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Truesdell P, Chang J, Coto Villa D, Dai M, Zhao Y, McIlwain R, Young S, Hiley S, Craig AW, Babak T. Pharmacogenomic discovery of genetically targeted cancer therapies optimized against clinical outcomes. NPJ Precis Oncol 2024; 8:186. [PMID: 39198692 PMCID: PMC11358483 DOI: 10.1038/s41698-024-00673-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 08/07/2024] [Indexed: 09/01/2024] Open
Abstract
Despite the clinical success of dozens of genetically targeted cancer therapies, the vast majority of patients with tumors caused by loss-of-function (LoF) mutations do not have access to these treatments. This is primarily due to the challenge of developing a drug that treats a disease caused by the absence of a protein target. The success of PARP inhibitors has solidified synthetic lethality (SL) as a means to overcome this obstacle. Recent mapping of SL networks using pooled CRISPR-Cas9 screens is a promising approach for expanding this concept to treating cancers driven by additional LoF drivers. In practice, however, translating signals from cell lines, where these screens are typically conducted, to patient outcomes remains a challenge. We developed a pharmacogenomic (PGx) approach called "Clinically Optimized Driver Associated-PGx" (CODA-PGX) that accurately predicts genetically targeted therapies with clinical-stage efficacy in specific LoF driver contexts. Using approved targeted therapies and cancer drugs with available real-world evidence and molecular data from hundreds of patients, we discovered and optimized the key screening principles predictive of efficacy and overall patient survival. In addition to establishing basic technical conventions, such as drug concentration and screening kinetics, we found that replicating the driver perturbation in the right context, as well as selecting patients where those drivers are genuine founder mutations, were key to accurate translation. We used CODA-PGX to screen a diverse collection of clinical stage drugs and report dozens of novel LoF genetically targeted opportunities; many validated in xenografts and by real-world evidence. Notable examples include treating STAG2-mutant tumors with Carboplatin, SMARCB1-mutant tumors with Oxaliplatin, and TP53BP1-mutant tumors with Etoposide or Bleomycin.
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Affiliation(s)
- Peter Truesdell
- Leapfrog Bio, San Mateo, USA
- Cancer Biology & Genetics, Queen's Cancer Research Institute; Queen's University, Kingston, Canada
| | | | | | - Meiou Dai
- Leapfrog Bio, San Mateo, USA
- Cancer Biology & Genetics, Queen's Cancer Research Institute; Queen's University, Kingston, Canada
| | - Yulei Zhao
- Cancer Biology & Genetics, Queen's Cancer Research Institute; Queen's University, Kingston, Canada
- Department of Cellular and Genetic Medicine, Frontier innovation center, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Robin McIlwain
- Leapfrog Bio, San Mateo, USA
- Cancer Biology & Genetics, Queen's Cancer Research Institute; Queen's University, Kingston, Canada
| | - Stephanie Young
- Cancer Biology & Genetics, Queen's Cancer Research Institute; Queen's University, Kingston, Canada
| | - Shawna Hiley
- Third Degree Science Communication, Edmonton, Canada
| | - Andrew W Craig
- Cancer Biology & Genetics, Queen's Cancer Research Institute; Queen's University, Kingston, Canada
| | - Tomas Babak
- Leapfrog Bio, San Mateo, USA.
- Department of Biology; Queen's University, Kingston, Canada.
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Huang R, Xu F, Su L, Lu Y, Liu W, Liu S, Yang L, Su L, Song W. PWP1 is overexpressed in hepatocellular carcinoma and facilitates liver cancer cell proliferation. Heliyon 2024; 10:e32409. [PMID: 38933950 PMCID: PMC11200354 DOI: 10.1016/j.heliyon.2024.e32409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Identification of novel biomarkers for prediction of disease course and prognosis is needed to reduce morbidity of liver hepatocellular carcinoma (LIHC/HCC) patients. Although dysregulated Periodic tryptophan protein 1 homolog (PWP1/endonuclein) expression has been detected in several tumors, the potential regulatory effect of PWP1 on LIHC remains uncertain. Here we evaluated the expression of PWP1 using multiple online platforms, and demonstrated that PWP1 upregulation was consistently observed in LIHC relative to non-tumor liver tissues and correlated with unfavorable prognosis. Moreover, HCC prognosis was significantly influenced by the methylation status of various CpG sites in the PWP1 gene. Lastly, we provide direct evidence that PWP1 acts as a driver of HCC progression by showing that siRNA-mediated PWP1 silencing significantly suppressed HCC cell proliferation in vitro. These data strongly suggest that PWP1 silencing may be an effective therapeutic strategy to treat LIHC.
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Affiliation(s)
- Rong Huang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Fu Xu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Luying Su
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yan Lu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Wei Liu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Shuaihu Liu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Ling Yang
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Inner Mongolia Key Laboratory of Medical Cell Biology, 1 Tong Dao Street, Hohhot, 010050, Inner Mongolia, China
| | - Liya Su
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Inner Mongolia Key Laboratory of Medical Cell Biology, 1 Tong Dao Street, Hohhot, 010050, Inner Mongolia, China
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
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Fogarty EA, Buchert EM, Ma Y, Nicely AB, Buttitta LA. Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592773. [PMID: 38766255 PMCID: PMC11100713 DOI: 10.1101/2024.05.06.592773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The mechanisms that maintain a non-cycling status in postmitotic tissues are not well understood. Many cell cycle genes have promoters and enhancers that remain accessible even when cells are terminally differentiated and in a non-cycling state, suggesting their repression must be maintained long term. In contrast, enhancer decommissioning has been observed for rate-limiting cell cycle genes in the Drosophila wing, a tissue where the cells die soon after eclosion, but it has been unclear if this also occurs in other contexts of terminal differentiation. In this study, we show that enhancer decommissioning also occurs at specific, rate-limiting cell cycle genes in the long-lived tissues of the Drosophila eye and brain, and we propose this loss of chromatin accessibility may help maintain a robust postmitotic state. We examined the decommissioned enhancers at specific rate-limiting cell cycle genes and show that they encode dynamic temporal and spatial expression patterns that include shared, as well as tissue-specific elements, resulting in broad gene expression with developmentally controlled temporal regulation. We extend our analysis to cell cycle gene expression and chromatin accessibility in the mammalian retina using a published dataset, and find that the principles of cell cycle gene regulation identified in terminally differentiating Drosophila tissues are conserved in the differentiating mammalian retina. We propose a robust, non-cycling status is maintained in long-lived postmitotic tissues through a combination of stable repression at most cell cycle gens, alongside enhancer decommissioning at specific rate-limiting cell cycle genes.
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Affiliation(s)
- Elizabeth A. Fogarty
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Elli M. Buchert
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Yiqin Ma
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Ava B. Nicely
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Laura A. Buttitta
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
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Fernández-Fernández J, Martín-Villanueva S, Perez-Fernandez J, de la Cruz J. The Role of Ribosomal Proteins eL15 and eL36 in the Early Steps of Yeast 60S Ribosomal Subunit Assembly. J Mol Biol 2023; 435:168321. [PMID: 37865285 DOI: 10.1016/j.jmb.2023.168321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
Ribosomal proteins have important roles in maintaining the structure and function of mature ribosomes, but they also drive crucial rearrangement reactions during ribosome biogenesis. The contribution of most, but not all, ribosomal proteins to ribosome synthesis has been previously analyzed in the yeast Saccharomyces cerevisiae. Herein, we characterize the role of yeast eL15 during 60S ribosomal subunit formation. In vivo depletion of eL15 results in a shortage of 60S subunits and the appearance of half-mer polysomes. This is likely due to defective processing of the 27SA3 to the 27SBS pre-rRNA and impaired subsequent processing of both forms of 27SB pre-rRNAs to mature 25S and 5.8S rRNAs. Indeed, eL15 depletion leads to the efficient turnover of the de novo formed 27S pre-rRNAs. Additionally, depletion of eL15 blocks nucleocytoplasmic export of pre-60S particles. Moreover, we have analyzed the impact of depleting either eL15 or eL36 on the composition of early pre-60S particles, thereby revealing that the depletion of eL15 or eL36 not only affects each other's assembly into pre-60S particles but also that of neighboring ribosomal proteins, including eL8. These intermediates also lack most ribosome assembly factors required for 27SA3 and 27SB pre-rRNA processing, named A3- and B-factors, respectively. Importantly, our results recapitulate previous ones obtained upon eL8 depletion. We conclude that assembly of eL15, together with that of eL8 and eL36, is a prerequisite to shape domain I of 5.8S/25S rRNA within early pre-60S particles, through their binding to this rRNA domain and the recruitment of specific groups of assembly factors.
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Affiliation(s)
- José Fernández-Fernández
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
| | - Jorge Perez-Fernandez
- Department of Biochemistry III, University of Regensburg, D-93051 Regensburg, Germany.
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain.
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Liu H, Xiu Z, Yang H, Ma Z, Yang D, Wang H, Tan BC. Maize Shrek1 encodes a WD40 protein that regulates pre-rRNA processing in ribosome biogenesis. THE PLANT CELL 2022; 34:4028-4044. [PMID: 35867001 PMCID: PMC9516035 DOI: 10.1093/plcell/koac216] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Ribosome biogenesis is a fundamental and highly orchestrated process that involves hundreds of ribosome biogenesis factors. Despite advances that have been made in yeast, the molecular mechanism of ribosome biogenesis remains largely unknown in plants. We uncovered a WD40 protein, Shrunken and Embryo Defective Kernel 1 (SHREK1), and showed that it plays a crucial role in ribosome biogenesis and kernel development in maize (Zea mays). The shrek1 mutant shows an aborted embryo and underdeveloped endosperm and embryo-lethal in maize. SHREK1 localizes mainly to the nucleolus and accumulates to high levels in the seed. Depleting SHREK1 perturbs pre-rRNA processing and causes imbalanced profiles of mature rRNA and ribosome. The expression pattern of ribosomal-related genes is significantly altered in shrek1. Like its yeast (Saccharomyces cerevisiae) ortholog Periodic tryptophan protein 1 (PWP1), SHREK1 physically interacts with ribosomal protein ZmRPL7a, a transient component of the PWP1-subcomplex involved in pre-rRNA processing in yeast. Additionally, SHREK1 may assist in the A3 cleavage of the pre-rRNA in maize by interacting with the nucleolar protein ZmPOP4, a maize homolog of the yeast RNase mitochondrial RNA-processing complex subunit. Overall, our work demonstrates a vital role of SHREK1 in pre-60S ribosome maturation, and reveals that impaired ribosome function accounts for the embryo lethality in shrek1.
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Affiliation(s)
- Hui Liu
- School of Life Sciences, The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, Shandong University, Qingdao 266237, China
| | - Zhihui Xiu
- School of Life Sciences, The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, Shandong University, Qingdao 266237, China
| | - Huanhuan Yang
- School of Life Sciences, The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, Shandong University, Qingdao 266237, China
| | - Zhaoxing Ma
- School of Life Sciences, The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, Shandong University, Qingdao 266237, China
| | - Dalin Yang
- School of Life Sciences, The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, Shandong University, Qingdao 266237, China
| | - Hongqiu Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
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6
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Approaches in Gene Coexpression Analysis in Eukaryotes. BIOLOGY 2022; 11:biology11071019. [PMID: 36101400 PMCID: PMC9312353 DOI: 10.3390/biology11071019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/22/2022]
Abstract
Simple Summary Genes whose expression levels rise and fall similarly in a large set of samples, may be considered coexpressed. Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. Coexpressed genes are clustered in smaller subnetworks, the predominant biological roles of which can be determined through enrichment analysis. By studying well-annotated gene partners, the attribution of new roles to genes of unknown function or assumption for participation in common metabolic pathways can be achieved, through a guilt-by-association approach. In this review, we present key issues in gene coexpression analysis, as well as the most popular tools that perform it. Abstract Gene coexpression analysis constitutes a widely used practice for gene partner identification and gene function prediction, consisting of many intricate procedures. The analysis begins with the collection of primary transcriptomic data and their preprocessing, continues with the calculation of the similarity between genes based on their expression values in the selected sample dataset and results in the construction and visualisation of a gene coexpression network (GCN) and its evaluation using biological term enrichment analysis. As gene coexpression analysis has been studied extensively, we present most parts of the methodology in a clear manner and the reasoning behind the selection of some of the techniques. In this review, we offer a comprehensive and comprehensible account of the steps required for performing a complete gene coexpression analysis in eukaryotic organisms. We comment on the use of RNA-Seq vs. microarrays, as well as the best practices for GCN construction. Furthermore, we recount the most popular webtools and standalone applications performing gene coexpression analysis, with details on their methods, features and outputs.
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Jiang JC, Rothnagel JA, Upton KR. Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer. Int J Mol Sci 2021; 22:5625. [PMID: 34070697 PMCID: PMC8199441 DOI: 10.3390/ijms22115625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/29/2022] Open
Abstract
L1 transposons occupy 17% of the human genome and are widely exapted for the regulation of human genes, particularly in breast cancer, where we have previously shown abundant cancer-specific transcription factor (TF) binding sites within the L1PA2 subfamily. In the current study, we performed a comprehensive analysis of TF binding activities in primate-specific L1 subfamilies and identified pervasive exaptation events amongst these evolutionarily related L1 transposons. By motif scanning, we predicted diverse and abundant TF binding potentials within the L1 transposons. We confirmed substantial TF binding activities in the L1 subfamilies using TF binding sites consolidated from an extensive collection of publicly available ChIP-seq datasets. Young L1 subfamilies (L1HS, L1PA2 and L1PA3) contributed abundant TF binding sites in MCF7 cells, primarily via their 5' UTR. This is expected as the L1 5' UTR hosts cis-regulatory elements that are crucial for L1 replication and mobilisation. Interestingly, the ancient L1 subfamilies, where 5' truncation was common, displayed comparable TF binding capacity through their 3' ends, suggesting an alternative exaptation mechanism in L1 transposons that was previously unnoticed. Overall, primate-specific L1 transposons were extensively exapted for TF binding in MCF7 breast cancer cells and are likely prominent genetic players modulating breast cancer transcriptional regulation.
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Affiliation(s)
| | | | - Kyle R. Upton
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (J.-C.J.); (J.A.R.)
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Yu K, Rodriguez M, Paul Z, Gordon E, Gu T, Rice K, Triplett EW, Keller-Wood M, Wood CE. Transfer of oral bacteria to the fetus during late gestation. Sci Rep 2021; 11:708. [PMID: 33436911 PMCID: PMC7804304 DOI: 10.1038/s41598-020-80653-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
The fetus develops in a privileged environment, as the placenta serves as both a gateway for nutrients and a barrier for pathogen transfer to the fetus. Regardless, recent evidence suggests the presence of bacterial DNA in both placenta and fetus, and we have reported that DNA and protein from small numbers of bacteria gain access to the fetus from the maternal bloodstream. Other routes of environmental bacterial transfer from the mother to fetus remain unknown, as well as the physiological relevance of their presence. In these experiments, we examine multiple routes by which bacterial cellular components can enter the fetus and the fetal response to influx of bacterial DNA and protein. We inoculated maternal sheep with genetically-labeled S. aureus (Staphylococcus aureus) using three routes: intravenously, orally, and intra-vaginally. The inoculum did not produce sepsis or fever in the ewes, therefore mimicking incidental exposure to bacteria during pregnancy. 3-5 days post inoculation, we assessed the presence of bacterial components in the fetal tissues and analyzed fetal brain tissue to identify any alterations in gene expression. Our results demonstrate that components of bacteria that were introduced into the maternal mouth were detected in the fetal brain and that they stimulated changes in gene expression. We conclude that an oral route of transmission is relevant for transfer of bacterial cellular components to the fetus.
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Affiliation(s)
- Kevin Yu
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1345 Center Drive, Room M552, Gainesville, FL, 32610, USA
| | - Michelle Rodriguez
- Department of Microbiology and Cell Science, University of Florida Institute of Food and Agricultural Sciences, Gainesville, USA
| | - Zubin Paul
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1345 Center Drive, Room M552, Gainesville, FL, 32610, USA
| | - Elizabeth Gordon
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1345 Center Drive, Room M552, Gainesville, FL, 32610, USA
| | - Tongjun Gu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
| | - Kelly Rice
- Department of Microbiology and Cell Science, University of Florida Institute of Food and Agricultural Sciences, Gainesville, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida Institute of Food and Agricultural Sciences, Gainesville, USA
| | - Maureen Keller-Wood
- Department of Pharmacodynamics, University of Florida College of Pharmacy, Gainesville, USA
| | - Charles E Wood
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, 1345 Center Drive, Room M552, Gainesville, FL, 32610, USA.
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Han XR, Sasaki N, Jackson SC, Wang P, Li Z, Smith MD, Xie L, Chen X, Zhang Y, Marzluff WF, Xiong Y. CRL4 DCAF1/VprBP E3 ubiquitin ligase controls ribosome biogenesis, cell proliferation, and development. SCIENCE ADVANCES 2020; 6:eabd6078. [PMID: 33355139 PMCID: PMC11206221 DOI: 10.1126/sciadv.abd6078] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/27/2020] [Indexed: 06/12/2023]
Abstract
Evolutionarily conserved DCAF1 is a major substrate receptor for the DDB1-CUL4-ROC1 E3 ubiquitin ligase (CRL4) and controls cell proliferation and development. The molecular basis for these functions is unclear. We show here that DCAF1 loss in multiple tissues and organs selectively eliminates proliferating cells and causes perinatal lethality, thymic atrophy, and bone marrow defect. Inducible DCAF1 loss eliminates proliferating, but not quiescent, T cells and MEFs. We identify the ribosome assembly factor PWP1 as a substrate of the CRL4DCAF1 ligase. DCAF1 loss results in PWP1 accumulation, impairing rRNA processing and ribosome biogenesis. Knockdown or overexpression of PWP1 can rescue defects or cause similar defects as DCAF1 loss, respectively, in ribosome biogenesis. DCAF1 loss increases free RPL11, resulting in L11-MDM2 association and p53 activation. Cumulatively, these results reveal a critical function for DCAF1 in ribosome biogenesis and define a molecular basis of DCAF1 function in cell proliferation and development.
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Affiliation(s)
- Xiao-Ran Han
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Naoya Sasaki
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah C Jackson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Pu Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhijun Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew D Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ling Xie
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xian Chen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yanping Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William F Marzluff
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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10
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Moradifard S, Hoseinbeyki M, Emam MM, Parchiniparchin F, Ebrahimi-Rad M. Association of the Sp1 binding site and -1997 promoter variations in COL1A1 with osteoporosis risk: The application of meta-analysis and bioinformatics approaches offers a new perspective for future research. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2020; 786:108339. [PMID: 33339581 DOI: 10.1016/j.mrrev.2020.108339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 08/11/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022]
Abstract
As a complex disease, osteoporosis is influenced by several genetic markers. Many studies have examined the link between the Sp1 binding site +1245 G > T (rs1800012) and -1997 G > T (rs1107946) variations in the COL1A1 gene with osteoporosis risk. However, the findings of these studies have been contradictory; therefore, we performed a meta-analysis to aggregate additional information and obtain increased statistical power to more efficiently estimate this correlation. A meta-analysis was conducted with studies published between 1991-2020 that were identified by a systematic electronic search of the Scopus and Clarivate Analytics databases. Studies with bone mineral density (BMD) data and complete genotypes of the single-nucleotide variations (SNVs) for the overall and postmenopausal female population were included in this meta-analysis and analyzed using the R metaphor package. A relationship between rs1800012 and significantly decreased BMD values at the lumbar spine and femoral neck was found in individuals carrying the "ss" versus the "SS" genotype in the overall population according to a random effects model (p < 0.0001). Similar results were also found in the postmenopausal female population (p = 0.003 and 0.0002, respectively). Such findings might be an indication of increased osteoporosis risk in both studied groups in individuals with the "ss" genotype. Although no association was identified between the -1997 G > T and low BMD in the overall population, those individuals with the "GT" genotype showed a higher level of BMD than those with "GG" in the subgroup analysis (p = 0.007). To determine which transcription factor (TF) might bind to the -1997 G > T in COL1A1, 45 TFs were identified based on bioinformatics predictions. According to the GSE35958 microarray dataset, 16 of 45 TFs showed differential expression profiles in osteoporotic human mesenchymal stem cells relative to normal samples from elderly donors. By identifying candidate TFs for the -1997 G > T site, our study offers a new perspective for future research.
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Affiliation(s)
| | | | - Mohammad Mehdi Emam
- Rheumatology Ward, Loghman Hospital, Shahid Beheshti Medical University (SBMU), Tehran, Iran
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Huang SSY, Makhlouf M, AbouMoussa EH, Ruiz Tejada Segura ML, Mathew LS, Wang K, Leung MC, Chaussabel D, Logan DW, Scialdone A, Garand M, Saraiva LR. Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting. Mol Metab 2020; 40:101038. [PMID: 32526449 PMCID: PMC7339127 DOI: 10.1016/j.molmet.2020.101038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/24/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Fasting regimens can promote health, mitigate chronic immunological disorders, and improve age-related pathophysiological parameters in animals and humans. Several ongoing clinical trials are using fasting as a potential therapy for various conditions. Fasting alters metabolism by acting as a reset for energy homeostasis, but the molecular mechanisms underlying the beneficial effects of short-term fasting (STF) are not well understood, particularly at the systems or multiorgan level. METHODS We performed RNA-sequencing in nine organs from mice fed ad libitum (0 h) or subjected to fasting five times (2-22 h). We applied a combination of multivariate analysis, differential expression analysis, gene ontology, and network analysis for an in-depth understanding of the multiorgan transcriptome. We used literature mining solutions, LitLab™ and Gene Retriever™, to identify the biological and biochemical terms significantly associated with our experimental gene set, which provided additional support and meaning to the experimentally derived gene and inferred protein data. RESULTS We cataloged the transcriptional dynamics within and between organs during STF and discovered differential temporal effects of STF among organs. Using gene ontology enrichment analysis, we identified an organ network sharing 37 common biological pathways perturbed by STF. This network incorporates the brain, liver, interscapular brown adipose tissue, and posterior-subcutaneous white adipose tissue; hence, we named it the brain-liver-fats organ network. Using Reactome pathways analysis, we identified the immune system, dominated by T cell regulation processes, as a central and prominent target of systemic modulations during STF in this organ network. The changes we identified in specific immune components point to the priming of adaptive immunity and parallel the fine-tuning of innate immune signaling. CONCLUSIONS Our study provides a comprehensive multiorgan transcriptomic profiling of mice subjected to multiple periods of STF and provides new insights into the molecular modulators involved in the systemic immunotranscriptomic changes that occur during short-term energy loss.
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Affiliation(s)
| | | | | | - Mayra L Ruiz Tejada Segura
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Marchioninistraße 25, 81377, München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | | | - Kun Wang
- Sidra Medicine, PO Box 26999, Doha, Qatar.
| | | | | | - Darren W Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Marchioninistraße 25, 81377, München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | | | - Luis R Saraiva
- Sidra Medicine, PO Box 26999, Doha, Qatar; Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA, 19104, USA.
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12
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Menendez L, Trecek T, Gopalakrishnan S, Tao L, Markowitz AL, Yu HV, Wang X, Llamas J, Huang C, Lee J, Kalluri R, Ichida J, Segil N. Generation of inner ear hair cells by direct lineage conversion of primary somatic cells. eLife 2020; 9:e55249. [PMID: 32602462 PMCID: PMC7326493 DOI: 10.7554/elife.55249] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
The mechanoreceptive sensory hair cells in the inner ear are selectively vulnerable to numerous genetic and environmental insults. In mammals, hair cells lack regenerative capacity, and their death leads to permanent hearing loss and vestibular dysfunction. Their paucity and inaccessibility has limited the search for otoprotective and regenerative strategies. Growing hair cells in vitro would provide a route to overcome this experimental bottleneck. We report a combination of four transcription factors (Six1, Atoh1, Pou4f3, and Gfi1) that can convert mouse embryonic fibroblasts, adult tail-tip fibroblasts and postnatal supporting cells into induced hair cell-like cells (iHCs). iHCs exhibit hair cell-like morphology, transcriptomic and epigenetic profiles, electrophysiological properties, mechanosensory channel expression, and vulnerability to ototoxin in a high-content phenotypic screening system. Thus, direct reprogramming provides a platform to identify causes and treatments for hair cell loss, and may help identify future gene therapy approaches for restoring hearing.
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Affiliation(s)
- Louise Menendez
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
| | - Talon Trecek
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Suhasni Gopalakrishnan
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
| | - Litao Tao
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Alexander L Markowitz
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
- USC Caruso Department of Otolaryngology – Head and Neck Surgery, University of Southern CaliforniaLos AngelesUnited States
| | - Haoze V Yu
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Xizi Wang
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Juan Llamas
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | | | - James Lee
- DRVision TechnologiesBellevueUnited States
| | - Radha Kalluri
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
- USC Caruso Department of Otolaryngology – Head and Neck Surgery, University of Southern CaliforniaLos AngelesUnited States
| | - Justin Ichida
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
| | - Neil Segil
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- USC Caruso Department of Otolaryngology – Head and Neck Surgery, University of Southern CaliforniaLos AngelesUnited States
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13
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Murad MW, Khan MA, Islam MS, Islam ABMMK. A switch in bidirectional histone mark leads to differential modulation of lincRNAs involved in neuronal and hematopoietic cell differentiation from their progenitors. J Cell Biochem 2020; 121:3451-3462. [DOI: 10.1002/jcb.29619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 12/09/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Md. Wahid Murad
- Department of Genetic Engineering and BiotechnologyUniversity of Dhaka Dhaka Bangladesh
| | | | - Md. Sajedul Islam
- Department of Genetic Engineering and BiotechnologyUniversity of Dhaka Dhaka Bangladesh
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14
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Abdallah F, Pichon C. Evidence on the direct correlation between miR-31 and IL-22 axis in IMQ-induced psoriasis. Exp Dermatol 2019; 28:1336-1340. [PMID: 31278779 DOI: 10.1111/exd.14001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/03/2019] [Accepted: 06/21/2019] [Indexed: 11/28/2022]
Abstract
Psoriatic skin is characterized by a deregulated profile of miRNAs that are contributing in disease development. In this study, we focus on miR-31, one of the upregulated miRNAs known to promote keratinocytes proliferation and migration. Moreover, miR-31 expression induction was dependent on a large panel of cytokines including IL-22. Here, we aimed at investigating the relationship between miR-31-5p and IL-22 axis; and by searching novel molecular target for miR-31-5p in keratinocytes. Our data identify a direct correlation between miR-31-5p and IL-22 in psoriasis with Pwp1 as new potential target. These findings confirm the important role of miR-31 in psoriasis onset and provide a basis for further investigations in miRNAs field in context of skin diseases.
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Affiliation(s)
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Orléans, France
- Université d'Orléans, Colleguim Sciences et Techniques, Orléans, France
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15
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Genome Wide Analysis of WD40 Proteins in Saccharomyces cerevisiae and Their Orthologs in Candida albicans. Protein J 2019; 38:58-75. [PMID: 30511317 DOI: 10.1007/s10930-018-9804-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The WD40 domain containing proteins are present in the lower organisms (Monera) to higher complex metazoans with involvement in diverse cellular processes. The WD40 repeats fold into β propeller structure due to which the proteins harbouring WD40 domains function as scaffold by offering platform for interactions, bring together diverse cellular proteins to form a single complex for mediating downstream effects. Multiple functions of WD40 domain containing proteins in lower eukaryote as in Fungi have been reported with involvement in vegetative and reproductive growth, virulence etc. In this article insilico analysis of the WDR proteins in the budding yeast Saccharomyces cerevisiae was performed. By WDSP software 83 proteins in S. cerevisiae were identified with at least one WD40 motif. WD40 proteins with 6 or more WD40 motifs were considered for further studies. The WD40 proteins in yeast which are involved in various biological processes show distribution on all chromosomes (16 chromosomes in yeast) except chromosome 1. Besides the WD40 domain some of these proteins also contain other protein domains which might be responsible for the diversity in the functions of WD40 proteins in the budding yeast. These proteins in budding yeast were analysed by DAVID and Blast2Go software for functional and domains categorization. Candida albicans, an opportunistic fungal pathogen also have orthologs of these WD40 proteins with possible similar functions. This is the first time genome wide analysis of WD40 proteins in lower eukaryote i.e. budding yeast. This data may be useful in further study of the functional diversity of yeast proteomes.
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16
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Bazan B, Wiktor M, Maszczak-Seneczko D, Olczak T, Kaczmarek B, Olczak M. Lysine at position 329 within a C-terminal dilysine motif is crucial for the ER localization of human SLC35B4. PLoS One 2018; 13:e0207521. [PMID: 30458018 PMCID: PMC6245738 DOI: 10.1371/journal.pone.0207521] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/01/2018] [Indexed: 12/21/2022] Open
Abstract
SLC35B4 belongs to the solute carrier 35 (SLC35) family whose best-characterized members display a nucleotide sugar transporting activity. Using an experimental model of HepG2 cells and indirect immunofluorescent staining, we verified that SLC35B4 was localized to the endoplasmic reticulum (ER). We demonstrated that dilysine motif, especially lysine at position 329, is crucial for the ER localization of this protein in human cells and therefore one should use protein C-tagging with caution. To verify the importance of the protein in glycoconjugates synthesis, we generated SLC35B4-deficient HepG2 cell line using CRISPR-Cas9 approach. Our data showed that knock-out of the SLC35B4 gene does not affect major UDP-Xyl- and UDP-GlcNAc-dependent glycosylation pathways.
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Affiliation(s)
- Bożena Bazan
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Maciej Wiktor
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | | | - Teresa Olczak
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Beata Kaczmarek
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Mariusz Olczak
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
- * E-mail:
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17
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Expression map of 78 brain-expressed mouse orphan GPCRs provides a translational resource for neuropsychiatric research. Commun Biol 2018; 1:102. [PMID: 30271982 PMCID: PMC6123746 DOI: 10.1038/s42003-018-0106-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/06/2018] [Indexed: 12/26/2022] Open
Abstract
Orphan G-protein-coupled receptors (oGPCRs) possess untapped potential for drug discovery. In the brain, oGPCRs are generally expressed at low abundance and their function is understudied. Expression profiling is an essential step to position oGPCRs in brain function and disease, however public databases provide only partial information. Here, we fine-map expression of 78 brain-oGPCRs in the mouse, using customized probes in both standard and supersensitive in situ hybridization. Images are available at http://ogpcr-neuromap.douglas.qc.ca. This searchable database contains over 8000 coronal brain sections across 1350 slides, providing the first public mapping resource dedicated to oGPCRs. Analysis with public mouse (60 oGPCRs) and human (56 oGPCRs) genome-wide datasets identifies 25 oGPCRs with potential to address emotional and/or cognitive dimensions of psychiatric conditions. We probe their expression in postmortem human brains using nanoString, and included data in the resource. Correlating human with mouse datasets reveals excellent suitability of mouse models for oGPCRs in neuropsychiatric research. Aliza Ehrlich et al. report the fine-mapping of orphan GPCR (oGPCR) transcripts in the mouse brain using in situ hybridization and provide a public resource for data mining. The authors also mapped 25 selected oGPCRs in human brains, identifying oGPCRs with high correlation between species and potential roles in neuropsychiatric disorders.
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18
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Shankar J, Cerqueira GC, Wortman JR, Clemons KV, Stevens DA. RNA-Seq Profile Reveals Th-1 and Th-17-Type of Immune Responses in Mice Infected Systemically with Aspergillus fumigatus. Mycopathologia 2018; 183:645-658. [PMID: 29500637 PMCID: PMC6067991 DOI: 10.1007/s11046-018-0254-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/19/2018] [Indexed: 01/15/2023]
Abstract
With the increasing numbers of immunocompromised hosts, Aspergillus fumigatus emerges as a lethal opportunistic fungal pathogen. Understanding innate and acquired immunity responses of the host is important for a better therapeutic strategy to deal with aspergillosis patients. To determine the transcriptome in the kidneys in aspergillosis, we employed RNA-Seq to obtain single 76-base reads of whole-genome transcripts of murine kidneys on a temporal basis (days 0; uninfected, 1, 2, 3 and 8) during invasive aspergillosis. A total of 6284 transcripts were downregulated, and 5602 were upregulated compared to baseline expression. Gene ontology enrichment analysis identified genes involved in innate and adaptive immune response, as well as iron binding and homeostasis, among others. Our results showed activation of pathogen recognition receptors, e.g., β-defensins, C-type lectins (e.g., dectin-1), Toll-like receptors (TLR-2, TLR-3, TLR-8, TLR-9 and TLR-13), as well as Ptx-3 and C-reactive protein among the soluble receptors. Upregulated transcripts encoding various differentiating cytokines and effector proinflammatory cytokines, as well as those encoding for chemokines and chemokine receptors, revealed Th-1 and Th-17-type immune responses. These studies form a basic dataset for experimental prioritization, including other target organs, to determine the global response of the host against Aspergillus infection.
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Affiliation(s)
- Jata Shankar
- Jaypee University of Information Technology, Solan, HP, India
- California Institute for Medical Research, San Jose, CA, USA
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Karl V Clemons
- California Institute for Medical Research, San Jose, CA, USA.
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
| | - David A Stevens
- California Institute for Medical Research, San Jose, CA, USA
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
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19
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Rothberg JLM, Maganti HB, Jrade H, Porter CJ, Palidwor GA, Cafariello C, Battaion HL, Khan ST, Perkins TJ, Paulson RF, Ito CY, Stanford WL. Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis. Cell Discov 2018; 4:21. [PMID: 29736258 PMCID: PMC5928144 DOI: 10.1038/s41421-018-0022-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 02/15/2018] [Accepted: 02/28/2018] [Indexed: 01/13/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) accessory proteins play substoichiometric, tissue-specific roles to recruit PRC2 to specific genomic loci or increase enzymatic activity, while PRC2 core proteins are required for complex stability and global levels of trimethylation of histone 3 at lysine 27 (H3K27me3). Here, we demonstrate a role for the classical PRC2 accessory protein Mtf2/Pcl2 in the hematopoietic system that is more akin to that of a core PRC2 protein. Mtf2-/- erythroid progenitors demonstrate markedly decreased core PRC2 protein levels and a global loss of H3K27me3 at promoter-proximal regions. The resulting de-repression of transcriptional and signaling networks blocks definitive erythroid development, culminating in Mtf2-/- embryos dying by e15.5 due to severe anemia. Gene regulatory network (GRN) analysis demonstrated Mtf2 directly regulates Wnt signaling in erythroblasts, leading to activated canonical Wnt signaling in Mtf2-deficient erythroblasts, while chemical inhibition of canonical Wnt signaling rescued Mtf2-deficient erythroblast differentiation in vitro. Using a combination of in vitro, in vivo and systems analyses, we demonstrate that Mtf2 is a critical epigenetic regulator of Wnt signaling during erythropoiesis and recast the role of polycomb accessory proteins in a tissue-specific context.
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Affiliation(s)
- Janet L. Manias Rothberg
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
- Ottawa Institute of Systems Biology, Ottawa, ON Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON Canada
| | - Harinad B. Maganti
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
- Ottawa Institute of Systems Biology, Ottawa, ON Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON Canada
| | - Hani Jrade
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
- Ottawa Institute of Systems Biology, Ottawa, ON Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON Canada
| | - Christopher J. Porter
- Ottawa Bioinformatics Core Facility, The Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
| | - Gareth A. Palidwor
- Ottawa Bioinformatics Core Facility, The Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
| | - Christopher Cafariello
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
- Ottawa Institute of Systems Biology, Ottawa, ON Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON Canada
| | - Hannah L. Battaion
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
- Ottawa Institute of Systems Biology, Ottawa, ON Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON Canada
| | - Safwat T. Khan
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
| | - Theodore J. Perkins
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON Canada
- Ottawa Bioinformatics Core Facility, The Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
| | - Robert F. Paulson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802 USA
| | - Caryn Y. Ito
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON Canada
| | - William L. Stanford
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6 Canada
- Ottawa Institute of Systems Biology, Ottawa, ON Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON Canada
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20
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Chen W, Xie Z, Yang F, Ye K. Stepwise assembly of the earliest precursors of large ribosomal subunits in yeast. Nucleic Acids Res 2017; 45:6837-6847. [PMID: 28402444 PMCID: PMC5499802 DOI: 10.1093/nar/gkx254] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/04/2017] [Indexed: 12/15/2022] Open
Abstract
Small ribosomal subunits are co-transcriptionally assembled on the nascent precursor rRNA in Saccharomyces cerevisiae. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is initially formed. Here, we affinity purified and analyzed a series of pre-60S particles assembled in vivo on plasmid-encoded pre-rRNA fragments of increasing lengths, revealing a spatiotemporal assembly map for 34 trans-acting assembly factors (AFs), 30 ribosomal proteins and 5S rRNA. The gradual association of AFs and ribosomal proteins with the pre-rRNA fragments strongly supports that the pre-60S is co-transcriptionally, rather than post-transcriptionally, assembled. The internal and external transcribed spacers ITS1, ITS2 and 3΄ ETS in pre-rRNA must be processed in pre-60S. We show that the processing machineries for ITS1 and ITS2 are primarily recruited by the 5΄ and 3΄ halves of pre-27S RNA, respectively. Nevertheless, processing of both ITS1 and ITS2 requires a complete 25S region. The 3΄ ETS plays a minor role in ribosome assembly, but is important for efficient rRNA processing and ribosome maturation. We also identified a distinct pre-60S state occurring before ITS2 processing. Our data reveal the elusive co-transcriptional assembly pathway of large ribosomal subunit.
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Affiliation(s)
- Wu Chen
- College of Biological Sciences, China Agricultural University, Beijing 100193, China.,National Institute of Biological Sciences, Beijing 102206, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhensheng Xie
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuquan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Abstract
Transcription factors (TFs) drive various biological processes ranging from embryonic development to carcinogenesis. Here, we employ a recently developed concatenated tandem array of consensus TF response elements (catTFRE) approach to profile the activated TFs in 24 adult and 8 fetal mouse tissues on proteome scale. A total of 941 TFs are quantitatively identified, representing over 60% of the TFs in the mouse genome. Using an integrated omics approach, we present a TF network in the major organs of the mouse, allowing data mining and generating knowledge to elucidate the roles of TFs in various biological processes, including tissue type maintenance and determining the general features of a physiological system. This study provides a landscape of TFs in mouse tissues that can be used to elucidate transcriptional regulatory specificity and programming and as a baseline that may facilitate understanding diseases that are regulated by TFs. While we have abundant data for transcription factor (TF) binding sites and TF expression at the mRNA level, our knowledge of TFs at the protein level and their DNA-binding activities is sparser. Here, the authors address this by using the catTFRE approach to profile active TFs in 24 adult and 8 fetal mouse tissues, and presenting the TF networks in major mouse organs.
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Tarifeño-Saldivia E, Lavergne A, Bernard A, Padamata K, Bergemann D, Voz ML, Manfroid I, Peers B. Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes. BMC Biol 2017; 15:21. [PMID: 28327131 PMCID: PMC5360028 DOI: 10.1186/s12915-017-0362-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/01/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Defining the transcriptome and the genetic pathways of pancreatic cells is of great interest for elucidating the molecular attributes of pancreas disorders such as diabetes and cancer. As the function of the different pancreatic cell types has been maintained during vertebrate evolution, the comparison of their transcriptomes across distant vertebrate species is a means to pinpoint genes under strong evolutionary constraints due to their crucial function, which have therefore preserved their selective expression in these pancreatic cell types. RESULTS In this study, RNA-sequencing was performed on pancreatic alpha, beta, and delta endocrine cells as well as the acinar and ductal exocrine cells isolated from adult zebrafish transgenic lines. Comparison of these transcriptomes identified many novel markers, including transcription factors and signaling pathway components, specific for each cell type. By performing interspecies comparisons, we identified hundreds of genes with conserved enriched expression in endocrine and exocrine cells among human, mouse, and zebrafish. This list includes many genes known as crucial for pancreatic cell formation or function, but also pinpoints many factors whose pancreatic function is still unknown. A large set of endocrine-enriched genes can already be detected at early developmental stages as revealed by the transcriptomic profiling of embryonic endocrine cells, indicating a potential role in cell differentiation. The actual involvement of conserved endocrine genes in pancreatic cell differentiation was demonstrated in zebrafish for myt1b, whose invalidation leads to a reduction of alpha cells, and for cdx4, selectively expressed in endocrine delta cells and crucial for their specification. Intriguingly, comparison of the endocrine alpha and beta cell subtypes from human, mouse, and zebrafish reveals a much lower conservation of the transcriptomic signatures for these two endocrine cell subtypes compared to the signatures of pan-endocrine and exocrine cells. These data suggest that the identity of the alpha and beta cells relies on a few key factors, corroborating numerous examples of inter-conversion between these two endocrine cell subtypes. CONCLUSION This study highlights both evolutionary conserved and species-specific features that will help to unveil universal and fundamental regulatory pathways as well as pathways specific to human and laboratory animal models such as mouse and zebrafish.
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Affiliation(s)
- Estefania Tarifeño-Saldivia
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, 4000 Sart Tilman, Liege, Belgium
| | - Arnaud Lavergne
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, 4000 Sart Tilman, Liege, Belgium
| | - Alice Bernard
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, 4000 Sart Tilman, Liege, Belgium
| | - Keerthana Padamata
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, 4000 Sart Tilman, Liege, Belgium
| | - David Bergemann
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, 4000 Sart Tilman, Liege, Belgium
| | - Marianne L Voz
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, 4000 Sart Tilman, Liege, Belgium
| | - Isabelle Manfroid
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, 4000 Sart Tilman, Liege, Belgium
| | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, 4000 Sart Tilman, Liege, Belgium.
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23
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Usmani A, Ganguli N, Jain SK, Ganguli N, Sarkar RK, Choubey M, Shukla M, Sarkar H, Majumdar SS. Robust generation of transgenic mice by simple hypotonic solution mediated delivery of transgene in testicular germ cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 3:16076. [PMID: 27933305 PMCID: PMC5142465 DOI: 10.1038/mtm.2016.76] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/28/2016] [Accepted: 10/04/2016] [Indexed: 11/10/2022]
Abstract
Our ability to decipher gene sequences has increased enormously with the advent of modern sequencing tools, but the ability to divulge functions of new genes have not increased correspondingly. This has caused a remarkable delay in functional interpretation of several newly found genes in tissue and age specific manner, limiting the pace of biological research. This is mainly due to lack of advancements in methodological tools for transgenesis. Predominantly practiced method of transgenesis by pronuclear DNA-microinjection is time consuming, tedious, and requires highly skilled persons for embryo-manipulation. Testicular electroporation mediated transgenesis requires use of electric current to testis. To this end, we have now developed an innovative technique for making transgenic mice by giving hypotonic shock to male germ cells for the gene delivery. Desired transgene was suspended in hypotonic Tris-HCl solution (pH 7.0) and simply injected in testis. This resulted in internalization of the transgene in dividing germ-cells residing at basal compartment of tubules leading to its integration in native genome of mice. Such males generated transgenic progeny by natural mating. Several transgenic animals can be generated with minimum skill within short span of time by this easily adaptable novel technique.
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Affiliation(s)
- Abul Usmani
- Embryo Biotechnology Laboratory, National Institute of Immunology, New Delhi, India; Department of Zoology, Dr. H. S. Gour University, Sagar, India
| | - Nirmalya Ganguli
- Embryo Biotechnology Laboratory, National Institute of Immunology , New Delhi, India
| | - Subodh K Jain
- Department of Zoology, Dr. H. S. Gour University , Sagar, India
| | - Nilanjana Ganguli
- Embryo Biotechnology Laboratory, National Institute of Immunology , New Delhi, India
| | - Rajesh Kumar Sarkar
- Embryo Biotechnology Laboratory, National Institute of Immunology , New Delhi, India
| | - Mayank Choubey
- Embryo Biotechnology Laboratory, National Institute of Immunology , New Delhi, India
| | - Mansi Shukla
- Embryo Biotechnology Laboratory, National Institute of Immunology , New Delhi, India
| | - Hironmoy Sarkar
- Embryo Biotechnology Laboratory, National Institute of Immunology , New Delhi, India
| | - Subeer S Majumdar
- Embryo Biotechnology Laboratory, National Institute of Immunology, New Delhi, India; National Institute of Animal Biotechnology, Hyderabad, Telangana, India
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24
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Shi W, Li K, Song L, Liu M, Wang Y, Liu W, Xia X, Qin Z, Zhen B, Wang Y, He F, Qin J, Ding C. Transcription Factor Response Elements on Tip: A Sensitive Approach for Large-Scale Endogenous Transcription Factor Quantitative Identification. Anal Chem 2016; 88:11990-11994. [DOI: 10.1021/acs.analchem.6b03150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Wenhao Shi
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Kai Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
- Department of Pathogeny Biology, School
of Basic Medical Sciences, North China University of Science and Technology, Tangshan 063009, Hebei, China
| | - Lei Song
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering
and Collaborative Innovation Center for Genetics and Development,
School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wanlin Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Xia Xia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Zhaoyu Qin
- State Key Laboratory of Genetic Engineering
and Collaborative Innovation Center for Genetics and Development,
School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Bei Zhen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Yi Wang
- Alkek Center for Molecular Discovery, Verna and Marrs
McLean Department of Biochemistry and Molecular Biology, Department
of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Fuchu He
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
- State Key Laboratory of Genetic Engineering
and Collaborative Innovation Center for Genetics and Development,
School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
- State Key Laboratory of Genetic Engineering
and Collaborative Innovation Center for Genetics and Development,
School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Alkek Center for Molecular Discovery, Verna and Marrs
McLean Department of Biochemistry and Molecular Biology, Department
of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Chen Ding
- State Key Laboratory of Proteomics, Beijing Proteome Research Center,
Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
- State Key Laboratory of Genetic Engineering
and Collaborative Innovation Center for Genetics and Development,
School of Life Sciences, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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25
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Lyons J, Herring CA, Banerjee A, Simmons AJ, Lau KS. Multiscale analysis of the murine intestine for modeling human diseases. Integr Biol (Camb) 2016; 7:740-57. [PMID: 26040649 DOI: 10.1039/c5ib00030k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
When functioning properly, the intestine is one of the key interfaces between the human body and its environment. It is responsible for extracting nutrients from our food and excreting our waste products. It provides an environment for a host of healthful microbes and serves as a first defense against pathogenic ones. These processes require tight homeostatic controls, which are provided by the interactions of a complex mix of epithelial, stromal, neural and immune cells, as well as the resident microflora. This homeostasis can be disrupted by invasive microbes, genetic lesions, and carcinogens, resulting in diseases such Clostridium difficile infection, inflammatory bowel disease (IBD) and cancer. Enormous strides have been made in understanding how this important organ functions in health and disease using everything from cell culture systems to animal models to human tissue samples. This has resulted in better therapies for all of these diseases, but there is still significant room for improvement. In the United States alone, 14,000 people per year die of C. difficile, up to 1.6 million people suffer from IBD, and more than 50,000 people die every year from colon cancer. Because these and other intestinal diseases arise from complex interactions between the different components of the gut ecosystem, we propose that systems approaches that address this complexity in an integrative manner may eventually lead to improved therapeutics that deliver lasting cures. This review will discuss the use of systems biology for studying intestinal diseases in vivo with particular emphasis on mouse models. Additionally, it will focus on established experimental techniques that have been used to drive this systems-level analysis, and emerging techniques that will push this field forward in the future.
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Affiliation(s)
- Jesse Lyons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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26
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Li Y, Liu H, Barta CL, Judge PD, Zhao L, Zhang WJ, Gong S, Beisel KW, He DZZ. Transcription Factors Expressed in Mouse Cochlear Inner and Outer Hair Cells. PLoS One 2016; 11:e0151291. [PMID: 26974322 PMCID: PMC4790917 DOI: 10.1371/journal.pone.0151291] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 02/25/2016] [Indexed: 11/24/2022] Open
Abstract
Regulation of gene expression is essential to determining the functional complexity and morphological diversity seen among different cells. Transcriptional regulation is a crucial step in gene expression regulation because the genetic information is directly read from DNA by sequence-specific transcription factors (TFs). Although several mouse TF databases created from genome sequences and transcriptomes are available, a cell type-specific TF database from any normal cell populations is still lacking. We identify cell type-specific TF genes expressed in cochlear inner hair cells (IHCs) and outer hair cells (OHCs) using hair cell-specific transcriptomes from adult mice. IHCs and OHCs are the two types of sensory receptor cells in the mammalian cochlea. We show that 1,563 and 1,616 TF genes are respectively expressed in IHCs and OHCs among 2,230 putative mouse TF genes. While 1,536 are commonly expressed in both populations, 73 genes are differentially expressed (with at least a twofold difference) in IHCs and 13 are differentially expressed in OHCs. Our datasets represent the first cell type-specific TF databases for two populations of sensory receptor cells and are key informational resources for understanding the molecular mechanism underlying the biological properties and phenotypical differences of these cells.
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Affiliation(s)
- Yi Li
- Department of Otorhinolaryngology—Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, 68178, United States of America
| | - Huizhan Liu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, 68178, United States of America
| | - Cody L. Barta
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, 68178, United States of America
| | - Paul D. Judge
- Department of Otorhinolaryngology—Head and Neck Surgery, University of Nebraska Medical Center, Omaha, NE, 68198, United States of America
| | - Lidong Zhao
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, 68178, United States of America
- Department of Otorhinolaryngology—Head and Neck Surgery, Chinese PLA General Hospital, Beijing, 100853, China
| | - Weiping J. Zhang
- Department of Pathophysiology, Second Military Medical University, Shanghai, 200433, China
| | - Shusheng Gong
- Department of Otorhinolaryngology—Head and Neck Surgery, Beijing Friendship Hospital, Beijing, China
| | - Kirk W. Beisel
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, 68178, United States of America
| | - David Z. Z. He
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, 68178, United States of America
- * E-mail:
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27
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A conserved MADS-box phosphorylation motif regulates differentiation and mitochondrial function in skeletal, cardiac, and smooth muscle cells. Cell Death Dis 2015; 6:e1944. [PMID: 26512955 PMCID: PMC5399178 DOI: 10.1038/cddis.2015.306] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/07/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022]
Abstract
Exposure to metabolic disease during fetal development alters cellular differentiation and perturbs metabolic homeostasis, but the underlying molecular regulators of this phenomenon in muscle cells are not completely understood. To address this, we undertook a computational approach to identify cooperating partners of the myocyte enhancer factor-2 (MEF2) family of transcription factors, known regulators of muscle differentiation and metabolic function. We demonstrate that MEF2 and the serum response factor (SRF) collaboratively regulate the expression of numerous muscle-specific genes, including microRNA-133a (miR-133a). Using tandem mass spectrometry techniques, we identify a conserved phosphorylation motif within the MEF2 and SRF Mcm1 Agamous Deficiens SRF (MADS)-box that regulates miR-133a expression and mitochondrial function in response to a lipotoxic signal. Furthermore, reconstitution of MEF2 function by expression of a neutralizing mutation in this identified phosphorylation motif restores miR-133a expression and mitochondrial membrane potential during lipotoxicity. Mechanistically, we demonstrate that miR-133a regulates mitochondrial function through translational inhibition of a mitophagy and cell death modulating protein, called Nix. Finally, we show that rodents exposed to gestational diabetes during fetal development display muscle diacylglycerol accumulation, concurrent with insulin resistance, reduced miR-133a, and elevated Nix expression, as young adult rats. Given the diverse roles of miR-133a and Nix in regulating mitochondrial function, and proliferation in certain cancers, dysregulation of this genetic pathway may have broad implications involving insulin resistance, cardiovascular disease, and cancer biology.
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28
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Yu Y, Fuscoe JC, Zhao C, Guo C, Jia M, Qing T, Bannon DI, Lancashire L, Bao W, Du T, Luo H, Su Z, Jones WD, Moland CL, Branham WS, Qian F, Ning B, Li Y, Hong H, Guo L, Mei N, Shi T, Wang KY, Wolfinger RD, Nikolsky Y, Walker SJ, Duerksen-Hughes P, Mason CE, Tong W, Thierry-Mieg J, Thierry-Mieg D, Shi L, Wang C. A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nat Commun 2015; 5:3230. [PMID: 24510058 PMCID: PMC3926002 DOI: 10.1038/ncomms4230] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 01/10/2014] [Indexed: 02/07/2023] Open
Abstract
The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNA-Seq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model. Gene expression is highly variable between tissues, and changes during development and with age. Here, the authors provide a comprehensive RNA-Seq analysis of the rat transcriptome, spanning eleven organs, four developmental stages and both sexes.
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Affiliation(s)
- Ying Yu
- 1] Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China [2]
| | - James C Fuscoe
- 1] National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA [2]
| | - Chen Zhao
- Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China
| | - Chao Guo
- Functional Genomics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Meiwen Jia
- Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China
| | - Tao Qing
- Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China
| | - Desmond I Bannon
- Army Institute of Public Health, U.S. Army Public Health Command, Aberdeen Proving Ground, Maryland 21010, USA
| | - Lee Lancashire
- Computation Biology and Bioinformatics, IP & Science, Thomson Reuters, London EC1N 8JS, UK
| | - Wenjun Bao
- SAS Institute Inc., Cary, North Carolina 27513, USA
| | - Tingting Du
- Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China
| | - Heng Luo
- Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China
| | - Zhenqiang Su
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | | | - Carrie L Moland
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | - William S Branham
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | - Feng Qian
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | - Yan Li
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | - Lei Guo
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | - Nan Mei
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | - Tieliu Shi
- The Center for Bioinformatics and The Institute of Biomedical Sciences, College of Life Science, Shanghai 200241, China
| | - Kevin Y Wang
- Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Yuri Nikolsky
- Computation Biology and Bioinformatics, IP & Science, Thomson Reuters, London EC1N 8JS, UK
| | - Stephen J Walker
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, USA
| | - Penelope Duerksen-Hughes
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
| | - Christopher E Mason
- Department of Physiology & Biophysics and the Institute for Computational Biomedicine, Cornell University, New York, New York 10021, USA
| | - Weida Tong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Leming Shi
- 1] Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China [2] National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA [3] Fudan-Zhangjiang Center for Clinical Genomics and Zhangjiang Center for Translational Medicine, Shanghai 201203, China
| | - Charles Wang
- Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
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Pazos Obregón F, Papalardo C, Castro S, Guerberoff G, Cantera R. Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach. BMC Genomics 2015; 16:694. [PMID: 26370122 PMCID: PMC4570697 DOI: 10.1186/s12864-015-1888-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 09/01/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Assembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Although roughly a thousand genes are expected to be important for this function in Drosophila melanogaster, just a few hundreds of them are known so far. RESULTS In this work we trained three learning algorithms to predict a "synaptic function" for genes of Drosophila using data from a whole-body developmental transcriptome published by others. Using statistical and biological criteria to analyze and combine the predictions, we obtained a gene catalogue that is highly enriched in genes of relevance for Drosophila synapse assembly and function but still not recognized as such. CONCLUSIONS The utility of our approach is that it reduces the number of genes to be tested through hypothesis-driven experimentation.
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Affiliation(s)
- Flavio Pazos Obregón
- Departamento de Biología del Neurodesarrollo, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, PC 11600, Montevideo, Uruguay.
| | - Cecilia Papalardo
- Instituto de Matemática y Estadística "Prof. Ing. Rafael Laguardia", Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay.
| | - Sebastián Castro
- Instituto de Matemática y Estadística "Prof. Ing. Rafael Laguardia", Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay.
| | - Gustavo Guerberoff
- Instituto de Matemática y Estadística "Prof. Ing. Rafael Laguardia", Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay.
| | - Rafael Cantera
- Departamento de Biología del Neurodesarrollo, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, PC 11600, Montevideo, Uruguay.
- Zoology Department, Stockholm University, Stockholm, Sweden.
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30
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Khan AUM, Mikut R, Reischl M. A Benchmark Data Set to Evaluate the Illumination Robustness of Image Processing Algorithms for Object Segmentation and Classification. PLoS One 2015; 10:e0131098. [PMID: 26191792 PMCID: PMC4508044 DOI: 10.1371/journal.pone.0131098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/28/2015] [Indexed: 12/02/2022] Open
Abstract
Developers of image processing routines rely on benchmark data sets to give qualitative comparisons of new image analysis algorithms and pipelines. Such data sets need to include artifacts in order to occlude and distort the required information to be extracted from an image. Robustness, the quality of an algorithm related to the amount of distortion is often important. However, using available benchmark data sets an evaluation of illumination robustness is difficult or even not possible due to missing ground truth data about object margins and classes and missing information about the distortion. We present a new framework for robustness evaluation. The key aspect is an image benchmark containing 9 object classes and the required ground truth for segmentation and classification. Varying levels of shading and background noise are integrated to distort the data set. To quantify the illumination robustness, we provide measures for image quality, segmentation and classification success and robustness. We set a high value on giving users easy access to the new benchmark, therefore, all routines are provided within a software package, but can as well easily be replaced to emphasize other aspects.
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Affiliation(s)
- Arif ul Maula Khan
- Institute for Applied Computer Science, Image and Data Analysis Group, Karlsruhe Institute of Technology, Karlsruhe, Baden-Wuerttemberg, Germany
| | - Ralf Mikut
- Institute for Applied Computer Science, Image and Data Analysis Group, Karlsruhe Institute of Technology, Karlsruhe, Baden-Wuerttemberg, Germany
| | - Markus Reischl
- Institute for Applied Computer Science, Image and Data Analysis Group, Karlsruhe Institute of Technology, Karlsruhe, Baden-Wuerttemberg, Germany
- * E-mail:
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31
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Abstract
The searching of human housekeeping (HK) genes has been a long quest since the emergence of transcriptomics, and is instrumental for us to understand the structure of genome and the fundamentals of biological processes. The resolved genes are frequently used in evolution studies and as normalization standards in quantitative gene-expression analysis. Within the past 20 years, more than a dozen HK-gene studies have been conducted, yet none of them sampled human tissues completely. We believe an integration of these results will help remove false positive genes owing to the inadequate sampling. Surprisingly, we only find one common gene across 15 examined HK-gene datasets comprising 187 different tissue and cell types. Our subsequent analyses suggest that it might not be appropriate to rigidly define HK genes as expressed in all tissue types that have diverse developmental, physiological, and pathological states. It might be beneficial to use more robustly identified HK functions for filtering criteria, in which the representing genes can be a subset of genome. These genes are not necessarily the same, and perhaps need not to be the same, everywhere in our body.
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Affiliation(s)
- Yijuan Zhang
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ding Li
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Bingyun Sun
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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32
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Ma S, Bohnert HJ, Dinesh-Kumar SP. AtGGM2014, an Arabidopsis gene co-expression network for functional studies. SCIENCE CHINA-LIFE SCIENCES 2015; 58:276-86. [PMID: 25682393 DOI: 10.1007/s11427-015-4803-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/25/2014] [Indexed: 12/19/2022]
Abstract
Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the ArrayExpress database, we constructed an Arabidopsis gene co-expression network, termed AtGGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. AtGGM2014 offers a constructive tool for plant systems biology studies.
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Affiliation(s)
- ShiSong Ma
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California, Davis, CA, 95616, USA,
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Comparison of Metabolic Network between Muscle and Intramuscular Adipose Tissues in Hanwoo Beef Cattle Using a Systems Biology Approach. Int J Genomics 2014; 2014:679437. [PMID: 25478565 PMCID: PMC4247929 DOI: 10.1155/2014/679437] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 10/07/2014] [Accepted: 10/30/2014] [Indexed: 12/16/2022] Open
Abstract
The interrelationship between muscle and adipose tissues plays a major role in determining the quality of carcass traits. The objective of this study was to compare metabolic differences between muscle and intramuscular adipose (IMA) tissues in the longissimus dorsi (LD) of Hanwoo (Bos taurus coreanae) using the RNA-seq technology and a systems biology approach. The LD sections between the 6th and 7th ribs were removed from nine (each of three cows, steers, and bulls) Hanwoo beef cattle (carcass weight of 430.2 ± 40.66 kg) immediately after slaughter. The total mRNA from muscle, IMA, and subcutaneous adipose and omental adipose tissues were isolated and sequenced. The reads that passed quality control were mapped onto the bovine reference genome (build bosTau6), and differentially expressed genes across tissues were identified. The KEGG pathway enrichment tests revealed the opposite direction of metabolic regulation between muscle and IMA. Metabolic gene network analysis clearly indicated that oxidative metabolism was upregulated in muscle and downregulated in IMA. Interestingly, pathways for regulating cell adhesion, structure, and integrity and chemokine signaling pathway were upregulated in IMA and downregulated in muscle. It is thus inferred that IMA may play an important role in the regulation of development and structure of the LD tissues and muscle/adipose communication.
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Verleyen W, Ballouz S, Gillis J. Measuring the wisdom of the crowds in network-based gene function inference. Bioinformatics 2014; 31:745-52. [DOI: 10.1093/bioinformatics/btu715] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res 2014; 24:1774-86. [PMID: 25258385 PMCID: PMC4216919 DOI: 10.1101/gr.177790.114] [Citation(s) in RCA: 442] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Alternative splicing (AS) of precursor RNAs is responsible for greatly expanding the regulatory and functional capacity of eukaryotic genomes. Of the different classes of AS, intron retention (IR) is the least well understood. In plants and unicellular eukaryotes, IR is the most common form of AS, whereas in animals, it is thought to represent the least prevalent form. Using high-coverage poly(A)+ RNA-seq data, we observe that IR is surprisingly frequent in mammals, affecting transcripts from as many as three-quarters of multiexonic genes. A highly correlated set of cis features comprising an “IR code” reliably discriminates retained from constitutively spliced introns. We show that IR acts widely to reduce the levels of transcripts that are less or not required for the physiology of the cell or tissue type in which they are detected. This “transcriptome tuning” function of IR acts through both nonsense-mediated mRNA decay and nuclear sequestration and turnover of IR transcripts. We further show that IR is linked to a cross-talk mechanism involving localized stalling of RNA polymerase II (Pol II) and reduced availability of spliceosomal components. Collectively, the results implicate a global checkpoint-type mechanism whereby reduced recruitment of splicing components coupled to Pol II pausing underlies widespread IR-mediated suppression of inappropriately expressed transcripts.
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Affiliation(s)
| | - Nuno L Barbosa-Morais
- Donnelly Centre, University of Toronto, Ontario, M5S 3E1, Canada; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Qun Pan
- Donnelly Centre, University of Toronto, Ontario, M5S 3E1, Canada
| | - Emil N Nachman
- Donnelly Centre, University of Toronto, Ontario, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Ontario, M5S 1A8, Canada
| | - Babak Alipanahi
- Department of Electrical and Computer Engineering, University of Toronto, Ontario, M5S 2E4, Canada
| | | | - Brendan Frey
- Department of Electrical and Computer Engineering, University of Toronto, Ontario, M5S 2E4, Canada
| | - Manuel Irimia
- Donnelly Centre, University of Toronto, Ontario, M5S 3E1, Canada;
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Ontario, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Ontario, M5S 1A8, Canada;
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Roles of Ebp2 and ribosomal protein L36 in ribosome biogenesis in Saccharomyces cerevisiae. Curr Genet 2014; 61:31-41. [PMID: 25119672 DOI: 10.1007/s00294-014-0442-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/10/2014] [Accepted: 07/29/2014] [Indexed: 01/08/2023]
Abstract
Ebp2 plays an essential role in biogenesis of 60S ribosomal subunits. We determined the genetic interactions between EBP2 and RPL36A/B, which encodes ribosomal protein L36a/b. RPL36A/B was a multicopy suppressor to ebp2 mutants, and the suppression was not common to defects in ribosome biogenesis resulting from other mutations of assembly factors. Disruption of RPL36A or RPL36B caused synthetic enhancement of the growth defect of the ebp2-14 allele at high temperatures. Disruption of RPL36B led to a more severe growth defect than that of RPL36A due to imbalances in the expression levels of the duplicated genes. Primer-extension analysis revealed that L36a/b is required for the processing of 27SA2, 27SA3, and 27SBL pre-rRNAs. Two-hybrid analysis indicated that Ebp2 interacts with ribosomal proteins L36a/b, L34a/b, and L8, which in mature ribosomes are located adjacent to each other in close proximity to the 3' end of 5.8S rRNA. These results suggest that Ebp2 functions cooperatively with ribosomal proteins L36, L34, and L8 in biogenesis of the 60S ribosomal subunit.
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Kraus P, V S, Yu HB, Xing X, Lim SL, Adler T, Pimentel JAA, Becker L, Bohla A, Garrett L, Hans W, Hölter SM, Janas E, Moreth K, Prehn C, Puk O, Rathkolb B, Rozman J, Adamski J, Bekeredjian R, Busch DH, Graw J, Klingenspor M, Klopstock T, Neff F, Ollert M, Stoeger T, Yildrim AÖ, Eickelberg O, Wolf E, Wurst W, Fuchs H, Gailus-Durner V, de Angelis MH, Lufkin T, Stanton LW. Pleiotropic functions for transcription factor zscan10. PLoS One 2014; 9:e104568. [PMID: 25111779 PMCID: PMC4128777 DOI: 10.1371/journal.pone.0104568] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/12/2014] [Indexed: 12/17/2022] Open
Abstract
The transcription factor Zscan10 had been attributed a role as a pluripotency factor in embryonic stem cells based on its interaction with Oct4 and Sox2 in in vitro assays. Here we suggest a potential role of Zscan10 in controlling progenitor cell populations in vivo. Mice homozygous for a Zscan10 mutation exhibit reduced weight, mild hypoplasia in the spleen, heart and long bones and phenocopy an eye malformation previously described for Sox2 hypomorphs. Phenotypic abnormalities are supported by the nature of Zscan10 expression in midgestation embryos and adults suggesting a role for Zscan10 in either maintaining progenitor cell subpopulation or impacting on fate choice decisions thereof.
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Affiliation(s)
- Petra Kraus
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
- Department of Biology, Clarkson University, Potsdam, New York, United States of America
| | - Sivakamasundari V
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Hong Bing Yu
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Xing Xing
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Siew Lan Lim
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Thure Adler
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Juan Antonio Aguilar Pimentel
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Klinikum rechts der Isar der Technischen Universität München, Klinik und Poliklinik für Dermatologie und Allergologie am Biederstein, Munich, Germany
| | - Lore Becker
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Alexander Bohla
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lillian Garrett
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Wolfgang Hans
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sabine M. Hölter
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Eva Janas
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Kristin Moreth
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cornelia Prehn
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Oliver Puk
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jan Rozman
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jerzy Adamski
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Raffi Bekeredjian
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine III, Division of Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Dirk H. Busch
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, Munich, Germany
| | - Jochen Graw
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Klingenspor
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Molecular Nutritional Medicine, Else Kröner-Fresenius Center, Technische Universität München, Freising-Weihenstephan, Germany
| | - Thomas Klopstock
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Frauke Neff
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Markus Ollert
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Klinikum rechts der Isar der Technischen Universität München, Klinik und Poliklinik für Dermatologie und Allergologie am Biederstein, Munich, Germany
| | - Tobias Stoeger
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ali Önder Yildrim
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Oliver Eickelberg
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Eckhard Wolf
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Developmental Biology, Technische Universität München, Freising-Weihenstephan, Germany
- Max Planck Institute of Psychiatry, Munich, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- Member of German Center for Diabetes Research, Neuherberg, Germany
| | - Thomas Lufkin
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
- Department of Biology, Clarkson University, Potsdam, New York, United States of America
| | - Lawrence W. Stanton
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
- * E-mail:
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Sodhi SS, Song KD, Ghosh M, Sharma N, Lee SJ, Kim JH, Kim N, Mongre RK, Adhikari P, Kim JY, Hong SP, Oh SJ, Jeong DK. Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native Pig. Gene 2014; 546:233-42. [PMID: 24910116 DOI: 10.1016/j.gene.2014.06.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/29/2014] [Accepted: 06/04/2014] [Indexed: 12/16/2022]
Abstract
RNA-seq is being rapidly adopted for the profiling of the transcriptomes in different areas of biology, especially in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds of Sus scrofa, is of particular interest for the current study. For the better understanding of the gene expression profiles of the liver and longissimus dorsi muscle, DEGs were identified via RNA-seq. Sequence reads were obtained from Illumina HiSeq2000 and mapped to the pig reference genome (Sscrofa10.2) using Tophat2. We identified 169 and 39 DEGs in the liver and muscle of JNP respectively, by comparison with Berkshire breed. Out of all identified genes, 41 genes in the liver and 9 genes in the muscle have given significant expression. Gene ontology (GO) terms of developmental process and KEGG pathway analysis showed that metabolic, immune response and protein binding were commonly enriched pathways in the two tissues. Further the heat map analysis by ArrayStar has shown the different levels of expression in JNP with respect to the Berkshire breed. The validation through real time PCR and western blotting also confirmed the differential expression of genes in both breeds. Genes pertaining to metabolic process and inflammatory and immune system are more enriched in Berkshire breed. This comparative transcriptome analysis of two tissues suggests a subset of novel marker genes which expressed differently between the JNP and Berkshire.
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Affiliation(s)
- Simrinder Singh Sodhi
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Ki-Duk Song
- The Animal Genomics and Breeding Center, Hankyong National University, Anseong-si, Gyeonggi-do 456-749, South Korea
| | - Mrinmoy Ghosh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Neelesh Sharma
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Sung Jin Lee
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Kangwon National University, Chuncheon 200-701, South Korea
| | - Jeong Hyun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Nameun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Raj Kumar Mongre
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Pradeep Adhikari
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Jin Young Kim
- Institute for Livestock Promotion, Jeju-do, Jeju 690-802, South Korea
| | - Sang Pyo Hong
- Institute for Livestock Promotion, Jeju-do, Jeju 690-802, South Korea
| | - Sung Jong Oh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Dong Kee Jeong
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea; Sustainable Agriculture Research Institute (SARI), Jeju National University, Jeju 690-756, South Korea.
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Nα-Acetyltransferase NatA Is Involved in Ribosome Synthesis inSaccharomyces cerevisiae. Biosci Biotechnol Biochem 2014; 77:631-8. [DOI: 10.1271/bbb.120860] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q. Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. Front Genet 2014; 5:123. [PMID: 24904632 PMCID: PMC4032932 DOI: 10.3389/fgene.2014.00123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 04/21/2014] [Indexed: 01/17/2023] Open
Abstract
Significant effort has been invested in network-based gene function prediction algorithms based on the guilt by association (GBA) principle. Existing approaches for assessing prediction performance typically compute evaluation metrics, either averaged across all functions being considered, or strictly from properties of the network. Since the success of GBA algorithms depends on the specific function being predicted, evaluation metrics should instead be computed for each function. We describe a novel method for computing the usefulness of a network by measuring its impact on gene function cross validation prediction performance across all gene functions. We have implemented this in software called Network Assessor, and describe its use in the GeneMANIA (GM) quality control system. Network Assessor is part of the GM command line tools.
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Affiliation(s)
- Jason Montojo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto Toronto, ON, Canada
| | - Khalid Zuberi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto Toronto, ON, Canada
| | - Quentin Shao
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto Toronto, ON, Canada
| | - Gary D Bader
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto Toronto, ON, Canada
| | - Quaid Morris
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto Toronto, ON, Canada
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Jonker MJ, de Leeuw WC, Marinković M, Wittink FRA, Rauwerda H, Bruning O, Ensink WA, Fluit AC, Boel CH, Jong MD, Breit TM. Absence/presence calling in microarray-based CGH experiments with non-model organisms. Nucleic Acids Res 2014; 42:e94. [PMID: 24771343 PMCID: PMC4066771 DOI: 10.1093/nar/gku343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknown order of probe targets. We therefore present an additional analysis approach, which does not depend on the structural information of a reference genome, and quantifies the presence or absence of a probe target in an unknown genome. The principle is that intensity values of target probes are compared with the intensities of negative-control probes and positive-control probes from a control hybridization, to determine if a probe target is absent or present. In a test, analyzing the genome content of a known bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful, demonstrated by receiver operating characteristic area under the curve values larger than 0.9995. We show its usability in various applications, such as comparing genome content and validating next-generation sequencing reads from eukaryotic non-model organisms.
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Affiliation(s)
- Martijs J Jonker
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Wim C de Leeuw
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Marino Marinković
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - Floyd R A Wittink
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Han Rauwerda
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Oskar Bruning
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
| | - Wim A Ensink
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Ad C Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - C H Boel
- Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mark de Jong
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands
| | - Timo M Breit
- MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands
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Abstract
Most fungal genomes are poorly annotated, and many fungal traits of industrial and biomedical relevance are not well suited to classical genetic screens. Assigning genes to phenotypes on a genomic scale thus remains an urgent need in the field. We developed an approach to infer gene function from expression profiles of wild fungal isolates, and we applied our strategy to the filamentous fungus Neurospora crassa. Using transcriptome measurements in 70 strains from two well-defined clades of this microbe, we first identified 2,247 cases in which the expression of an unannotated gene rose and fell across N. crassa strains in parallel with the expression of well-characterized genes. We then used image analysis of hyphal morphologies, quantitative growth assays, and expression profiling to test the functions of four genes predicted from our population analyses. The results revealed two factors that influenced regulation of metabolism of nonpreferred carbon and nitrogen sources, a gene that governed hyphal architecture, and a gene that mediated amino acid starvation resistance. These findings validate the power of our population-transcriptomic approach for inference of novel gene function, and we suggest that this strategy will be of broad utility for genome-scale annotation in many fungal systems. IMPORTANCE Some fungal species cause deadly infections in humans or crop plants, and other fungi are workhorses of industrial chemistry, including the production of biofuels. Advances in medical and industrial mycology require an understanding of the genes that control fungal traits. We developed a method to infer functions of uncharacterized genes by observing correlated expression of their mRNAs with those of known genes across wild fungal isolates. We applied this strategy to a filamentous fungus and predicted functions for thousands of unknown genes. In four cases, we experimentally validated the predictions from our method, discovering novel genes involved in the metabolism of nutrient sources relevant for biofuel production, as well as colony morphology and starvation resistance. Our strategy is straightforward, inexpensive, and applicable for predicting gene function in many fungal species.
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Ribosome assembly factors Pwp1 and Nop12 are important for folding of 5.8S rRNA during ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 2014; 34:1863-77. [PMID: 24636992 DOI: 10.1128/mcb.01322-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Previous work from our lab suggests that a group of interdependent assembly factors (A(3) factors) is necessary to create early, stable preribosomes. Many of these proteins bind at or near internal transcribed spacer 2 (ITS2), but in their absence, ITS1 is not removed from rRNA, suggesting long-range communication between these two spacers. By comparing the nonessential assembly factors Nop12 and Pwp1, we show that misfolding of rRNA is sufficient to perturb early steps of biogenesis, but it is the lack of A(3) factors that results in turnover of early preribosomes. Deletion of NOP12 significantly inhibits 27SA(3) pre-rRNA processing, even though the A(3) factors are present in preribosomes. Furthermore, pre-rRNAs are stable, indicating that the block in processing is not sufficient to trigger turnover. This is in contrast to the absence of Pwp1, in which the A(3) factors are not present and pre-rRNAs are unstable. In vivo RNA structure probing revealed that the pre-rRNA processing defects are due to misfolding of 5.8S rRNA. In the absence of Nop12 and Pwp1, rRNA helix 5 is not stably formed. Interestingly, the absence of Nop12 results in the formation of an alternative yet unproductive helix 5 when cells are grown at low temperatures.
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Williams MD, Wong W, Rixon A, Satoor SN, Hardikar AA, Joglekar MV. Pdx1 (GFP/w) mice for isolation, characterization, and differentiation of pancreatic progenitor cells. Methods Mol Biol 2014; 1194:271-288. [PMID: 25064109 DOI: 10.1007/978-1-4939-1215-5_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
It is well known that human cells are diverse with respect to their epigenome, transcriptome, and proteome. In the context of regenerative medicine, it is important for the transplanted cells or tissues to faithfully recapitulate their intended tissue type in each of these respects. Whether the cells chosen for such an application are embryonic, postnatal, or induced pluripotent stem cells, the transplanted product must behave in a predictable and reliable manner to be a safe and effective treatment option. Irrespective of the choice of cells used in such an application, the characterization and understanding of the developmental cues responsible for establishing and maintaining the desired cell phenotype are essential.Animal models are extremely important in understanding the development of a specific tissue, which can then be subsequently extrapolated to human studies. Generation of transgenic animal models with whole-body gene knockout, conditional knockout, constitutive fluorescent gene reporters, and Cre-Lox-based conditional and lineage reporters has revolutionized the field of developmental biology. An intrinsically complex network of the actions and interactions of the multitude of different signalling cascades is required for development. A thorough understanding of such networks, gained through studies on transgenic animal models, is essential for the development of the techniques necessary to reliably differentiate a given stem or progenitor cell population into a specific cell type, such as an islet-like, insulin-producing cell aggregate.In this chapter, we describe the use of GFP (green fluorescent protein)-based reporter mice for isolation of cells of choice, analyzing gene expression in those cells as well as their use for screening signalling molecules to understand their effect on differentiation.
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Affiliation(s)
- Michael D Williams
- NHMRC Clinical Trials Centre, The University of Sydney, Medical Foundation Building, Camperdown, NSW, 2050, Australia
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Dembowski JA, Ramesh M, McManus CJ, Woolford JL. Identification of the binding site of Rlp7 on assembling 60S ribosomal subunits in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2013; 19:1639-47. [PMID: 24129494 PMCID: PMC3884665 DOI: 10.1261/rna.041194.113] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Eukaryotic ribosome assembly requires over 200 assembly factors that facilitate rRNA folding, ribosomal protein binding, and pre-rRNA processing. One such factor is Rlp7, an essential RNA binding protein required for consecutive pre-rRNA processing steps for assembly of yeast 60S ribosomal subunits: exonucleolytic processing of 27SA3 pre-rRNA to generate the 5' end of 5.8S rRNA and endonucleolytic cleavage of the 27SB pre-rRNA to initiate removal of internal transcribed spacer 2 (ITS2). To better understand the functions of Rlp7 in 27S pre-rRNA processing steps, we identified where it crosslinks to pre-rRNA. We found that Rlp7 binds at the junction of ITS2 and the ITS2-proximal stem, between the 3' end of 5.8S rRNA and the 5' end of 25S rRNA. Consistent with Rlp7 binding to this neighborhood during assembly, two-hybrid and affinity copurification assays showed that Rlp7 interacts with other assembly factors that bind to or near ITS2 and the proximal stem. We used in vivo RNA structure probing to demonstrate that the proximal stem forms prior to Rlp7 binding and that Rlp7 binding induces RNA conformational changes in ITS2 that may chaperone rRNA folding and regulate 27S pre-rRNA processing. Our findings contradict the hypothesis that Rlp7 functions as a placeholder for ribosomal protein L7, from which Rlp7 is thought to have evolved in yeast. The binding site of Rlp7 is within eukaryotic-specific RNA elements, which are not found in bacteria. Thus, we propose that Rlp7 coevolved with these RNA elements to facilitate eukaryotic-specific functions in ribosome assembly and pre-rRNA processing.
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Shan L, Wu Q, Li Y, Shang H, Guo K, Wu J, Wei H, Zhao J, Yu J, Li MH. Transcriptome profiling identifies differentially expressed genes in postnatal developing pituitary gland of miniature pig. DNA Res 2013; 21:207-16. [PMID: 24282060 PMCID: PMC3989491 DOI: 10.1093/dnares/dst051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In recent years, Tibetan pig and Bama pig are popularly used as animal models for medical researches. However, little genomic information is available for the two breeds, particularly regarding gene expression pattern at the whole-transcriptome level. In this study, we characterized the pituitary transcriptome profile along their postnatal developmental stages within and between the two breeds in order to illustrate the differential dynamics and functions of differentially expressed genes. We obtained a total of ∼300 million 80-bp paired-end reads, detected 15 715 previously annotated genes. Most of the genes (90.33%) were shared between the two breeds with the main functions in metabolic process. Four hormone genes (GH, PRL, LHB, and FSHB) were detected in all samples with extremely high levels of expression. Functional differences between the three developmental stages (infancy, puberty and adulthood) in each breed were dominantly presented by the gene expressions at the first stage. That is, Bama pig was over-represented in the genes involved in the cellular process, while Tibetan pig was over-represented in the genes represented by the reproductive process. The identified SNPs indicated that the divergence between the miniature pig breeds and the large pig (Duroc) were greater than that between the two miniature pig breeds. This study substantially expands our knowledge concerning the genes transcribed in the pig pituitary gland and provides an overview of pituitary transcriptome dynamics throughout the period of postnatal development.
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Affiliation(s)
- Lei Shan
- 1Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Eksi R, Li HD, Menon R, Wen Y, Omenn GS, Kretzler M, Guan Y. Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PLoS Comput Biol 2013; 9:e1003314. [PMID: 24244129 PMCID: PMC3820534 DOI: 10.1371/journal.pcbi.1003314] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 09/19/2013] [Indexed: 12/13/2022] Open
Abstract
Integrating large-scale functional genomic data has significantly accelerated our understanding of gene functions. However, no algorithm has been developed to differentiate functions for isoforms of the same gene using high-throughput genomic data. This is because standard supervised learning requires ‘ground-truth’ functional annotations, which are lacking at the isoform level. To address this challenge, we developed a generic framework that interrogates public RNA-seq data at the transcript level to differentiate functions for alternatively spliced isoforms. For a specific function, our algorithm identifies the ‘responsible’ isoform(s) of a gene and generates classifying models at the isoform level instead of at the gene level. Through cross-validation, we demonstrated that our algorithm is effective in assigning functions to genes, especially the ones with multiple isoforms, and robust to gene expression levels and removal of homologous gene pairs. We identified genes in the mouse whose isoforms are predicted to have disparate functionalities and experimentally validated the ‘responsible’ isoforms using data from mammary tissue. With protein structure modeling and experimental evidence, we further validated the predicted isoform functional differences for the genes Cdkn2a and Anxa6. Our generic framework is the first to predict and differentiate functions for alternatively spliced isoforms, instead of genes, using genomic data. It is extendable to any base machine learner and other species with alternatively spliced isoforms, and shifts the current gene-centered function prediction to isoform-level predictions. In mammalian genomes, a single gene can be alternatively spliced into multiple isoforms which greatly increase the functional diversity of the genome. In the human, more than 95% of multi-exon genes undergo alternative splicing. It is hard to computationally differentiate the functions for the splice isoforms of the same gene, because they are almost always annotated with the same functions and share similar sequences. In this paper, we developed a generic framework to identify the ‘responsible’ isoform(s) for each function that the gene carries out, and therefore predict functional assignment on the isoform level instead of on the gene level. Within this generic framework, we implemented and evaluated several related algorithms for isoform function prediction. We tested these algorithms through both computational evaluation and experimental validation of the predicted ‘responsible’ isoform(s) and the predicted disparate functions of the isoforms of Cdkn2a and of Anxa6. Our algorithm represents the first effort to predict and differentiate isoforms through large-scale genomic data integration.
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Affiliation(s)
- Ridvan Eksi
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Hong-Dong Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yuchen Wen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (GSO); (MK); (YG)
| | - Matthias Kretzler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (GSO); (MK); (YG)
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (GSO); (MK); (YG)
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Woolford JL, Baserga SJ. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 2013; 195:643-81. [PMID: 24190922 PMCID: PMC3813855 DOI: 10.1534/genetics.113.153197] [Citation(s) in RCA: 558] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/26/2013] [Indexed: 01/09/2023] Open
Abstract
Ribosomes are highly conserved ribonucleoprotein nanomachines that translate information in the genome to create the proteome in all cells. In yeast these complex particles contain four RNAs (>5400 nucleotides) and 79 different proteins. During the past 25 years, studies in yeast have led the way to understanding how these molecules are assembled into ribosomes in vivo. Assembly begins with transcription of ribosomal RNA in the nucleolus, where the RNA then undergoes complex pathways of folding, coupled with nucleotide modification, removal of spacer sequences, and binding to ribosomal proteins. More than 200 assembly factors and 76 small nucleolar RNAs transiently associate with assembling ribosomes, to enable their accurate and efficient construction. Following export of preribosomes from the nucleus to the cytoplasm, they undergo final stages of maturation before entering the pool of functioning ribosomes. Elaborate mechanisms exist to monitor the formation of correct structural and functional neighborhoods within ribosomes and to destroy preribosomes that fail to assemble properly. Studies of yeast ribosome biogenesis provide useful models for ribosomopathies, diseases in humans that result from failure to properly assemble ribosomes.
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Affiliation(s)
- John L. Woolford
- Department of Biological Sciences, Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Susan J. Baserga
- Molecular Biophysics and Biochemistry, Genetics and Therapeutic Radiology, Yale University, New Haven, Connecticut 06520-8024
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Ferg M, Armant O, Yang L, Dickmeis T, Rastegar S, Strähle U. Gene transcription in the zebrafish embryo: regulators and networks. Brief Funct Genomics 2013; 13:131-43. [PMID: 24152666 DOI: 10.1093/bfgp/elt044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The precise spatial and temporal control of gene expression is a key process in the development, maintenance and regeneration of the vertebrate body. A substantial proportion of vertebrate genomes encode genes that control the transcription of the genetic information into mRNA. The zebrafish is particularly well suited to investigate gene regulatory networks underlying the control of gene expression during development due to the external development of its transparent embryos and the increasingly sophisticated tools for genetic manipulation available for this model system. We review here recent data on the analysis of cis-regulatory modules, transcriptional regulators and their integration into gene regulatory networks in the zebrafish, using the developing spinal cord as example.
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Affiliation(s)
- Marco Ferg
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany.
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50
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Bastos HP, Clarke LA, Couto FM. Annotation extension through protein family annotation coherence metrics. Front Genet 2013; 4:201. [PMID: 24130572 PMCID: PMC3795322 DOI: 10.3389/fgene.2013.00201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/22/2013] [Indexed: 11/23/2022] Open
Abstract
Protein functional annotation consists in associating proteins with textual descriptors elucidating their biological roles. The bulk of annotation is done via automated procedures that ultimately rely on annotation transfer. Despite a large number of existing protein annotation procedures the ever growing protein space is never completely annotated. One of the facets of annotation incompleteness derives from annotation uncertainty. Often when protein function cannot be predicted with enough specificity it is instead conservatively annotated with more generic terms. In a scenario of protein families or functionally related (or even dissimilar) sets this leads to a more difficult task of using annotations to compare the extent of functional relatedness among all family or set members. However, we postulate that identifying sub-sets of functionally coherent proteins annotated at a very specific level, can help the annotation extension of other incompletely annotated proteins within the same family or functionally related set. As an example we analyse the status of annotation of a set of CAZy families belonging to the Polysaccharide Lyase class. We show that through the use of visualization methods and semantic similarity based metrics it is possible to identify families and respective annotation terms within them that are suitable for possible annotation extension. Based on our analysis we then propose a semi-automatic methodology leading to the extension of single annotation terms within these partially annotated protein sets or families.
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Affiliation(s)
- Hugo P Bastos
- LaSIGE, Department of Informatics, Faculdade de Ciências, Universidade de Lisboa Lisboa, Portugal
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