A Mulaw
- Medical Faculty, University of Ulm, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Clinic Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054, Erlangen, Bayern, Germany
| | - Jochen H Weishaupt
- Division for Neurodegenerative Diseases, Neurology Department, University Medicine Mannheim, Heidelberg University, 68167, Mannheim, Baden-Wuerttemberg, Germany
| | - Albert C Ludolph
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
- German Center for Neurodegenerative Diseases (DZNE), 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Veselin Grozdanov
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Karin M Danzer
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany.
- German Center for Neurodegenerative Diseases (DZNE), 89081, Ulm, Baden-Wuerttemberg, Germany.
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14
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Yang L, Yan Y, Li J, Zhou C, Jin J, Zhang T, Wu H, Li X, Wang W, Yuan L, Zhang X, Gao J. (Tn5-)FISH-based imaging in the era of 3D/spatial genomics. Biophys Rep 2023; 9:15-25. [PMID: 37426200 PMCID: PMC10323772 DOI: 10.52601/bpr.2023.220025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/20/2023] [Indexed: 07/11/2023] Open
Abstract
3D genomics mainly focuses on the 3D position of single genes at the cell level, while spatial genomics focuses more on the tissue level. In this exciting new era of 3D/spatial genomics, half-century old FISH and its derivative methods, including Tn5-FISH, play important roles. In this review, we introduce the Tn5-FISH we developed recently, and present six different applications published by our collaborators and us, based on (Tn5-)FISH, which can be either general BAC clone-based FISH or Tn5-FISH. In these interesting cases, (Tn5-)FISH demonstrated its vigorous ability of targeting sub-chromosomal structures across different diseases and cell lines (leukemia, mESCs (mouse embryonic stem cells), and differentiation cell lines). Serving as an effective tool to image genomic structures at the kilobase level, Tn5-FISH holds great potential to detect chromosomal structures in a high-throughput manner, thus bringing the dawn for new discoveries in the great era of 3D/spatial genomics.
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Affiliation(s)
- Liheng Yang
- Seaver College, Pepperdine University, CA 90263, USA
| | - Yan Yan
- Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, BNRist, Department of Automation, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Beijing 100084, China
| | - JunLin Li
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100084, China
| | - Cheng Zhou
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jinlan Jin
- Department of Critical Care Medicine, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518034, China
| | - Tongmei Zhang
- Medical Oncology, Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Haokaifeng Wu
- Centre for Regenerative Medicine and Health, HongKong Institute of Science & Innovation, Chinese Academy of Sciences, HongKong SAR, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510000, China
| | - Xingang Li
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
| | - Wei Wang
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
| | - Li Yuan
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100084, China
| | - Xu Zhang
- Beijing Institute of Collaborative Innovation, Beijing 100094, China
| | - Juntao Gao
- Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
- Bioinformatics Division, BNRist, Department of Automation, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Beijing 100084, China
- Institute for TCM-X, Beijing 100084, China
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15
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Zhu X, Huang Q, Luo J, Kong D, Zhang Y. Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology. Comput Struct Biotechnol J 2023; 21:1728-1737. [PMID: 36890880 PMCID: PMC9986247 DOI: 10.1016/j.csbj.2023.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Gene regulatory networks are now at the forefront of precision biology, which can help researchers better understand how genes and regulatory elements interact to control cellular gene expression, offering a more promising molecular mechanism in biological research. Interactions between the genes and regulatory elements involve different promoters, enhancers, transcription factors, silencers, insulators, and long-range regulatory elements, which occur at a ∼10 µm nucleus in a spatiotemporal manner. In this way, three-dimensional chromatin conformation and structural biology are critical for interpreting the biological effects and the gene regulatory networks. In the review, we have briefly summarized the latest processes in three-dimensional chromatin conformation, microscopic imaging, and bioinformatics, and we have presented the outlook and future directions for these three aspects.
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Affiliation(s)
- Xiusheng Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qitong Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
| | - Jing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Dashuai Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,College of Life Science and Engineering, Foshan University, Foshan, China
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16
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Subramanian S, George TP, George J, Thomas T. Ensemble learning based assessment of the role of transcription factors in gene expression. Comput Biol Med 2023; 152:106455. [PMID: 36566628 DOI: 10.1016/j.compbiomed.2022.106455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Cancer cells are formed when the associated, active genes fail to function the way they are meant to function. Multiple genes collectively control cell growth by activating a proper set of genes. Regulation of gene expression is controlled through the combined effort of multiple regulatory elements. Transcription of each gene is affected differently according to the combinatorial patterns of regulatory elements bound in the nearby regions. Identifying and analysing such patterns will give a better insight into the cell function. The main focus of this study is on developing a computational model to predict the functional role of transcriptional factors residing between divergent gene pairs. Acute Myeloid Leukaemia (AML) gene expression data from GEO and the two TFs EP300 and CTCF binding data calibrated in k562 cell line from ENCODE consortium are taken as a case study.
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Affiliation(s)
| | | | - Jeslin George
- Department of Statistical Sciences, Kannur University, India.
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17
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Goes CP, Kanno TY, Yan CYI. In Embryo Gene Reporter Assays for Evaluation of Cis-Regulatory Regions. Methods Mol Biol 2023; 2599:227-239. [PMID: 36427153 DOI: 10.1007/978-1-0716-2847-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Gene expression reporter assays measure the relevance of cis-regulatory elements and DNA-binding proteins in modulating transcriptional activity. Commonly, they are performed in cell lines. However, regulation of transcriptional activity during development is complex and dynamic, and not many cell lines reproduce the embryonic conditions. Thus, conclusions derived from cell line data provide limited information about embryonic development. On the other hand, one of the major hurdles for embryonic assays is delivering reporter plasmids in a tissue-specific manner. In this sense, the chick embryo is a good model system to perform these assays. Electroporation of chick embryos provides temporal and spatially controlled plasmid delivery. Further, it is a well-established, easy, and an economical procedure. Here, we describe in detail how to measure in the chick neural tube (1) enhancer activity with GFP, (2) enhancer activity with luciferase, and (3) 3'UTR activity with luciferase.
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Affiliation(s)
- Carolina Purcell Goes
- Department of Cell and Developmental Biology, Biomedical Sciences Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Tatiane Y Kanno
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - C Y Irene Yan
- Department of Cell and Developmental Biology, Biomedical Sciences Institute, Universidade de São Paulo, São Paulo, Brazil.
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Lee BH, Wu Z, Rhie SK. Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C. Epigenetics Chromatin 2022; 15:41. [PMID: 36544209 PMCID: PMC9768916 DOI: 10.1186/s13072-022-00473-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Regulatory elements such as promoters, enhancers, and insulators interact each other to mediate molecular processes. To capture chromatin interactions of regulatory elements, 3C-derived methods such as Hi-C and Micro-C are developed. Here, we generated and analyzed Hi-C, Micro-C, and promoter capture Micro-C datasets with different sequencing depths to study chromatin interactions of regulatory elements and nucleosome positions in human prostate cancer cells. RESULTS Compared to Hi-C, Micro-C identifies more high-resolution loops, including ones around structural variants. By evaluating the effect of sequencing depth, we revealed that more than 2 billion reads of Micro-C are needed to detect chromatin interactions at 1 kb resolution. Moreover, we found that deep-sequencing identifies additional long-range loops that are longer than 1 Mb in distance. Furthermore, we found that more than 50% of the loops are involved in insulators while less than 10% of the loops are promoter-enhancer loops. To comprehensively capture chromatin interactions that promoters are involved in, we performed promoter capture Micro-C. Promoter capture Micro-C identifies loops near promoters with a lower amount of sequencing reads. Sequencing of 160 million reads of promoter capture Micro-C resulted in reaching a plateau of identifying loops. However, there was still a subset of promoters that are not involved in loops even after deep-sequencing. By integrating Micro-C with NOMe-seq and ChIP-seq, we found that active promoters involved in loops have a more accessible region with lower levels of DNA methylation and more highly phased nucleosomes, compared to active promoters that are not involved in loops. CONCLUSION We determined the required sequencing depth for Micro-C and promoter capture Micro-C to generate high-resolution chromatin interaction maps and loops. We also investigated the effect of sequencing coverage of Hi-C, Micro-C, and promoter capture Micro-C on detecting chromatin loops. Our analyses suggest the presence of distinct regulatory element groups, which are differently involved in nucleosome positions and chromatin interactions. This study does not only provide valuable insights on understanding chromatin interactions of regulatory elements, but also present guidelines for designing research projects on chromatin interactions among regulatory elements.
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Affiliation(s)
- Beoung Hun Lee
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Zexun Wu
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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19
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Chen S, Liu S, Shi S, Jiang Y, Cao M, Tang Y, Li W, Liu J, Fang L, Yu Y, Zhang S. Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits. BMC Biol 2022; 20:273. [PMID: 36482458 PMCID: PMC9730597 DOI: 10.1186/s12915-022-01459-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/07/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Insights into the genetic basis of complex traits and disease in both human and livestock species have been achieved over the past decade through detection of genetic variants in genome-wide association studies (GWAS). A majority of such variants were found located in noncoding genomic regions, and though the involvement of numerous regulatory elements (REs) has been predicted across multiple tissues in domesticated animals, their evolutionary conservation and effects on complex traits have not been fully elucidated, particularly in ruminants. Here, we systematically analyzed 137 epigenomic and transcriptomic datasets of six mammals, including cattle, sheep, goats, pigs, mice, and humans, and then integrated them with large-scale GWAS of complex traits. RESULTS Using 40 ChIP-seq datasets of H3K4me3 and H3K27ac, we detected 68,479, 58,562, 63,273, 97,244, 111,881, and 87,049 REs in the liver of cattle, sheep, goats, pigs, humans and mice, respectively. We then systematically characterized the dynamic functional landscapes of these REs by integrating multi-omics datasets, including gene expression, chromatin accessibility, and DNA methylation. We identified a core set (n = 6359) of ruminant-specific REs that are involved in liver development, metabolism, and immune processes. Genes with more complex cis-REs exhibited higher gene expression levels and stronger conservation across species. Furthermore, we integrated expression quantitative trait loci (eQTLs) and GWAS from 44 and 52 complex traits/diseases in cattle and humans, respectively. These results demonstrated that REs with different degrees of evolutionary conservation across species exhibited distinct enrichments for GWAS signals of complex traits. CONCLUSIONS We systematically annotated genome-wide functional REs in liver across six mammals and demonstrated the evolution of REs and their associations with transcriptional output and conservation. Detecting lineage-specific REs allows us to decipher the evolutionary and genetic basis of complex phenotypes in livestock and humans, which may benefit the discovery of potential biomedical models for functional variants and genes of specific human diseases.
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Affiliation(s)
- Siqian Chen
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuli Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China ,grid.494629.40000 0004 8008 9315 School of Life Sciences, Westlake University, Hangzhou, China
| | - Shaolei Shi
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yifan Jiang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Mingyue Cao
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yongjie Tang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wenlong Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianfeng Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lingzhao Fang
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit at the Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK ,grid.7048.b0000 0001 1956 2722Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark
| | - Ying Yu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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20
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Girdhar K, Rahman S, Dong P, Fullard JF, Roussos P. The Neuroepigenome: Implications of Chemical and Physical Modifications of Genomic DNA in Schizophrenia. Biol Psychiatry 2022; 92:443-449. [PMID: 35750513 DOI: 10.1016/j.biopsych.2022.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/14/2022] [Accepted: 04/27/2022] [Indexed: 11/02/2022]
Abstract
Schizophrenia is a chronic mental illness with a substantial genetic component. To unfold the complex etiology of schizophrenia, it is important to understand the interplay between genetic and nongenetic factors. Genetic factors involve variation in the DNA sequences of protein-coding genes, which directly contribute to phenotypic traits, and variation in noncoding sequences, which comprise 98% of the genome and contain DNA elements known to play a role in regulating gene expression. The epigenome refers to the chemical modifications on both DNA and the structural proteins that package DNA into the nucleus, which together regulate gene expression in specific cell types, conditions, and developmental stages. The dynamic nature of the epigenome makes it an ideal tool to investigate the relationship between inherited genetic mutations associated with schizophrenia and altered gene regulation throughout the course of brain development. In this review, we focus on the current understanding of the role of epigenetic marks and their three-dimensional nuclear organization in the developmental trajectory of distinct brain cell types to decipher the complex gene regulatory mechanisms that are disrupted in schizophrenia.
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Affiliation(s)
- Kiran Girdhar
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Samir Rahman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pengfei Dong
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, New York; Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, New York.
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21
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Suhorukova AV, Tyurin AA, Pavlenko OS, Mustafayev ON, Sinelnikov IG, Goldenkova-Pavlova IV. Development of dual reporter vector system for estimating translational activity of regulatory elements. BMC Plant Biol 2022; 22:356. [PMID: 35864445 PMCID: PMC9306140 DOI: 10.1186/s12870-022-03735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND For the needs of modern biotechnology, a quantitative approach to the control of regulatory elements at all stages of gene expression has long become indispensable. Such a control regime is impossible without a quantitative analysis of the role of each regulatory element or pattern used. Therefore, it seems important to modify and develop the accuracy, reproducibility, and availability of methods for quantifying the contribution of each regulatory code to the implementation of genetic information. RESULTS A new vector system for transient expression in plants is described; this system is intended for quantitative analysis of the contribution of regulatory elements to transcription and translation efficiencies. The proposed vector comprises two expression cassettes carrying reporter genes (of the Clostridium thermocellum thermostable lichenase and E. coli β-glucuronidase) under the control of different promoters. Herewith we also propose a new method for quantification of the effect of tested regulatory elements on expression, which relies on assessment of the enzyme activities of reporter proteins taking into account the transcription of their genes. CONCLUSIONS In our view, this approach makes it possible to precisely determine the amounts of reporter proteins and their transcripts at all stages of expression. The efficiency of the proposed system has been validated by the analysis of the roles of known translation enhancers at the stages of transcription and translation.
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Affiliation(s)
- Aleksandra V. Suhorukova
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A. Tyurin
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga S. Pavlenko
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Orkhan N. Mustafayev
- Genetic resources institute, Azerbaijan National Academy of Sciences, Baku, Azerbaijan
| | - Igor G. Sinelnikov
- Laboratory of enzyme biotechnology, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, Moscow, Russia
| | - Irina V. Goldenkova-Pavlova
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
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22
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Mikec Š, Šimon M, Morton NM, Atanur SS, Konc J, Dovč P, Horvat S, Kunej T. Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines. Mol Biol Rep 2022; 49:4619-4631. [PMID: 35347545 DOI: 10.1007/s11033-022-07309-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/25/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Adipose tissue hypoxia and members of the hypoxia-inducible factor alpha (HIFA) are involved in development of obesity. However, the mechanism and functions of HIF3A, one of three HIFA paralogs, in fat deposition have not been sufficiently studied. METHODS AND RESULTS In the present study, we investigated whether Hif3a sequence variants are associated with divergent fat deposition in mouse selection lines for fatness and leanness. Sequencing and RFLP were used to analyse sequence variants within Hif3a. To identify candidate regulatory variants, we performed literature screening and used databases and bioinformatics tools like Ensembl, MethPrimer, TargetScanMouse, miRDB, PolyAsite, RISE, LncRRIsearch, RNAfold, PredictProtein, CAIcal, and switches.ELM Resource. There are 90 sequence variants in Hif3a between the two mouse lines. While most Fat line variants locate within intronic regions, Lean line variants are mainly in 3' UTR. We constructed a map of Hif3a potential regulatory regions and identified 39 regulatory variants by integrating data on constrained and regulatory elements, CpGs, and miRNAs and lncRNAs binding sites. Moreover, 3' UTR and two exonic variants may influence mRNA stability, translation rate and protein functionality. We propose as priority candidates for further functional studies a missense (rs37398126) and synonymous (rs37739792) variants, and intronic (rs47471302) variant that overlap conserved element in promoter region and predicted lncRNAs binding site. CONCLUSION The results indicate a potential involvement of Hif3a in fat deposition. Additionally, approach used in the present study may serve as a general guideline for constructing an integrative gene map for prioritizing candidate gene variants with phenotypic effects.
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Affiliation(s)
- Špela Mikec
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Martin Šimon
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nicholas M Morton
- The Queen's Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Santosh S Atanur
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK.,Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Janez Konc
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia.
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia.
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23
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Cinkornpumin JK, Hossain I, Pastor WA. Mapping Chromatin Accessibility in Human Naïve Pluripotent Stem Cells Using ATAC-Seq. Methods Mol Biol 2022; 2416:201-211. [PMID: 34870838 DOI: 10.1007/978-1-0716-1908-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Regulatory elements, such as promoters and enhancers, typically show reduced nucleosome occupancy, which is a feature that is commonly referred to as "open chromatin". The distribution of open chromatin sites can provide important clues about the transcription factors and regulatory networks that drive gene expression in a given cell. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a rapid and robust method for mapping open chromatin sites. ATAC-seq data can also discern the binding sites of nucleosomes and transcription factors. In this chapter, we describe how to produce and assess the quality of ATAC-seq libraries that are generated from naïve human pluripotent stem cells.
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Affiliation(s)
| | | | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada.
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24
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Nim HT, Dang L, Thiyagarajah H, Bakopoulos D, See M, Charitakis N, Sibbritt T, Eichenlaub MP, Archer SK, Fossat N, Burke RE, Tam PPL, Warr CG, Johnson TK, Ramialison M. A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease. Genome Biol 2021; 22:335. [PMID: 34906219 PMCID: PMC8672579 DOI: 10.1186/s13059-021-02539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. RESULTS We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. CONCLUSIONS Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.
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Affiliation(s)
- Hieu T. Nim
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
| | - Louis Dang
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Harshini Thiyagarajah
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Daniel Bakopoulos
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Michael See
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Natalie Charitakis
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Tennille Sibbritt
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Michael P. Eichenlaub
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Stuart K. Archer
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Nicolas Fossat
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
- Present address: Copenhagen Hepatitis C Program, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Present address: Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Richard E. Burke
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Patrick P. L. Tam
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Coral G. Warr
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
- School of Molecular Sciences, La Trobe University, Bundoora, Victoria 3083 Australia
| | - Travis K. Johnson
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
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25
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Wang H, Ji Y, Ding Z, Guo W, Zou Y. Gene expression profiling and functional analysis of ventricular tissues from murine transverse aortic constriction. Gene 2021; 813:146093. [PMID: 34896521 DOI: 10.1016/j.gene.2021.146093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/22/2021] [Accepted: 11/23/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Transverse aortic constriction (TAC) model is widely used to study pressure overload-induced cardiac remodeling. However, the conserved transcriptional features of TAC model and the underlying regulatory mechanisms remain unclear. METHODS In this study, we screened out the high-quality microarray data for ventricular tissue from murine TAC model. The transcriptional changes in ventricular tissue were analyzed by identifying the common differently expressed genes (DEGs) and enriched gene sets. We also analyzed the protein-protein interaction and mRNA-mRNA association of DEGs. Furthermore, the potential regulatory elements of the DEGs were explored through comparative analysis between mouse and human. RESULTS 265 common DEGs and 45 enriched canonical pathways were identified in murine TAC model. 201 DEGs had the protein-protein interaction, whereas 96 DEGs had mRNA-mRNA association. 99 transcription factor (TF)-mRNA and 2997 microRNA (miRNA)-mRNA regulatory relationships were retrieved. CONCLUSIONS In pressure overload-induced cardiac remodeling, inflammation, fibrosis, metabolic remodeling and hypoxia were significant features. Approaches to intervene these phenomena may have therapeutic values. TFs and miRNAs are important regulator elements of DEGs in both mouse and human. Examination of miRNAs is a promising tool to detect the occurrence of pressure overload-induced cardiac remodeling in patients.
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Affiliation(s)
- Hao Wang
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuyao Ji
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhiwen Ding
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yunzeng Zou
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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Abstract
Sex determination is the process by which an initial bipotential gonad adopts either a testicular or ovarian cell fate. The inability to properly complete this process leads to a group of developmental disorders classified as disorders of sex development (DSD). To date, dozens of genes were shown to play roles in mammalian sex determination, and mutations in these genes can cause DSD in humans or gonadal sex reversal/dysfunction in mice. However, exome sequencing currently provides genetic diagnosis for only less than half of DSD patients. This points towards a major role for the non-coding genome during sex determination. In this review, we highlight recent advances in our understanding of non-coding, cis-acting gene regulatory elements and discuss how they may control transcriptional programmes that underpin sex determination in the context of the 3-dimensional folding of chromatin. As a paradigm, we focus on the Sox9 gene, a prominent pro-male factor and one of the most extensively studied genes in gonadal cell fate determination.
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Affiliation(s)
- Meshi Ridnik
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Stefan Schoenfelder
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
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27
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Patel ZM, Hughes TR. Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms. Genome Biol 2021; 22:285. [PMID: 34620190 PMCID: PMC8496038 DOI: 10.1186/s13059-021-02503-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 09/16/2021] [Indexed: 01/07/2023] Open
Abstract
Background Mammalian genomes contain millions of putative regulatory sequences, which are delineated by binding of multiple transcription factors. The degree to which spacing and orientation constraints among transcription factor binding sites contribute to the recognition and identity of regulatory sequence is an unresolved but important question that impacts our understanding of genome function and evolution. Global mechanisms that underlie phenomena including the size of regulatory sequences, their uniqueness, and their evolutionary turnover remain poorly described. Results Here, we ask whether models incorporating different degrees of spacing and orientation constraints among transcription factor binding sites are broadly consistent with several global properties of regulatory sequence. These properties include length, sequence diversity, turnover rate, and dominance of specific TFs in regulatory site identity and cell type specification. Models with and without spacing and orientation constraints are generally consistent with all observed properties of regulatory sequence, and with regulatory sequences being fundamentally small (~ 1 nucleosome). Uniqueness of regulatory regions and their rapid evolutionary turnover are expected under all models examined. An intriguing issue we identify is that the complexity of eukaryotic regulatory sites must scale with the number of active transcription factors, in order to accomplish observed specificity. Conclusions Models of transcription factor binding with or without spacing and orientation constraints predict that regulatory sequences should be fundamentally short, unique, and turn over rapidly. We posit that the existence of master regulators may be, in part, a consequence of evolutionary pressure to limit the complexity and increase evolvability of regulatory sites. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02503-y.
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Affiliation(s)
- Zain M Patel
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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Ullastres A, Merenciano M, González J. Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila. Genome Biol 2021; 22:265. [PMID: 34521452 PMCID: PMC8439047 DOI: 10.1186/s13059-021-02471-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
Background Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements. Results In this work, we use a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identify 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validate three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions is consistent with an increased survival to infection. Indeed, for one of the insertions, we show that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion is deleted from its native genomic context. Conclusions We show that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, transposable elements are likely to play a role in immune response in other organisms as well. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02471-3.
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Affiliation(s)
- Anna Ullastres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
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Abstract
Epigenetic marks do not change the sequence of DNA but affect gene expression in a cell-type specific manner by altering the activities of regulatory elements. Development of new molecular biology assays, sequencing technologies, and computational approaches enables us to profile the human epigenome in three-dimensional structure genome-wide. Here we describe various molecular biology techniques and bioinformatic tools that have been developed to measure the activities of regulatory elements and their chromatin interactions. Moreover, we list currently available three-dimensional epigenomic data sets that are generated in various human cell types and tissues to assist in the design and analysis of research projects.
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Affiliation(s)
- Beoung Hun Lee
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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30
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Choi HJ, Jin SD, Rengaraj D, Kim JH, Pain B, Han JY. Differential transcriptional regulation of the NANOG gene in chicken primordial germ cells and embryonic stem cells. J Anim Sci Biotechnol 2021; 12:40. [PMID: 33658075 PMCID: PMC7931612 DOI: 10.1186/s40104-021-00563-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/26/2021] [Indexed: 01/06/2023] Open
Abstract
Background NANOG is a core transcription factor (TF) in embryonic stem cells (ESCs) and primordial germ cells (PGCs). Regulation of the NANOG gene by TFs, epigenetic factors, and autoregulatory factors is well characterized in ESCs, and transcriptional regulation of NANOG is well established in these cells. Although NANOG plays a key role in germ cells, the molecular mechanism underlying its transcriptional regulation in PGCs has not been studied. Therefore, we investigated the mechanism that regulates transcription of the chicken NANOG (cNANOG) gene in PGCs and ESCs. Results We first identified the transcription start site of cNANOG by 5′-rapid amplification of cDNA ends PCR analysis. Then, we measured the promoter activity of various 5′ flanking regions of cNANOG in chicken PGCs and ESCs using the luciferase reporter assay. cNANOG expression required transcriptional regulatory elements, which were positively regulated by POU5F3 (OCT4) and SOX2 and negatively regulated by TP53 in PGCs. The proximal region of the cNANOG promoter contains a positive transcriptional regulatory element (CCAAT/enhancer-binding protein (CEBP)-binding site) in ESCs. Furthermore, small interfering RNA-mediated knockdown demonstrated that POU5F3, SOX2, and CEBP played a role in cell type-specific transcription of cNANOG. Conclusions We show for the first time that different trans-regulatory elements control transcription of cNANOG in a cell type-specific manner. This finding might help to elucidate the mechanism that regulates cNANOG expression in PGCs and ESCs.
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Affiliation(s)
- Hee Jung Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So Dam Jin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Deivendran Rengaraj
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin Hwa Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Bertrand Pain
- Univ Lyon, Universite ́Lyon 1, INSERM, INRAE, Stem Cell and Brain Research Institute, U1208, USC1361, 69500, Bron, France
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. .,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan.
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31
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Eicher T, Chan J, Luu H, Machiraju R, Mathé EA. Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements. BMC Bioinformatics 2021; 22:35. [PMID: 33516170 PMCID: PMC7847148 DOI: 10.1186/s12859-021-03976-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Assigning chromatin states genome-wide (e.g. promoters, enhancers, etc.) is commonly performed to improve functional interpretation of these states. However, computational methods to assign chromatin state suffer from the following drawbacks: they typically require data from multiple assays, which may not be practically feasible to obtain, and they depend on peak calling algorithms, which require careful parameterization and often exclude the majority of the genome. To address these drawbacks, we propose a novel learning technique built upon the Self-Organizing Map (SOM), Self-Organizing Map with Variable Neighborhoods (SOM-VN), to learn a set of representative shapes from a single, genome-wide, chromatin accessibility dataset to associate with a chromatin state assignment in which a particular RE is prevalent. These shapes can then be used to assign chromatin state using our workflow. RESULTS We validate the performance of the SOM-VN workflow on 14 different samples of varying quality, namely one assay each of A549 and GM12878 cell lines and two each of H1 and HeLa cell lines, primary B-cells, and brain, heart, and stomach tissue. We show that SOM-VN learns shapes that are (1) non-random, (2) associated with known chromatin states, (3) generalizable across sets of chromosomes, and (4) associated with magnitude and multimodality. We compare the accuracy of SOM-VN chromatin states against the Clustering Aggregation Tool (CAGT), an unsupervised method that learns chromatin accessibility signal shapes but does not associate these shapes with REs, and we show that overall precision and recall is increased when learning shapes using SOM-VN as compared to CAGT. We further compare enhancer state assignments from SOM-VN in signals above a set threshold to enhancer state assignments from Predicting Enhancers from ATAC-seq Data (PEAS), a deep learning method that assigns enhancer chromatin states to peaks. We show that the precision-recall area under the curve for the assignment of enhancer states is comparable to PEAS. CONCLUSIONS Our work shows that the SOM-VN workflow can learn relationships between REs and chromatin accessibility signal shape, which is an important step toward the goal of assigning and comparing enhancer state across multiple experiments and phenotypic states.
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Affiliation(s)
- Tara Eicher
- Department of Biomedical Informatics, The Ohio State University College of Medicine, 370 W. 9th Avenue, Columbus, OH, 43210, USA
- Department of Computer Science and Engineering, The Ohio State University College of Engineering, 2015 Neil Avenue, Columbus, OH, 43210, USA
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, 9800 Medical Center Dr., Rockville, MD, 20892, USA
| | - Jany Chan
- Department of Biomedical Informatics, The Ohio State University College of Medicine, 370 W. 9th Avenue, Columbus, OH, 43210, USA
| | - Han Luu
- Department of Biomedical Informatics, The Ohio State University College of Medicine, 370 W. 9th Avenue, Columbus, OH, 43210, USA
| | - Raghu Machiraju
- Department of Biomedical Informatics, The Ohio State University College of Medicine, 370 W. 9th Avenue, Columbus, OH, 43210, USA.
- Department of Computer Science and Engineering, The Ohio State University College of Engineering, 2015 Neil Avenue, Columbus, OH, 43210, USA.
- Department of Pathology, The Ohio State University College of Medicine, 1645 Neil Ave, Columbus, OH, 43210, USA.
- Translational Data Analytics Institute, The Ohio State University, 1760 Neil Ave., Columbus, OH, 43210, USA.
| | - Ewy A Mathé
- Department of Biomedical Informatics, The Ohio State University College of Medicine, 370 W. 9th Avenue, Columbus, OH, 43210, USA.
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, 9800 Medical Center Dr., Rockville, MD, 20892, USA.
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Abstract
The ATAC-seq assay has emerged as the most useful, versatile, and widely adaptable method for profiling accessible chromatin regions and tracking the activity of cis-regulatory elements (cREs) in eukaryotes. Thanks to its great utility, it is now being applied to map active chromatin in the context of a very wide diversity of biological systems and questions. In the course of these studies, considerable experience working with ATAC-seq data has accumulated and a standard set of computational tasks that need to be carried for most ATAC-seq analyses has emerged. Here, we review and provide examples of common such analytical procedures (including data processing, quality control, peak calling, identifying differentially accessible open chromatin regions, and variable transcription factor (TF) motif accessibility) and discuss recommended optimal practices.
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Serebreni L, Stark A. Insights into gene regulation: From regulatory genomic elements to DNA-protein and protein-protein interactions. Curr Opin Cell Biol 2020; 70:58-66. [PMID: 33385708 DOI: 10.1016/j.ceb.2020.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/19/2020] [Accepted: 11/29/2020] [Indexed: 01/19/2023]
Abstract
Transcription is orchestrated by non-coding regulatory elements embedded in chromatin, which exist within the larger context of chromosome topology. Here, we review recent insights into the functions of non-coding regulatory elements and their protein interactors during transcription control. A picture emerges in which the topological environment constraints enhancer-promoter interactions and specific enhancer-bound proteins with distinct promoter-compatibilities refine target promoter choice. Such compatibilities are encoded within the sequences of enhancers and promoters and realized by diverse transcription factors and cofactors with distinct biochemical activities. An emerging property of transcription factors and cofactors is the formation of nuclear microenvironments or membraneless compartments that can have properties of phase-separated liquids. These environments are able to selectively enrich certain proteins and small molecules over others. Further investigation into the interaction of transcriptional regulators with themselves and regulatory DNA elements will help reveal the complexities of gene regulation within the context of the nucleus.
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Affiliation(s)
- Leonid Serebreni
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
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34
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Chattopadhyay A, Abdul Kader Jailani A, Roy A, Mukherjee SK, Mandal B. Prediction of putative regulatory elements in the subgenomic promoters of cucumber green mottle mosaic virus and their interactions with the RNA dependent RNA polymerase domain. Virusdisease 2020; 31:503-516. [PMID: 33381623 DOI: 10.1007/s13337-020-00640-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 10/27/2020] [Indexed: 11/26/2022] Open
Abstract
Characterization of the subgenomic RNA (sgRNA) promoter of many plant viruses is important to understand the expression of downstream genes and also to configure their genome into a suitable virus gene-vector system. Cucumber green mottle mosaic virus (CGMMV, genus Tobamovirus) is one of the RNA viruses, which is extensively being exploited as the suitable gene silencing and protein expression vector. Even though, characters of the sgRNA promoters (SGPs) of CGMMV are yet to be addressed. In the present study, we predicted the SGP for the movement protein (MP) and coat protein (CP) of CGMMV. Further, we identified the key regulatory elements in the SGP regions of MP and CP, and their interactions with the core RNA dependent RNA polymerase (RdRp) domain of CGMMV was deciphered. The modeled structure of core RdRp contains two palm (1-41 aa, and 63-109 aa), one finger (42-62 aa) subdomains with three conserved RdRp motifs that played important role in binding to the SGP nucleic acids. RdRp strongly preferred the double helix form of the stem region in the stem and loop (SL) structures, and the internal bulge elements. In MP-SGP, a total of six elements was identified; of them, the affinity of binding to - 26 nt to - 17 nt site (CGCGGAAAAG) was higher through the formation of strong hydrogen bonds with LYS16, TYR17, LYS19, SER20, etc. of the motif A in the palm subdomain of RdRp. Similar strong interactions were noticed in the internal bulge (CAACUUU) located at + 33 to + 39 nt adjacent to the translation start site (TLSS) (+ 1). These could be proposed as the putative core promoter elements in MP-SGP. Likewise, total five elements were predicted within - 114 nt to + 144 nt region of CP-SGP with respect to CP-TLSS. Of them, RdRp preferred to bind at the small hairpin located at - 60 nt to - 43 nt (UUGGAGGUUUAGCCUCCA) in the upstream region, and at the complex duplex structure spanning between + 99 and + 114 nt in the downstream region, thus indicating the distribution of core promoter within - 60 nt to + 114 nt region of CP-SGP with respect to TLSS (+ 1) of the CP; whereas, the - 114 nt to + 144 nt region of CP-SGP might be necessary for the full activity of the CP-SGP. Our in silico prediction certifies the gravity of these nucleotide stretches as the RNA regulatory elements and identifies their potentiality for binding with of palm and finger sub-domain of RdRp. Identification of such elements will be helpful to anticipate the critical length of the SGPs. Our finding will not only be helpful to delineate the SGPs of CGMMV but also their subsequent application in the efficient construction of virus gene-vector for the expression of foreign protein in plant.
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Affiliation(s)
- Anirudha Chattopadhyay
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - A Abdul Kader Jailani
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Anirban Roy
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Sunil Kumar Mukherjee
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
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35
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Bondareva O, Tsaryk R, Bojovic V, Odenthal-Schnittler M, Siekmann AF, Schnittler HJ. Identification of atheroprone shear stress responsive regulatory elements in endothelial cells. Cardiovasc Res 2020; 115:1487-1499. [PMID: 30785199 DOI: 10.1093/cvr/cvz027] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/14/2018] [Accepted: 02/19/2019] [Indexed: 12/21/2022] Open
Abstract
AIMS Oscillatory shear stress (OSS) is an atheroprone haemodynamic force that occurs in areas of vessel irregularities and is implicated in the pathogenesis of atherosclerosis. Changes in signalling and transcriptional programme in response to OSS have been vigorously studied; however, the underlying changes in the chromatin landscape controlling transcription remain to be elucidated. Here, we investigated the changes in the regulatory element (RE) landscape of endothelial cells under atheroprone OSS conditions in an in vitro model. METHODS AND RESULTS Analyses of H3K27ac chromatin immunoprecipitation-Seq enrichment and RNA-Seq in primary human umbilical vein endothelial cells 6 h after onset of OSS identified 2806 differential responsive REs and 33 differentially expressed genes compared with control cells kept under static conditions. Furthermore, gene ontology analyses of putative RE-associated genes uncovered enrichment of WNT/HIPPO pathway and cytoskeleton reorganization signatures. Transcription factor (TF) binding motif analysis within RE sequences identified over-representation of ETS, Zinc finger, and activator protein 1 TF families that regulate cell cycle, proliferation, and apoptosis, implicating them in the development of atherosclerosis. Importantly, we confirmed the activation of EGR1 as well as the YAP/TAZ complex early (6 h) after onset of OSS in both cultured human vein and artery endothelial cells and, by undertaking luciferase assays, functionally verified their role in RE activation in response to OSS. CONCLUSIONS Based on the identification and verification of specific responsive REs early upon OSS exposure, we propose an expanded mechanism of how OSS might contribute to the development of atherosclerosis.
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Affiliation(s)
- Olga Bondareva
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, Münster, Germany.,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), Westfälische Wilhelms University of Münster, Waldeyerstrasse 15, Münster, Germany
| | - Roman Tsaryk
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), Westfälische Wilhelms University of Münster, Waldeyerstrasse 15, Münster, Germany.,Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Vesna Bojovic
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, Münster, Germany
| | - Maria Odenthal-Schnittler
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, Münster, Germany.,Department of Ophthalmology, Westfälische Wilhelms University of Münster, Faculty of Medicine, Domagkstrasse 15, Muenster, Germany
| | - Arndt F Siekmann
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), Westfälische Wilhelms University of Münster, Waldeyerstrasse 15, Münster, Germany.,Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany.,Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania, USA
| | - Hans-J Schnittler
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, Münster, Germany.,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), Westfälische Wilhelms University of Münster, Waldeyerstrasse 15, Münster, Germany
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Niu W, Bo QY, Niu J, Niu ZC, Peng C, Zou XQ, Zhang ZY. Identification of integrin β6 gene promoter and analysis of its transcription regulation in colon cancer cells. World J Gastrointest Oncol 2020; 12:526-534. [PMID: 32461784 PMCID: PMC7235184 DOI: 10.4251/wjgo.v12.i5.526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/29/2020] [Accepted: 04/18/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The integrin β6 gene, which is expressed in epithelial cancer, plays a pivotal role in various aspects of cancer progression. The present research for integrin β6 regulation mainly focuses on the post-transcription and translation related regulation mechanism and its role in tumorigenesis. The mechanisms of how the integrin β6 gene is regulated transcriptionally, and the promoter and transcription factors responsible for basic transcription of integrin β6 gene remain unknown.
AIM To clone and characterize the integrin β6 promoter.
METHODS Software analysis was used to predict the region of integrin β6 promoter. Luciferase reporter plasmids, which contained the integrin β6 promoter, were constructed. Element deletion analysis was performed to identify the location of core promoter and binding sites for transcription factors.
RESULTS The regulatory elements for the transcription of the integrin β6 gene were located between -286 and -85 and contained binding sites for transcription factors such as STAT3 and Ets-1.
CONCLUSION For the first time, we found the region of β6 core promoter and demonstrated the binding sites for transcription factors such as Ets-1 and STAT3, which are important for integrin β6 promoter transcription activity. These findings are important for investigating the mechanism of integrin β6 activation in cancer progression.
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Affiliation(s)
- Wei Niu
- Department of Hepatobiliary Surgery, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
| | - Qi-Yu Bo
- Department of Nursing, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
| | - Jun Niu
- Department of Hepatobiliary Surgery, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
| | - Zheng-Chuan Niu
- Department of Hepatobiliary Surgery, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
| | - Cheng Peng
- Department of Hepatobiliary Surgery, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
| | - Xue-Qing Zou
- Department of Hepatobiliary Surgery, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
| | - Zhao-Yang Zhang
- Department of Emergency Surgery, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
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Thiery A, Buzzi AL, Streit A. Cell fate decisions during the development of the peripheral nervous system in the vertebrate head. Curr Top Dev Biol 2020; 139:127-67. [PMID: 32450959 DOI: 10.1016/bs.ctdb.2020.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Sensory placodes and neural crest cells are among the key cell populations that facilitated the emergence and diversification of vertebrates throughout evolution. Together, they generate the sensory nervous system in the head: both form the cranial sensory ganglia, while placodal cells make major contributions to the sense organs-the eye, ear and olfactory epithelium. Both are instrumental for integrating craniofacial organs and have been key to drive the concentration of sensory structures in the vertebrate head allowing the emergence of active and predatory life forms. Whereas the gene regulatory networks that control neural crest cell development have been studied extensively, the signals and downstream transcriptional events that regulate placode formation and diversity are only beginning to be uncovered. Both cell populations are derived from the embryonic ectoderm, which also generates the central nervous system and the epidermis, and recent evidence suggests that their initial specification involves a common molecular mechanism before definitive neural, neural crest and placodal lineages are established. In this review, we will first discuss the transcriptional networks that pattern the embryonic ectoderm and establish these three cell fates with emphasis on sensory placodes. Second, we will focus on how sensory placode precursors diversify using the specification of otic-epibranchial progenitors and their segregation as an example.
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38
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Martinelli RP, Rodriguez JM, Daurelio LD, Esteban L. In silico identification of novel transcription factors associated with CYP27B1 transcriptional regulation in LPS-challenged mononuclear phagocytes. J Steroid Biochem Mol Biol 2020; 199:105590. [PMID: 32001361 DOI: 10.1016/j.jsbmb.2020.105590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/13/2019] [Accepted: 01/13/2020] [Indexed: 01/08/2023]
Abstract
Renal and extrarenal production of the active form of vitamin D, 1,25-dihydroxyvitamin D (1,25(OH)2D), is catalyzed by CYP27B1, an enzyme also called 1-α-hydroxylase. The overproduction of 1,25(OH)2D has been described in granulomatous diseases. High circulating concentrations of 1,25(OH)2D can lead to hypercalcemia. The aim of this work was to characterize the transcriptional regulation of CYP27B1 in human mononuclear phagocytes exposed to LPS due to its relevance to understanding the hypercalcemia and ectopic calcifications associated with chronic inflammatory diseases such as tuberculosis and other granulomatous diseases. The human CYP27B1 promoter analysis identified binding sites for published TF, SNPs, novel putative TFBS and conserved sites compared to mice. Then, using microarray data, a meta-analysis was performed to obtain a global view of the gene expression in LPS-challenged dendritic cells, monocytes and macrophages. Finally, two experiments, GSE40885 and time series GSE19765, were analyzed in-depth using differential expression analysis which permitted the identification of TF co-expressed with CYP27B1. This work allowed us to formulate a CYP27B1 transcriptional regulation model for LPS-challenged monocytes/macrophages. The importance of two TF families, NFKB and CEBPB, was confirmed. Data also suggests that PLAGL2 and STAT4 which are novel TF could participate in the CYP27B1 transcriptional regulation in cells exposed to LPS. These TF, in turn, would be interacting with regions that present polymorphisms in the general population which might explain the pathological phenotypes associated with altered vitamin D metabolism.
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Affiliation(s)
- Romina P Martinelli
- Departamento de Química Biológica, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Cátedra de Genética Humana, Facultad de Medicina, Universidad Abierta Interamericana, Rosario, Santa Fe, Argentina.
| | - Julia M Rodriguez
- Departamento de Química Biológica, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Lucas D Daurelio
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Investigaciones en Fisiología y Biología Molecular Vegetal (LIFiBVe), Cátedra de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Santa Fe, Argentina.
| | - Luis Esteban
- Departamento de Química Biológica, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina.
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39
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Abstract
Background Non-synonymous mutations altering tumor suppressor genes and oncogenes are widely studied. However, synonymous mutations, which do not alter the protein sequence, are rarely investigated in melanoma genome studies. Methods We explored the role of somatic synonymous mutations in melanoma samples from TCGA (The Cancer Genome Atlas). The pathogenic synonymous mutation and neutral synonymous mutation data were used to assess the significance of pathogenic synonymous mutations in melanoma likely to affect genetic regulatory elements using Fisher’s exact test. Poisson distribution probabilities of each gene were used to mine the genes with multiple potential functional synonymous mutations affecting regulatory elements. Results Concentrating on five types of genetic regulatory functions, we found that the mutational patterns of pathogenic synonymous mutations are mostly involved in exonic splicing regulators in near-splicing sites or inside DNase I hypersensitivity sites or non-optimal codon. Moreover, the sites of miRNA binding alteration exhibit a significantly lower rate of evolution than other sites. Finally, 12 genes were hit by recurrent potentially functional synonymous mutations, which showed statistical significance in the pathogenic mutations. Among them, nine genes (DNAH5, ADCY8, GRIN2A, KSR2, TECTA, RIMS2, XKR6, MYH1, SCN10A) have been reported to be mutated in melanoma, and other three genes (SLC9A2, CASR, SLC8A3) have a great potential to impact melanoma. Conclusion These findings confirm the functional consequences of somatic synonymous mutations in melanoma, emphasizing the significance of research in future studies.
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Affiliation(s)
- Di Zhang
- College of information science and engineering, Shaoguan University, Shaoguan, Guangdong, China.,Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
| | - Junfeng Xia
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China.
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Wani SH, Kumar V, Khare T, Guddimalli R, Parveda M, Solymosi K, Suprasanna P, Kavi Kishor PB. Engineering salinity tolerance in plants: progress and prospects. Planta 2020; 251:76. [PMID: 32152761 DOI: 10.1007/s00425-020-03366-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/24/2020] [Indexed: 05/20/2023]
Abstract
There is a need to integrate conceptual framework based on the current understanding of salt stress responses with different approaches for manipulating and improving salt tolerance in crop plants. Soil salinity exerts significant constraints on global crop production, posing a serious challenge for plant breeders and biotechnologists. The classical transgenic approach for enhancing salinity tolerance in plants revolves by boosting endogenous defence mechanisms, often via a single-gene approach, and usually involves the enhanced synthesis of compatible osmolytes, antioxidants, polyamines, maintenance of hormone homeostasis, modification of transporters and/or regulatory proteins, including transcription factors and alternative splicing events. Occasionally, genetic manipulation of regulatory proteins or phytohormone levels confers salinity tolerance, but all these may cause undesired reduction in plant growth and/or yields. In this review, we present and evaluate novel and cutting-edge approaches for engineering salt tolerance in crop plants. First, we cover recent findings regarding the importance of regulatory proteins and transporters, and how they can be used to enhance salt tolerance in crop plants. We also evaluate the importance of halobiomes as a reservoir of genes that can be used for engineering salt tolerance in glycophytic crops. Additionally, the role of microRNAs as critical post-transcriptional regulators in plant adaptive responses to salt stress is reviewed and their use for engineering salt-tolerant crop plants is critically assessed. The potentials of alternative splicing mechanisms and targeted gene-editing technologies in understanding plant salt stress responses and developing salt-tolerant crop plants are also discussed.
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Affiliation(s)
- Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Anantnag, Jammu and Kashmir, 192 101, India.
| | - Vinay Kumar
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | - Tushar Khare
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | | | | | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, ELTE-Eötvös Loránd University, Budapest, 1053, Hungary
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - P B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science Technology and Research, Vadlamudi, Guntur, 522 213, India
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41
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Abstract
Background Metabolic diseases such as obesity are known to be driven by both environmental and genetic factors. Although genome-wide association studies of common variants and their impact on complex traits have provided some biological insight into disease etiology, identified genetic variants have been found to contribute only a small proportion to disease heritability, and to map mainly to non-coding regions of the genome. To link variants to function, association studies of cellular traits, such as epigenetic marks, in disease-relevant tissues are commonly applied. Scope of the review We review large-scale efforts to generate genome-wide maps of coordinated epigenetic marks and their utility in complex disease dissection with a focus on DNA methylation. We contrast DNA methylation profiling methods and discuss the advantages of using targeted methods for single-base resolution assessments of methylation levels across tissue-specific regulatory regions to deepen our understanding of contributing factors leading to complex diseases. Major conclusions Large-scale assessments of DNA methylation patterns in metabolic disease-linked study cohorts have provided insight into the impact of variable epigenetic variants in disease etiology. In-depth profiling of epigenetic marks at regulatory regions, particularly at tissue-specific elements, will be key to dissect the genetic and environmental components contributing to metabolic disease onset and progression. Changes in epigenetic marks have been linked to metabolic disease phenotypes. Disease-linked sites of variable DNA methylation status are enriched in distal regulatory regions of disease-linked tissues. Distal regulatory elements remain underrepresented in popular array-based methylation profiling technologies. Novel next-generation capture methods provide cost-effective solutions to assess the impact of DNA methylation in metabolic diseases specifically at regulatory elements. Improvements in methodologies to account for tissue heterogeneity and causality will be crucial in future epigenome-wide association studies.
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Affiliation(s)
- Fiona Allum
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0C7, Canada; McGill University and Genome Quebec Innovation Centre, Montréal, Québec, H3A 0G1, Canada
| | - Elin Grundberg
- Children's Mercy Kansas City, Kansas City, MO, 64108, United States.
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Liu Y, He Y, Wang Y, Liu M, Jiang M, Gao R, Wang G. Synthetic promoter for efficient and muscle-specific expression of exogenous genes. Plasmid 2019; 106:102441. [PMID: 31676335 DOI: 10.1016/j.plasmid.2019.102441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 02/05/2023]
Abstract
Synthetic promoters (SPs) have many advantages over their natural counterparts, especially with regard to transcriptional activity and tissue specificity. Here, we report a new strategy to construct SPs for efficient and muscle-specific gene expression. First, 19 nucleic acid motifs classified to 3 kinds of transcriptional regulatory elements were rationally selected. A recombinant promoter library was constructed by randomly assembling these motifs. Second, the transcriptional activities of ~1200 SPs were screened by intramuscular expression of several reporter genes in different cell lines for activity higher than that of the cytomegalovirus (CMV) promoter, with SP-301 finally identified as the strongest. A single intramuscular injection of mice with an SP-301 plasmid expressing mouse growth hormone releasing hormone accelerated mouse growth significantly over 24 days. Third, the muscle specificity of SP-301 was confirmed in transgenic mice. Finally, in comparison with the CMV promoter, SP-301 accelerated translocation and increased the level of plasmid in the nuclei of myoblast cells to a greater extent than in non-muscle cells. Altogether, the study has provided a more rational strategy to construct efficient and tissue-specific promoters, with the promoter SP-301 exhibiting promising potential for establishing an intramuscular gene expression system for therapeutic applications.
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Affiliation(s)
- Yili Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China; National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, China; College of Life Science and Technology, Southwest Minzu University, Chengdu, Sichuan, China
| | - Yutong He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, China
| | - Yong Wang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, Sichuan, China
| | - Ming Liu
- Department of Medical Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mingfeng Jiang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, Sichuan, China
| | - Rong Gao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Gang Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan, China.
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Gong XX, Yan BY, Tan YR, Gao X, Wang D, Zhang H, Wang P, Li SJ, Wang Y, Zhou LY, Liu JP. Identification of cis-regulatory regions responsible for developmental and hormonal regulation of HbHMGS1 in transgenic Arabidopsis thaliana. Biotechnol Lett 2019; 41:1077-1091. [PMID: 31236789 DOI: 10.1007/s10529-019-02703-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/21/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVES 3-Hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase (HMGS) is an important enzyme in mevalonate (MVA) pathway of isoprenoid biosynthesis, which regulates the rubber biosynthetic pathway in rubber tree (Hevea brasiliensis) in coordination with HMG-CoA reductase (HMGR). However, little information is available about the regulation of HMGS gene expression. To understand the mechanism controlling the HbHMGS1 gene expression, we characterized the HbHMGS1 promoter sequence in transgenic plants with the β-glucuronidase (GUS) reporter gene. RESULTS GUS activity analysis of the transgenic plants showed that the HbHMGS1 promoter is active in all organs of the transgenic Arabidopsis plants during various developmental stages (from 6 to 45-day-old). Deletion of different portions of the upstream HbHMGS1 promoter identified sequences responsible for either positive or negative regulation of the GUS expression. Particularly, the - 454 bp HbHMGS1 promoter resulted in a 2.19-fold increase in promoter activity compared with the CaMV 35S promoter, suggesting that the - 454 bp HbHMGS1 promoter is a super-strong near-constitutive promoter. In addition, a number of promoter regions important for the responsiveness to ethylene, methyl jasmonate (MeJA) and gibberellic acid (GA) were identified. CONCLUSION The - 454 bp HbHMGS1 promoter has great application potential in plant transformation studies as an alternative to the CaMV 35S promoter. The HbHMGS1 promoter may play important roles in regulating ethylene-, MeJA- and GA-mediated gene expression. The functional complexity of cis-elements revealed by this study remains to be elucidated.
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Affiliation(s)
- Xiao-Xiao Gong
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Bing-Yu Yan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Yu-Rong Tan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Xuan Gao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Dan Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Heng Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Peng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Shuang-Jiang Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Yi Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Lu-Yao Zhou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Jin-Ping Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China.
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Chahal G, Tyagi S, Ramialison M. Navigating the non-coding genome in heart development and Congenital Heart Disease. Differentiation 2019; 107:11-23. [PMID: 31102825 DOI: 10.1016/j.diff.2019.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/14/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Congenital Heart Disease (CHD) is characterised by a wide range of cardiac defects, from mild to life-threatening, which occur in babies worldwide. To date, there is no cure to CHD, however, progress in surgery has reduced its mortality allowing children affected by CHD to reach adulthood. In an effort to understand its genetic basis, several studies involving whole-genome sequencing (WGS) of patients with CHD have been undertaken and generated a great wealth of information. The majority of putative causative mutations identified in WGS studies fall into the non-coding part of the genome. Unfortunately, due to the lack of understanding of the function of these non-coding mutations, it is challenging to establish a causal link between the non-coding mutation and the disease. Thus, here we review the state-of-the-art approaches to interpret non-coding mutations in the context of CHD and address the following questions: What are the non-coding sequences important for cardiac function? Which technologies are used to identify them? Which resources are available to analyse them? What mutations are expected in these non-coding sequences? Learning from developmental process, what is their expected role in CHD?
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Affiliation(s)
- Gulrez Chahal
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia
| | - Sonika Tyagi
- School of Biological Sciences, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Australian Genome Research Facility, 305 Grattan Street, Melbourne, VIC, 3000, Australia.
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia.
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Bertini V, Valetto A, Baldinotti F, Azzarà A, Cambi F, Toschi B, Giacomina A, Gatti GL, Gana S, Caligo MA, Bertelloni S. Blepharophimosis, Ptosis, Epicanthus Inversus Syndrome: New Report with a 197-kb Deletion Upstream of FOXL2 and Review of the Literature. Mol Syndromol 2019; 10:147-153. [PMID: 31191203 DOI: 10.1159/000497092] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2018] [Indexed: 11/19/2022] Open
Abstract
Blepharophimosis, ptosis, and epicanthus inversus syndrome (BPES) is due to heterozygous FOXL2 intragenic mutations in about 70% of the patients, whereas total or partial gene deletions account for a minority of cases. Alteration of FOXL2 regulatory elements has been rarely described in patients with BPES. In this study, a prepubertal girl with BPES due to a 197-kb de novo deletion of the regulatory elements upstream of FOXL2 is reported. This girl presented with additional clinical features such as a soft cleft palate and microcephaly; thus, this copy number variant might have other somatic effects. The present deletion encompasses 2 coding genes (MRPS22 and COPB2), whose homozygous mutations have been associated with microcephaly. In our case, the sequences of the non-deleted allele were normal, ruling out a compound genetic defect. Normal levels of new biomarkers of ovarian reserve (anti-müllerian hormone, inhibin B) likely indicate an early diagnosis of type 2 BPES, but an evolutive gonadal damage will be excluded only by long-term follow-up. Additional reports of microdeletions upstream of FOXL2 are needed to better define the underlying genetic mechanism and the related phenotypic spectrum; the ability of the new hormonal markers to predict ovarian function in adolescence and adulthood should be confirmed.
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Affiliation(s)
- Veronica Bertini
- SOD Citogenetica, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Angelo Valetto
- SOD Citogenetica, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Fulvia Baldinotti
- SOD Genetica Molecolare, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Alessia Azzarà
- SOD Citogenetica, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Francesca Cambi
- SOD Citogenetica, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Benedetta Toschi
- Sezione Genetica Medica, Medicina Interna 1, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | | | - Gian L Gatti
- U.O. Chirurgia Plastica, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Simone Gana
- Sezione Genetica Medica, Medicina Interna 1, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Maria A Caligo
- SOD Genetica Molecolare, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Silvano Bertelloni
- Pediatric Division, Department of Obstetrics, Gynecology and Pediatrics, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
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Abstract
The bipotential nature of cell types in the early developing gonad and the process of sex determination leading to either testis or ovary differentiation makes this an interesting system in which to study transcriptional regulation of gene expression and cell fate decisions. SOX9 is a transcription factor with multiple roles during development, including being a key player in mediating testis differentiation and therefore subsequent male development. Loss of Sox9 expression in both humans and mice results in XY female development, whereas its inappropriate activation in XX embryonic gonads can give male development. Multiple cases of Disorders of Sex Development in human patients or sex reversal in mice and other vertebrates can be explained by mutations affecting upstream regulators of Sox9 expression, such as the product of the Y chromosome gene Sry that triggers testis differentiation. Other cases are due to mutations in the Sox9 gene itself, including its own regulatory region. Indeed, rearrangements in and around the Sox9 genomic locus indicate the presence of multiple critical enhancers and the complex nature of its regulation. Here we summarize what is known about the role of Sox9 and its regulation during gonad development, including recently discovered critical enhancers. We also discuss higher order chromatin organization and how this might be involved. We end with some interesting future directions that have the potential to further enrich our understanding on the complex, multi-layered regulation controlling Sox9 expression in the gonads.
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Affiliation(s)
- Nitzan Gonen
- The Francis Crick Institute, London, United Kingdom.
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47
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Garcia-Moreno SA, Futtner CR, Salamone IM, Gonen N, Lovell-Badge R, Maatouk DM. Gonadal supporting cells acquire sex-specific chromatin landscapes during mammalian sex determination. Dev Biol 2018; 446:168-179. [PMID: 30594505 DOI: 10.1016/j.ydbio.2018.12.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/09/2018] [Accepted: 12/24/2018] [Indexed: 12/22/2022]
Abstract
Cis-regulatory elements are critical for the precise spatiotemporal regulation of genes during development. However, identifying functional regulatory sites that drive cell differentiation in vivo has been complicated by the high numbers of cells required for whole-genome epigenetic assays. Here, we identified putative regulatory elements during sex determination by performing ATAC-seq and ChIP-seq for H3K27ac in purified XX and XY gonadal supporting cells before and after sex determination in mice. We show that XX and XY supporting cells initiate sex determination with similar chromatin landscapes and acquire sex-specific regulatory elements as they commit to the male or female fate. To validate our approach, we identified a functional gonad-specific enhancer downstream of Bmp2, an ovary-promoting gene. This work increases our understanding of the complex regulatory network underlying mammalian sex determination and provides a powerful resource for identifying non-coding regulatory elements that could harbor mutations that lead to Disorders of Sexual Development.
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Affiliation(s)
| | - Christopher R Futtner
- Department of Endocrinology, Northwestern University, Chicago, IL 60611, United States.
| | - Isabella M Salamone
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Nitzan Gonen
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Danielle M Maatouk
- Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL 60611, United States
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48
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Plágaro AH, Pearman PB, Kaberdin VR. Defining the transcription landscape of the Gram-negative marine bacterium Vibrio harveyi. Genomics 2018; 111:1547-1556. [PMID: 30423347 DOI: 10.1016/j.ygeno.2018.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/13/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022]
Abstract
Vibrio harveyi is a Gram-negative pathogenic bacterium ubiquitously present in natural aquatic systems. Although environmental adaptability in V. harveyi may be enabled by profound reprogramming of gene expression previously observed during responses to starvation, suboptimal temperatures and other stress factors, the key characteristics of V. harveyi transcripts and operons, such as their boundaries and size as well as location of small RNA genes, remain largely unknown. To reveal the main features of the V. harveyi transcriptome, total RNA of this organism was analyzed by differential RNA sequencing (dRNA-seq). Analysis of the dRNA-seq data made it possible to define the primary transcriptome of V. harveyi along with cis-acting regulatory elements (riboswitches and leader sequences) and new genes. The latter encode a number of putative polypeptides and new phylogenetically conserved antisense RNAs potentially involved in the post-transcriptional control of gene expression.
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Affiliation(s)
- Ander Hernández Plágaro
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain.
| | - Peter B Pearman
- Department of Plant Biology and Ecology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), 48620 Plentzia, Spain.
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49
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Lyons-Weiler J, Ricketson R. Reconsideration of the immunotherapeutic pediatric safe dose levels of aluminum. J Trace Elem Med Biol 2018; 48:67-73. [PMID: 29773196 DOI: 10.1016/j.jtemb.2018.02.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 12/31/2017] [Accepted: 02/26/2018] [Indexed: 12/21/2022]
Abstract
FDA regulations require safety testing of constituent ingredients in drugs (21 CFR 610.15). With the exception of extraneous proteins, no component safety testing is required for vaccines or vaccine schedules. The dosing of aluminum in vaccines is based on the production of antibody titers, not safety science. Here we estimate a Pediatric Dose Limit that considers body weight. We identify several serious historical missteps in past analyses of provisional safe levels of aluminum in vaccines, and provide updates relevant to infant aluminum exposure in the pediatric schedule considering pediatric body weight. When aluminum doses are estimated from Federal Regulatory Code given body weight, exposure from the current vaccine schedule are found to exceed our estimate of a weight-corrected Pediatric Dose Limit. Our calculations show that the levels of aluminum suggested by the currently used limits place infants at risk of acute, repeated, and possibly chronic exposures of toxic levels of aluminum in modern vaccine schedules. Individual adult exposures are on par with Provisional Tolerable Weekly Intake "limits", but some individuals may be aluminum intolerant due to genetics or previous exposures. Vaccination in neonates and low birth-weight infants must be re-assessed; other implications for the use of aluminum-containing vaccines, and additional limitations in our understanding of neurotoxicity and safety levels of aluminum in biologics are discussed.
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Affiliation(s)
- James Lyons-Weiler
- Institute for Pure and Applied Knowledge, 2912 Kilcairn Lane, Allison, PA 15101, United States.
| | - Robert Ricketson
- Hale O'mana'o Research, 19 West Edwards Street, Edmond, OK 73003, United States.
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50
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Mahmood T, Tahir T, Munir F, Shinwari ZK. Characterization of regulatory elements in OsRGLP2 gene promoter from different rice accessions through sequencing and in silico evaluation. Comput Biol Chem 2018; 73:206-12. [PMID: 29501997 DOI: 10.1016/j.compbiolchem.2018.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 02/17/2018] [Accepted: 02/20/2018] [Indexed: 12/18/2022]
Abstract
Germins and germin-like proteins from cupin superfamily contribute resistance to heat denaturation, chemical degradation and against plant pathogens, further functions in plant growth and development. In this study, from three different Oryza sativa accessions KS-282 and Pak 7178 and Pak 7865, OsRGLP2 gene promoter region was amplified, sequenced and analyzed. Sequencing data was evaluated via different computational tools. The regulatory elements were predicted by Consite tool and mapping was done. Many transcription factors binding sites were discovered in OsRGLP2 gene promoter; among these factors, HFH-1 having a significant role in germination was picked for further investigation. To study the interaction between HFH-1 and corresponding regulatory factors, HADDOCK Webserver was used. Graphical models for the interactions of HFH-1 and related regulatory elements were studied by graphic molecular system PyMOL. Mapping of cis-acting regulatory elements in OsRGLP2 gene promoter from three rice accessions showed differences in their position and copy number. Important regulatory elements found in OsRGLP2 promoter region were TATA, CAAT Box, ARR1, GATA, AGAAA, CAAT and DNA-binding One Zinc Finger (Dof) factors, few of them contribute to the regulation of plant defensive system, light responses, developmental and growth activities. Furthermore, during DNA interaction studies, it was found that HFH-1 transcription factor participates in hydrogen bonds formation with thymine and adenine bases.
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