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Holmes EC, Krammer F, Goodrum FD. Virology-The next fifty years. Cell 2024; 187:5128-5145. [PMID: 39303682 DOI: 10.1016/j.cell.2024.07.025] [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: 02/29/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 09/22/2024]
Abstract
Virology has made enormous advances in the last 50 years but has never faced such scrutiny as it does today. Herein, we outline some of the major advances made in virology during this period, particularly in light of the COVID-19 pandemic, and suggest some areas that may be of research importance in the next 50 years. We focus on several linked themes: cataloging the genomic and phenotypic diversity of the virosphere; understanding disease emergence; future directions in viral disease therapies, vaccines, and interventions; host-virus interactions; the role of viruses in chronic diseases; and viruses as tools for cell biology. We highlight the challenges that virology will face moving forward-not just the scientific and technical but also the social and political. Although there are inherent limitations in trying to outline the virology of the future, we hope this article will help inspire the next generation of virologists.
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Affiliation(s)
- Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Felicia D Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, AZ, USA
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2
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Liu L, Manley JL. Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3' ends. RNA (NEW YORK, N.Y.) 2024; 30:1122-1140. [PMID: 38986572 PMCID: PMC11331416 DOI: 10.1261/rna.080108.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
The cleavage and polyadenylation specificity factor (CPSF) complex plays a central role in the formation of mRNA 3' ends, being responsible for the recognition of the poly(A) signal sequence, the endonucleolytic cleavage step, and recruitment of poly(A) polymerase. CPSF has been extensively studied for over three decades, and its functions and those of its individual subunits are becoming increasingly well-defined, with much current research focusing on the impact of these proteins on the normal functioning or disease/stress states of cells. In this review, we provide an overview of the general functions of CPSF and its subunits, followed by a discussion of how they exert their functions in a surprisingly diverse variety of biological processes and cellular conditions. These include transcription termination, small RNA processing, and R-loop prevention/resolution, as well as more generally cancer, differentiation/development, and infection/immunity.
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Affiliation(s)
- Lizhi Liu
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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3
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Murari E, Meadows D, Cuda N, Mangone M. A comprehensive analysis of 3'UTRs in Caenorhabditis elegans. Nucleic Acids Res 2024; 52:7523-7538. [PMID: 38917330 PMCID: PMC11260456 DOI: 10.1093/nar/gkae543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/29/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
3'Untranslated regions (3'UTRs) are essential portions of genes containing elements necessary for pre-mRNA 3'end processing and are involved in post-transcriptional gene regulation. Despite their importance, they remain poorly characterized in eukaryotes. Here, we have used a multi-pronged approach to extract and curate 3'UTR data from 11533 publicly available datasets, corresponding to the entire collection of Caenorhabditis elegans transcriptomes stored in the NCBI repository from 2009 to 2023. We have also performed high throughput cloning pipelines to identify and validate rare 3'UTR isoforms and incorporated and manually curated 3'UTR isoforms from previously published datasets. This updated C. elegans 3'UTRome (v3) is the most comprehensive resource in any metazoan to date, covering 97.4% of the 20362 experimentally validated protein-coding genes with refined and updated 3'UTR boundaries for 23489 3'UTR isoforms. We also used this novel dataset to identify and characterize sequence elements involved in pre-mRNA 3'end processing and update miRNA target predictions. This resource provides important insights into the 3'UTR formation, function, and regulation in eukaryotes.
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Affiliation(s)
- Emma Murari
- The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, USA
| | - Dalton Meadows
- The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, USA
| | - Nicholas Cuda
- The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, USA
| | - Marco Mangone
- The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA
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Genç B, Nho B, Seung H, Helmold B, Park H, Gözütok Ö, Kim S, Park J, Ye S, Lee H, Lee N, Yu SS, Kim S, Lee J, Özdinler H. Novel rAAV vector mediated intrathecal HGF delivery has an impact on neuroimmune modulation in the ALS motor cortex with TDP-43 pathology. Gene Ther 2023; 30:560-574. [PMID: 36823441 DOI: 10.1038/s41434-023-00383-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/21/2022] [Accepted: 01/23/2023] [Indexed: 02/25/2023]
Abstract
Recombinant adeno-associated virus (rAAV)-based gene therapies offer an immense opportunity for rare diseases, such as amyotrophic lateral sclerosis (ALS), which is defined by the loss of the upper and the lower motor neurons. Here, we describe generation, characterization, and utilization of a novel vector system, which enables expression of the active form of hepatocyte growth factor (HGF) under EF-1α promoter with bovine growth hormone (bGH) poly(A) sequence and is effective with intrathecal injections. HGF's role in promoting motor neuron survival had been vastly reported. Therefore, we investigated whether intrathecal delivery of HGF would have an impact on one of the most common pathologies of ALS: the TDP-43 pathology. Increased astrogliosis, microgliosis and progressive upper motor neuron loss are important consequences of ALS in the motor cortex with TDP-43 pathology. We find that cortex can be modulated via intrathecal injection, and that expression of HGF reduces astrogliosis, microgliosis in the motor cortex, and help restore ongoing UMN degeneration. Our findings not only introduce a novel viral vector for the treatment of ALS, but also demonstrate modulation of motor cortex by intrathecal viral delivery, and that HGF treatment is effective in reducing astrogliosis and microgliosis in the motor cortex of ALS with TDP-43 pathology.
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Affiliation(s)
- Barış Genç
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA
| | - Boram Nho
- School of Biological Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea
| | - Hana Seung
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea
| | - Benjamin Helmold
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA
| | - Huiwon Park
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea
| | - Öge Gözütok
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA
| | - Seunghyun Kim
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea
| | - Jinil Park
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea
| | - Sanghyun Ye
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea
| | - Haneul Lee
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea
| | - Nayeon Lee
- School of Biological Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seung-Shin Yu
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea
| | - Sunyoung Kim
- School of Biological Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea
| | - Junghun Lee
- School of Biological Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
- Helixmith Co., Ltd., R&D Center, 21, Magokjungang 8-ro 7-gil, Gangseo-gu, Seoul, 07794, Republic of Korea.
| | - Hande Özdinler
- Department of Neurology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL, 60611, USA.
- Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University, Evanston, IL, 60208, USA.
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5
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Gutierrez PA, Wei J, Sun Y, Tong L. Molecular basis for the recognition of the AUUAAA polyadenylation signal by mPSF. RNA (NEW YORK, N.Y.) 2022; 28:1534-1541. [PMID: 36130077 PMCID: PMC9745836 DOI: 10.1261/rna.079322.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
The polyadenylation signal (PAS) is a key sequence element for 3'-end cleavage and polyadenylation of messenger RNA precursors (pre-mRNAs). This hexanucleotide motif is recognized by the mammalian polyadenylation specificity factor (mPSF), consisting of CPSF160, WDR33, CPSF30, and Fip1 subunits. Recent studies have revealed how the AAUAAA PAS, the most frequently observed PAS, is recognized by mPSF. We report here the structure of human mPSF in complex with the AUUAAA PAS, the second most frequently identified PAS. Conformational differences are observed for the A1 and U2 nucleotides in AUUAAA compared to the A1 and A2 nucleotides in AAUAAA, while the binding modes of the remaining 4 nt are essentially identical. The 5' phosphate of U2 moves by 2.6 Å and the U2 base is placed near the six-membered ring of A2 in AAUAAA, where it makes two hydrogen bonds with zinc finger 2 (ZF2) of CPSF30, which undergoes conformational changes as well. We also attempted to determine the binding modes of two rare PAS hexamers, AAGAAA and GAUAAA, but did not observe the RNA in the cryo-electron microscopy density. The residues in CPSF30 (ZF2 and ZF3) and WDR33 that recognize PAS are disordered in these two structures.
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Affiliation(s)
- Pedro A Gutierrez
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jia Wei
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Yadong Sun
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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6
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Loke ASW, Lambert PF, Spurgeon ME. Current In Vitro and In Vivo Models to Study MCPyV-Associated MCC. Viruses 2022; 14:2204. [PMID: 36298759 PMCID: PMC9607385 DOI: 10.3390/v14102204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/01/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022] Open
Abstract
Merkel cell polyomavirus (MCPyV) is the only human polyomavirus currently known to cause human cancer. MCPyV is believed to be an etiological factor in at least 80% of cases of the rare but aggressive skin malignancy Merkel cell carcinoma (MCC). In these MCPyV+ MCC tumors, clonal integration of the viral genome results in the continued expression of two viral proteins: the viral small T antigen (ST) and a truncated form of the viral large T antigen. The oncogenic potential of MCPyV and the functional properties of the viral T antigens that contribute to neoplasia are becoming increasingly well-characterized with the recent development of model systems that recapitulate the biology of MCPyV+ MCC. In this review, we summarize our understanding of MCPyV and its role in MCC, followed by the current state of both in vitro and in vivo model systems used to study MCPyV and its contribution to carcinogenesis. We also highlight the remaining challenges within the field and the major considerations related to the ongoing development of in vitro and in vivo models of MCPyV+ MCC.
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Affiliation(s)
| | | | - Megan E. Spurgeon
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine & Public Health, University of Wisconsin, Madison, WI 53705, USA
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Fang L, Guo L, Zhang M, Li X, Deng Z. Analysis of Polyadenylation Signal Usage with Full-Length Transcriptome in Spodoptera frugiperda (Lepidoptera: Noctuidae). INSECTS 2022; 13:803. [PMID: 36135504 PMCID: PMC9505298 DOI: 10.3390/insects13090803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
During the messenger RNA (mRNA) maturation process, RNA polyadenylation is a key step, and is coupled to the termination of transcription. Various cis-acting elements near the cleavage site and their binding factors would affect the process of polyadenylation, and AAUAAA, a highly conserved hexamer, was the most important polyadenylation signal (PAS). PAS usage is one of the critical modification determinants targeted at mRNA post-transcription. The full-length transcriptome has recently generated a massive amount of sequencing data, revealing poly(A) variation and alternative polyadenylation (APA) in Spodoptera frugiperda. We identified 50,616 polyadenylation signals in Spodoptera frugiperda via analysis of full-length transcriptome combined with expression Sequence Tags Technology (EST). The polyadenylation signal usage in Spodoptera frugiperda is conserved, and it is similar to that of flies and other animals. AAUAAA and AUUAAA are the most highly conserved polyadenylation signals of all polyadenylation signals we identified. Additionally, we found the U/GU-rich downstream sequence element (DSE) in the cleavage site. These results demonstrate that APA in Spodoptera frugiperda plays a significant role in root growth and development. This is the first polyadenylation signal usage analysis in agricultural pests, which can deepen our understanding of Spodoptera frugiperda and provide a theoretical basis for pest control.
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Affiliation(s)
- Liying Fang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lina Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Min Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xianchun Li
- Department of Entomology, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
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8
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Stenglein MD. The Case for Studying New Viruses of New Hosts. Annu Rev Virol 2022; 9:157-172. [PMID: 35671564 DOI: 10.1146/annurev-virology-100220-112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mark D Stenglein
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA;
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9
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Small DNA tumor viruses and human cancer: Preclinical models of virus infection and disease. Tumour Virus Res 2022; 14:200239. [PMID: 35636683 PMCID: PMC9194455 DOI: 10.1016/j.tvr.2022.200239] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/05/2022] [Accepted: 05/25/2022] [Indexed: 01/13/2023] Open
Abstract
Human tumor viruses cause various human cancers that account for at least 15% of the global cancer burden. Among the currently identified human tumor viruses, two are small DNA tumor viruses: human papillomaviruses (HPVs) and Merkel cell polyomavirus (MCPyV). The study of small DNA tumor viruses (adenoviruses, polyomaviruses, and papillomaviruses) has facilitated several significant biological discoveries and established some of the first animal models of virus-associated cancers. The development and use of preclinical in vivo models to study HPVs and MCPyV and their role in human cancer is the focus of this review. Important considerations in the design of animal models of small DNA tumor virus infection and disease, including host range, cell tropism, choice of virus isolates, and the ability to recapitulate human disease, are presented. The types of infection-based and transgenic model strategies that are used to study HPVs and MCPyV, including their strengths and limitations, are also discussed. An overview of the current models that exist to study HPV and MCPyV infection and neoplastic disease are highlighted. These comparative models provide valuable platforms to study various aspects of virus-associated human disease and will continue to expand knowledge of human tumor viruses and their relationship with their hosts.
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10
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Zhang Y, Song J, Zhang M, Deng Z. Analysis Polyadenylation Signal Usage in Sus scrofa. Animals (Basel) 2022; 12:ani12020194. [PMID: 35049816 PMCID: PMC8773104 DOI: 10.3390/ani12020194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/01/2022] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
RNA polyadenylation is an important step in the messenger RNA (mRNA) maturation process, and the first step is recognizing the polyadenylation signal (PAS). The PAS type and distribution is a key determinant of post-transcriptional mRNA modification and gene expression. However, little is known about PAS usage and alternative polyadenylation (APA) regulation in livestock species. Recently, sequencing technology has enabled the generation of a large amount of sequencing data revealing variation in poly(A) signals and APA regulation in Sus scrofa. We identified 62,491 polyadenylation signals in Sus scrofa using expressed sequence tag (EST) sequences combined with RNA-seq analysis. The composition and usage frequency of polyadenylation signal in Sus scrofa is similar with that of human and mouse. The most highly conserved polyadenylation signals are AAUAAA and AUUAAA, used for over 63.35% of genes. In addition, we also analyzed the U/GU-rich downstream sequence (DSE) element, located downstream of the cleavage site. Our results indicate that APA regulation was widely occurred in Sus scrofa, as in other organisms. Our result was useful for the accurate annotation of RNA 3' ends in Sus scrofa and the analysis of polyadenylation signal usage in Sus scrofa would give the new insights into the mechanisms of transcriptional regulation.
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Affiliation(s)
- Yuting Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.Z.); (M.Z.)
| | - Jingwen Song
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China;
| | - Min Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.Z.); (M.Z.)
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China;
| | - Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.Z.); (M.Z.)
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China;
- Correspondence:
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11
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Fenno LE, Levy R, Yizhar O. Molecular Optimization of Rhodopsin-Based Tools for Neuroscience Applications. Methods Mol Biol 2022; 2501:289-310. [PMID: 35857234 DOI: 10.1007/978-1-0716-2329-9_14] [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] [Indexed: 06/15/2023]
Abstract
There is no question that genetically encoded tools have revolutionized neuroscience. These include optically modulated tools for writing-in (optogenetics) and reading-out (calcium, voltage, and neurotransmitter indicators) neural activity as well as precision expression of these reagents using virally mediated delivery. With few exceptions, these powerful approaches are derived from naturally occurring molecules that are sourced from diverse organisms that span all kingdoms of life. Successful expression of genetic tools in standard neuroscience model organisms requires optimizing gene structure, taking into account differences in both protein translation and trafficking. Myriad approaches have resolved these two challenges, resulting in order-of-magnitude increases in functional expression. In this chapter, we focus on synthesizing prior experience in successfully enabling the transition of genes across kingdoms with a goal of facilitating the production of the next generation of molecular tools for neuroscience. We then provide a detailed protocol that allows expression and testing of novel genetically encoded tools in mammalian cell lines and primary cultured neurons.
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Affiliation(s)
- Lief E Fenno
- Departments of Psychiatry and Neuroscience, University of Texas Austin Dell Medical School, Austin, TX, USA
| | - Rivka Levy
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel.
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12
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Trotman JB, Lee DM, Cherney RE, Kim SO, Inoue K, Schertzer MD, Bischoff SR, Cowley DO, Calabrese J. Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity. Nucleic Acids Res 2020; 48:10500-10517. [PMID: 32986830 PMCID: PMC7544216 DOI: 10.1093/nar/gkaa789] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/20/2020] [Accepted: 09/12/2020] [Indexed: 12/22/2022] Open
Abstract
The Xist lncRNA requires Repeat A, a conserved RNA element located in its 5' end, to induce gene silencing during X-chromosome inactivation. Intriguingly, Repeat A is also required for production of Xist. While silencing by Repeat A requires the protein SPEN, how Repeat A promotes Xist production remains unclear. We report that in mouse embryonic stem cells, expression of a transgene comprising the first two kilobases of Xist (Xist-2kb) causes transcriptional readthrough of downstream polyadenylation sequences. Readthrough required Repeat A and the ∼750 nucleotides downstream, did not require SPEN, and was attenuated by splicing. Despite associating with SPEN and chromatin, Xist-2kb did not robustly silence transcription, whereas a 5.5-kb Xist transgene robustly silenced transcription and read through its polyadenylation sequence. Longer, spliced Xist transgenes also induced robust silencing yet terminated efficiently. Thus, in contexts examined here, Xist requires sequence elements beyond its first two kilobases to robustly silence transcription, and the 5' end of Xist harbors SPEN-independent transcriptional antiterminator activity that can repress proximal cleavage and polyadenylation. In endogenous contexts, this antiterminator activity may help produce full-length Xist RNA while rendering the Xist locus resistant to silencing by the same repressive complexes that the lncRNA recruits to other genes.
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Affiliation(s)
- Jackson B Trotman
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - David M Lee
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, Chapel Hill, NC 27599, USA
| | - Rachel E Cherney
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, Chapel Hill, NC 27599, USA
| | - Susan O Kim
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Kaoru Inoue
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Megan D Schertzer
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, Chapel Hill, NC 27599, USA
| | - Steven R Bischoff
- Animal Models Core, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Dale O Cowley
- Animal Models Core, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - J Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
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13
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Characterization of the effects of terminators and introns on recombinant gene expression in the basidiomycete Ceriporiopsis subvermispora. J Microbiol 2020; 58:1037-1045. [DOI: 10.1007/s12275-020-0213-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 01/06/2023]
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14
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Phillips BL, Banerjee A, Sanchez BJ, Di Marco S, Gallouzi IE, Pavlath GK, Corbett AH. Post-transcriptional regulation of Pabpn1 by the RNA binding protein HuR. Nucleic Acids Res 2019; 46:7643-7661. [PMID: 29939290 PMCID: PMC6125628 DOI: 10.1093/nar/gky535] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/08/2018] [Indexed: 01/14/2023] Open
Abstract
RNA processing is critical for proper spatial and temporal control of gene expression. The ubiquitous nuclear polyadenosine RNA binding protein, PABPN1, post-transcriptionally regulates multiple steps of gene expression. Mutations in the PABPN1 gene expanding an N-terminal alanine tract in the PABPN1 protein from 10 alanines to 11–18 alanines cause the muscle-specific disease oculopharyngeal muscular dystrophy (OPMD), which affects eyelid, pharynx, and proximal limb muscles. Previous work revealed that the Pabpn1 transcript is unstable, contributing to low steady-state Pabpn1 mRNA and protein levels in vivo, specifically in skeletal muscle, with even lower levels in muscles affected in OPMD. Thus, low levels of PABPN1 protein could predispose specific tissues to pathology in OPMD. However, no studies have defined the mechanisms that regulate Pabpn1 expression. Here, we define multiple cis-regulatory elements and a trans-acting factor, HuR, which regulate Pabpn1 expression specifically in mature muscle in vitro and in vivo. We exploit multiple models including C2C12 myotubes, primary muscle cells, and mice to determine that HuR decreases Pabpn1 expression. Overall, we have uncovered a mechanism in mature muscle that negatively regulates Pabpn1 expression in vitro and in vivo, which could provide insight to future studies investigating therapeutic strategies for OPMD treatment.
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Affiliation(s)
- Brittany L Phillips
- Department of Biology, Emory University, Atlanta, GA 30322, USA.,Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Ayan Banerjee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Brenda J Sanchez
- Department of Biochemistry, Goodman Cancer Center, McGill University, Montreal, Quebec, Canada
| | - Sergio Di Marco
- Department of Biochemistry, Goodman Cancer Center, McGill University, Montreal, Quebec, Canada
| | - Imed-Eddine Gallouzi
- Department of Biochemistry, Goodman Cancer Center, McGill University, Montreal, Quebec, Canada.,Hamad Bin Khalifa University (HBKU), Life Sciences Division, College of Sciences and Engineering, Education City, Doha, Qatar
| | - Grace K Pavlath
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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15
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DiMaio D. Small size, big impact: how studies of small DNA tumour viruses revolutionized biology. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180300. [PMID: 30955494 PMCID: PMC6501907 DOI: 10.1098/rstb.2018.0300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2018] [Indexed: 01/19/2023] Open
Abstract
Intense study of three families of small tumour viruses with double-stranded DNA genomes, carried out over 50 years, has had a profound impact on biology. The polyomaviruses and papillomaviruses have circular DNA genomes of approximately 5000 and approximately 8000 base-pairs, respectively, and thus encode only a handful of proteins. Adenoviruses have a 32 000-base-pair linear DNA genome, still far smaller than the three billion-base-pair human genome. Members of all three virus families can transform cultured cells to tumorigenicity and cause tumours in experimental animals. Several human papillomaviruses (HPV) and at least one polyomavirus are oncogenic in humans. Early analysis of these viruses, particularly the polyomavirus SV40, led to the development of many powerful experimental tools, including restriction mapping, site-directed mutagenesis, gene transfer, genome-wide sequencing and recombinant DNA. These tools have since been refined and used to study cellular genes, revolutionizing our understanding of biology. These tools were also applied to the viruses themselves. Analysis of the virus life cycle and the effect of these viruses on cells yielded important new insights into many aspects of gene expression, DNA replication, cell biology and carcinogenesis. These studies have also led to vaccination strategies to prevent infection and cancer in humans. This article is part of the theme issue 'Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses'.
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Affiliation(s)
- Daniel DiMaio
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
- Yale Cancer Center, PO Box 208028, New Haven, CT 06520-8028, USA
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16
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Hill CH, Boreikaitė V, Kumar A, Casañal A, Kubík P, Degliesposti G, Maslen S, Mariani A, von Loeffelholz O, Girbig M, Skehel M, Passmore LA. Activation of the Endonuclease that Defines mRNA 3' Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex. Mol Cell 2019; 73:1217-1231.e11. [PMID: 30737185 PMCID: PMC6436931 DOI: 10.1016/j.molcel.2018.12.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/02/2018] [Accepted: 12/21/2018] [Indexed: 01/19/2023]
Abstract
Cleavage and polyadenylation factor (CPF/CPSF) is a multi-protein complex essential for formation of eukaryotic mRNA 3' ends. CPF cleaves pre-mRNAs at a specific site and adds a poly(A) tail. The cleavage reaction defines the 3' end of the mature mRNA, and thus the activity of the endonuclease is highly regulated. Here, we show that reconstitution of specific pre-mRNA cleavage with recombinant yeast proteins requires incorporation of the Ysh1 endonuclease into an eight-subunit "CPFcore" complex. Cleavage also requires the accessory cleavage factors IA and IB, which bind substrate pre-mRNAs and CPF, likely facilitating assembly of an active complex. Using X-ray crystallography, electron microscopy, and mass spectrometry, we determine the structure of Ysh1 bound to Mpe1 and the arrangement of subunits within CPFcore. Together, our data suggest that the active mRNA 3' end processing machinery is a dynamic assembly that is licensed to cleave only when all protein factors come together at the polyadenylation site.
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Affiliation(s)
- Chris H Hill
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - Ana Casañal
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Peter Kubík
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Ottilie von Loeffelholz
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, Université de Strasbourg, Strasbourg, France; Centre National de la Recherche Scientifique UMR 7104, Illkirch, Université de Strasbourg, Strasbourg, France; INSERM U964, Illkirch, Université de Strasbourg, Strasbourg, France
| | - Mathias Girbig
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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17
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Toledano T, Vitenshtein A, Stern-Ginossar N, Seidel E, Mandelboim O. Decay of the Stress-Induced Ligand MICA Is Controlled by the Expression of an Alternative 3′ Untranslated Region. THE JOURNAL OF IMMUNOLOGY 2018. [DOI: 10.4049/jimmunol.1700968] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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18
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Neve J, Patel R, Wang Z, Louey A, Furger AM. Cleavage and polyadenylation: Ending the message expands gene regulation. RNA Biol 2017; 14:865-890. [PMID: 28453393 PMCID: PMC5546720 DOI: 10.1080/15476286.2017.1306171] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/02/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022] Open
Abstract
Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3'end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes. Here, we review how pA sites are recognized and comprehensively summarize how APA is regulated and creates mRNA isoform profiles that are characteristic for cell types, tissues, cellular states and disease.
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Affiliation(s)
- Jonathan Neve
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Radhika Patel
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Zhiqiao Wang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Alastair Louey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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19
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VanBelzen DJ, Malik AS, Henthorn PS, Kornegay JN, Stedman HH. Mechanism of Deletion Removing All Dystrophin Exons in a Canine Model for DMD Implicates Concerted Evolution of X Chromosome Pseudogenes. Mol Ther Methods Clin Dev 2017; 4:62-71. [PMID: 28344992 PMCID: PMC5363321 DOI: 10.1016/j.omtm.2016.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/07/2016] [Indexed: 01/19/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a lethal, X-linked, muscle-wasting disorder caused by mutations in the large, 2.4-Mb dystrophin gene. The majority of DMD-causing mutations are sporadic, multi-exon, frameshifting deletions, with the potential for variable immunological tolerance to the dystrophin protein from patient to patient. While systemic gene therapy holds promise in the treatment of DMD, immune responses to vectors and transgenes must first be rigorously evaluated in informative preclinical models to ensure patient safety. A widely used canine model for DMD, golden retriever muscular dystrophy, expresses detectable amounts of near full-length dystrophin due to alternative splicing around an intronic point mutation, thereby confounding the interpretation of immune responses to dystrophin-derived gene therapies. Here we characterize a naturally occurring deletion in a dystrophin-null canine, the German shorthaired pointer. The deletion spans 5.6 Mb of the X chromosome and encompasses all coding exons of the DMD and TMEM47 genes. The sequences surrounding the deletion breakpoints are virtually identical, suggesting that the deletion occurred through a homologous recombination event. Interestingly, the deletion breakpoints are within loci that are syntenically conserved among mammals, yet the high homology among this subset of ferritin-like loci is unique to the canine genome, suggesting lineage-specific concerted evolution of these atypical sequence elements.
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Affiliation(s)
- D. Jake VanBelzen
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alock S. Malik
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paula S. Henthorn
- Section of Medical Genetics, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Joe N. Kornegay
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Hansell H. Stedman
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael Crescenz Veterans Administration Medical Center, Philadelphia, PA 19104, USA
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20
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Streamlined scanning for enhancer elements in Drosophila melanogaster. Biotechniques 2016; 60:141-4. [PMID: 26956092 DOI: 10.2144/000114391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/09/2015] [Indexed: 11/23/2022] Open
Abstract
Enhancer elements in most eukaryotic organisms are often positioned at a great distance away from the transcription start site of the gene they regulate. Complex three-dimensional chromatin organization and insulators usually guide and limit the range of an enhancer's regulatory activity to a specific genetic locus. Rigorous testing of an entire genomic locus is often required in order to uncover the complete set of cis-regulatory modules (CRMs) regulating a gene, especially those with complex and dynamic expression patterns. Here we report a fast and efficient method for enhancer element identification by scanning large genomic regions using transgenic reporter genes.
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21
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Salem TZ, Seaborn CP, Turney CM, Xue J, Shang H, Cheng XW. The Influence of SV40 polyA on Gene Expression of Baculovirus Expression Vector Systems. PLoS One 2015; 10:e0145019. [PMID: 26659470 PMCID: PMC4686012 DOI: 10.1371/journal.pone.0145019] [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: 09/15/2015] [Accepted: 11/25/2015] [Indexed: 01/17/2023] Open
Abstract
The simian virus 40 polyadenylation signal (SV40 polyA) has been routinely inserted downstream of the polyhedrin promoter in many baculovirus expression vector systems (BEVS). In the baculovirus prototype Autographa californica multiple nucleopolyhedrovirus (AcMNPV), the polyhedrin promoter (very late promoter) transcribes its gene by a viral RNA polymerase therefore there is no supporting evidence that SV40 polyA is required for the proper gene expression under the polyhedrin promoter. Moreover, the effect of the SV40 polyA sequence on the polyhedrin promoter activity has not been tested either at its natural polyhedrin locus or in other loci in the viral genome. In order to test the significance of adding the SV40 polyA sequence on gene expression, the expression of the enhanced green fluorescent protein (egfp) was evaluated with and without the presence of SV40 polyA under the control of the polyhedrin promoter at different genomic loci (polyherin, ecdysteroid UDP-glucosyltransferase (egt), and gp37). In this study, spectrofluorometry and western blot showed reduction of EGFP protein for all recombinant viruses with SV40 polyA, whereas qPCR showed an increase in the egfp mRNA levels. Therefore, we conclude that SV40 polyA increases mRNA levels but decreases protein production in the BEVS when the polyhedrin promoter is used at different loci. This work suggests that SV40 polyA in BEVSs should be replaced by an AcMNPV late gene polyA for optimal protein production or left untouched for optimal RNA production (RNA interference applications).
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Affiliation(s)
- Tamer Z. Salem
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
- Biomedical Sciences, University of Science and Technology at Zewail City, Giza, Egypt
- Department of Microbial Molecular Biology, AGERI, ARC, Giza, Egypt
- * E-mail: (TZS); (XC)
| | - Craig P. Seaborn
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
| | - Colin M. Turney
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
| | - Jianli Xue
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
| | - Hui Shang
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
| | - Xiao-Wen Cheng
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
- * E-mail: (TZS); (XC)
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22
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Zulliger R, Conley SM, Naash MI. Non-viral therapeutic approaches to ocular diseases: An overview and future directions. J Control Release 2015; 219:471-487. [PMID: 26439665 PMCID: PMC4699668 DOI: 10.1016/j.jconrel.2015.10.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 12/31/2022]
Abstract
Currently there are no viable treatment options for patients with debilitating inherited retinal degeneration. The vast variability in disease-inducing mutations and resulting phenotypes has hampered the development of therapeutic interventions. Gene therapy is a logical approach, and recent work has focused on ways to optimize vector design and packaging to promote optimized expression and phenotypic rescue after intraocular delivery. In this review, we discuss ongoing ocular clinical trials, which currently use viral gene delivery, but focus primarily on new advancements in optimizing the efficacy of non-viral gene delivery for ocular diseases. Non-viral delivery systems are highly customizable, allowing functionalization to improve cellular and nuclear uptake, bypassing cellular degradative machinery, and improving gene expression in the nucleus. Non-viral vectors often yield transgene expression levels lower than viral counterparts, however their favorable safety/immune profiles and large DNA capacity (critical for the delivery of large ocular disease genes) make their further development a research priority. Recent work on particle coating and vector engineering presents exciting ways to overcome limitations of transient/low gene expression levels, but also highlights the fact that further refinements are needed before use in the clinic.
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Affiliation(s)
- Rahel Zulliger
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204-5060, United States
| | - Shannon M Conley
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States
| | - Muna I Naash
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204-5060, United States.
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23
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Nerlich A, Ruangkiattikul N, Laarmann K, Janze N, Dittrich-Breiholz O, Kracht M, Goethe R. C/EBPβ is a transcriptional key regulator of IL-36α in murine macrophages. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:966-78. [PMID: 26066982 DOI: 10.1016/j.bbagrm.2015.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/15/2015] [Accepted: 06/01/2015] [Indexed: 12/25/2022]
Abstract
Interleukin (IL)-36α - one of the novel members of the IL-1 family of cytokines - is a potent regulator of dendritic and T cells and plays an important role in inflammatory processes like experimental skin inflammation in mice and in mouse models for human psoriasis. Here, we demonstrate that C/EBPβ, a transcription factor required for the selective expression of inflammatory genes, is a key activator of the Il36A gene in murine macrophages. RNAi-mediated suppression of C/EBPβ expression in macrophages (C/EBPβ(low) cells) significantly impaired Il36A gene induction following challenge with LPS. Despite the presence of five predicted C/EBP binding sites, luciferase reporter assays demonstrated that C/EBPβ confers responsiveness to LPS primarily through a half-CRE•C/EBP element in the proximal Il36A promoter. Electrophoretic mobility shift assays showed that C/EBPβ but not CREB proteins interact with this critical half-CRE•C/EBP element. In addition, overexpression of C/EBPβ in C/EBPβ(low) cells enhanced the expression of Il36A whereas CREB-1 had no effect. Finally, chromatin immunoprecipitation confirmed that C/EBPβ but neither CREB-1, ATF-2 nor ATF4 is directly recruited to the proximal promoter region of the Il36A gene. Together, these findings demonstrate an essential role of C/EBPβ in the regulation of the Il36A gene via the proximal half-CRE•C/EBP element in response to inflammatory stimuli.
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Affiliation(s)
- Andreas Nerlich
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany.
| | - Nanthapon Ruangkiattikul
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | - Kristin Laarmann
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | - Nina Janze
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | | | - Michael Kracht
- Rudolf -Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
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24
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Sladitschek HL, Neveu PA. MXS-Chaining: A Highly Efficient Cloning Platform for Imaging and Flow Cytometry Approaches in Mammalian Systems. PLoS One 2015; 10:e0124958. [PMID: 25909630 PMCID: PMC4409215 DOI: 10.1371/journal.pone.0124958] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/19/2015] [Indexed: 11/25/2022] Open
Abstract
The continuous improvement of imaging technologies has driven the development of sophisticated reporters to monitor biological processes. Such constructs should ideally be assembled in a flexible enough way to allow for their optimization. Here we describe a highly reliable cloning method to efficiently assemble constructs for imaging or flow cytometry applications in mammalian cell culture systems. We bioinformatically identified a list of restriction enzymes whose sites are rarely found in human and mouse cDNA libraries. From the best candidates, we chose an enzyme combination (MluI, XhoI and SalI: MXS) that enables iterative chaining of individual building blocks. The ligation scar resulting from the compatible XhoI- and SalI-sticky ends can be translated and hence enables easy in-frame cloning of coding sequences. The robustness of the MXS-chaining approach was validated by assembling constructs up to 20 kb long and comprising up to 34 individual building blocks. By assessing the success rate of 400 ligation reactions, we determined cloning efficiency to be 90% on average. Large polycistronic constructs for single-cell imaging or flow cytometry applications were generated to demonstrate the versatility of the MXS-chaining approach. We devised several constructs that fluorescently label subcellular structures, an adapted version of FUCCI (fluorescent, ubiquitination-based cell cycle indicator) optimized to visualize cell cycle progression in mouse embryonic stem cells and an array of artificial promoters enabling dosage of doxycyline-inducible transgene expression. We made publicly available through the Addgene repository a comprehensive set of MXS-building blocks comprising custom vectors, a set of fluorescent proteins, constitutive promoters, polyadenylation signals, selection cassettes and tools for inducible gene expression. Finally, detailed guidelines describe how to chain together prebuilt MXS-building blocks and how to generate new customized MXS-building blocks.
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Affiliation(s)
- Hanna L. Sladitschek
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, Germany
| | - Pierre A. Neveu
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, Germany
- * E-mail:
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25
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Singh A, Meena M, Kumar D, Dubey AK, Hassan MI. Structural and functional analysis of various globulin proteins from soy seed. Crit Rev Food Sci Nutr 2015; 55:1491-502. [PMID: 24915310 DOI: 10.1080/10408398.2012.700340] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Storage proteins of soybean mostly consist of globulins, which are classified according to their sedimentation coefficient. Among 4 major types: 2S, 7S, 11S, and 15S of globulins, 7S and 11S constitute major fraction. The 11S fraction consists only of glycinin and 7S fraction majorly consists of β-conglycinin, small amounts of γ-conglycinin and basic 7S globulin (Bg7S). Glycinin exist as a hexamer while β-conglycinin as a trimer and Bg7S as a tetramer. Glycinin subunits are coded by 5 genes of a family, whereas about 15 genes are present for β-conglycinin subunits. Bg7S gene is present in four copies in soybean genome. Synthesis of all proteins takes place as a single polypeptide chain, which is cleaved after folding to yield different chains or subunits. Glycinin and β-Conglycinin are made for storage purpose. However, Bg7S has potential xylanase inhibition activity and protein kinase activity. Primary structure of Bg7S reveals 12 conserved cysteine residues involved in forming 6 disulfide bonds, which provides appreciable stability to protein. Secondary structure is predominately rich in β-sheets with few alpha helices. Bg7S shares structural similarity with various aspartic-proteases. In this review, our aim is to discuss sequence, structure, and function of various globulins present in Glycine max.
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Affiliation(s)
- Amandeep Singh
- a Division of Biotechnology, Netaji Subhas Institute of Technology , Azad Hind Fauz Marg, Sector-3, Dwarka, New Delhi , India
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26
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Li XQ, Du D. Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals. BMC Evol Biol 2014; 14:162. [PMID: 25052519 PMCID: PMC4360255 DOI: 10.1186/s12862-014-0162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
Background The polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mRNA polyadenylation [poly(A)] sites are still uncharacterized in most species. The evolutionary tendency for poly(A) site selection is still largely unknown. Results We analyzed the poly(A) site regions of 31 species or phyla. Different groups of species showed different poly(A) signal motifs: UUACUU at the poly(A) site in the parasite Trypanosoma cruzi; UGUAAC (approximately 13 bases upstream of the site) in the alga Chlamydomonas reinhardtii; UGUUUG (or UGUUUGUU) at mainly the fourth base downstream of the poly(A) site in the parasite Blastocystis hominis; and AAUAAA at approximately 16 bases and approximately 19 bases upstream of the poly(A) site in animals and plants, respectively. Polyadenylation signal motifs are usually several hundred times more abundant around poly(A) sites than in whole genomes. These predominant motifs usually had very specific locations, whether upstream of, at, or downstream of poly(A) sites, depending on the species or phylum. The poly(A) site was usually an adenosine (A) in all analyzed species except for B. hominis, and there was weak A predominance in C. reinhardtii. Fungi, animals, plants, and the protist Phytophthora infestans shared a general base abundance pattern (or base composition pattern) of “U-rich—A-rich—U-rich—Poly(A) site—U-rich regions”, or U-A-U-A-U for short, with some variation for each kingdom or subkingdom. Conclusion This study identified the poly(A) signal motifs, motif locations, and base composition patterns around mRNA poly(A) sites in protists, fungi, plants, and animals and provided insight into poly(A) site evolution.
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Affiliation(s)
- Xiu-Qing Li
- Molecular Genetics Laboratory, Potato Research Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada.
| | - Donglei Du
- Quantitative Methods Research Group, Faculty of Business Administration, University of New Brunswick, 7 Macaulay Lane, Fredericton, NB, E3B 5A3, Canada.
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27
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Laishram RS. Poly(A) polymerase (PAP) diversity in gene expression--star-PAP vs canonical PAP. FEBS Lett 2014; 588:2185-97. [PMID: 24873880 PMCID: PMC6309179 DOI: 10.1016/j.febslet.2014.05.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/02/2014] [Accepted: 05/15/2014] [Indexed: 01/09/2023]
Abstract
Almost all eukaryotic mRNAs acquire a poly(A) tail at the 3'-end by a concerted RNA processing event: cleavage and polyadenylation. The canonical PAP, PAPα, was considered the only nuclear PAP involved in general polyadenylation of mRNAs. A phosphoinositide-modulated nuclear PAP, Star-PAP, was then reported to regulate a select set of mRNAs in the cell. In addition, several non-canonical PAPs have been identified with diverse cellular functions. Further, canonical PAP itself exists in multiple isoforms thus illustrating the diversity of PAPs. In this review, we compare two nuclear PAPs, Star-PAP and PAPα with a general overview of PAP diversity in the cell. Emerging evidence suggests distinct niches of target pre-mRNAs for the two PAPs and that modulation of these PAPs regulates distinct cellular functions.
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Affiliation(s)
- Rakesh S Laishram
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
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Slattery M, Voutev R, Ma L, Nègre N, White KP, Mann RS. Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning. PLoS Genet 2013; 9:e1003753. [PMID: 24039600 PMCID: PMC3764184 DOI: 10.1371/journal.pgen.1003753] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/10/2013] [Indexed: 12/19/2022] Open
Abstract
The Yorkie/Yap transcriptional coactivator is a well-known regulator of cellular proliferation in both invertebrates and mammals. As a coactivator, Yorkie (Yki) lacks a DNA binding domain and must partner with sequence-specific DNA binding proteins in the nucleus to regulate gene expression; in Drosophila, the developmental regulators Scalloped (Sd) and Homothorax (Hth) are two such partners. To determine the range of target genes regulated by these three transcription factors, we performed genome-wide chromatin immunoprecipitation experiments for each factor in both the wing and eye-antenna imaginal discs. Strong, tissue-specific binding patterns are observed for Sd and Hth, while Yki binding is remarkably similar across both tissues. Binding events common to the eye and wing are also present for Sd and Hth; these are associated with genes regulating cell proliferation and “housekeeping” functions, and account for the majority of Yki binding. In contrast, tissue-specific binding events for Sd and Hth significantly overlap enhancers that are active in the given tissue, are enriched in Sd and Hth DNA binding sites, respectively, and are associated with genes that are consistent with each factor's previously established tissue-specific functions. Tissue-specific binding events are also significantly associated with Polycomb targeted chromatin domains. To provide mechanistic insights into tissue-specific regulation, we identify and characterize eye and wing enhancers of the Yki-targeted bantam microRNA gene and demonstrate that they are dependent on direct binding by Hth and Sd, respectively. Overall these results suggest that both Sd and Hth use distinct strategies – one shared between tissues and associated with Yki, the other tissue-specific, generally Yki-independent and associated with developmental patterning – to regulate distinct gene sets during development. The Hippo tumor suppressor pathway controls proliferation in a tissue-nonspecific fashion in Drosophila epithelial progenitor tissues via the transcriptional coactivator Yorkie (Yki). However, despite the tissue-nonspecific role that Yki plays in tissue growth, the transcription factors that recruit Yki to DNA, most notably Scalloped (Sd) and Homothorax (Hth), are important regulators of developmental patterning with many tissue-specific functions. Thus, these three transcriptional regulators – Yki, Sd, and Hth – provide a model for exploring the properties of protein-DNA interactions that regulate both tissue-shared and tissue-specific functions. With this goal in mind, we identified the positions in the fly genome that are bound by Yki, Sd, and Hth in the progenitors of the wing and eye-antenna structures of the fly. These data not only provide a global view of the Yki gene regulatory network, they reveal an unusual amount of tissue specificity in the genomic regions targeted by Sd and Hth, but not Yki. The data also reveal that tissue-specific binding is very likely to overlap tissue-specific enhancer regions, provide important clues for how tissue-specific Sd and Hth binding occurs, and support the idea that gene regulatory networks are plastic, with spatial differences in binding significantly impacting network structures.
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Affiliation(s)
- Matthew Slattery
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Roumen Voutev
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Lijia Ma
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Nicolas Nègre
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Université de Montpellier 2 and INRA, UMR1333 DGIMI, Montpellier, France
| | - Kevin P. White
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Richard S. Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- * E-mail:
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Voelter-Mahlknecht S, Mahlknecht U. Cloning, chromosomal characterization and FISH mapping of the NAD(+)-dependent histone deacetylase gene sirtuin 5 in the mouse. Int J Oncol 2013; 43:237-45. [PMID: 23673559 DOI: 10.3892/ijo.2013.1939] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 03/22/2013] [Indexed: 11/06/2022] Open
Abstract
Sirtuin 5 (SIRT5) is a nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase, belonging to the silent information regulator 2 (Sir2) family of sirtuin histone deacetylases (sirtuins). The yeast Sir2 protein and its mammalian derivatives are important in epigenetic gene silencing, DNA repair and recombination, cell cycle, microtubule organization and in the regulation of aging. In mammals, 7 sirtuin isoforms have been identified to date of which three (SIRT3, SIRT4 and SIRT5) are localized in the mitochondria, which serve as the center of energy management and the initiation of cellular apoptosis. In the study presented herein, we report the genomic organization and chromosomal localization of the murine sirt5 gene. We have isolated and characterized the murine sirt5 genomic sequence, which spans a region of 24,449 bp and which has one single genomic locus. The murine sirt5 gene consists of 8 exons and encodes a 310-aa protein with a predictive mo-lecular weight of 34.1 kDa and an isoelectric point of 8.90. For the murine sirt5 gene only one single genomic locus has been identified. The gene has been localized to mouse chromosome 13A4 and is flanked by STS-marker 164522 (synonymous WI MRC-RH: 506859).
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Affiliation(s)
- Susanne Voelter-Mahlknecht
- Institute of Occupational and Social Medicine and Health Services Research, University of Tuebingen, D-72074 Tuebingen, Germany.
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Abstract
Recent studies have revealed widespread mRNA alternative polyadenylation (APA) in eukaryotes and its dynamic spatial and temporal regulation. APA not only generates proteomic and functional diversity, but also plays important roles in regulating gene expression. Global deregulation of APA has been demonstrated in a variety of human diseases. Recent exciting advances in the field have been made possible in a large part by high throughput analyses using newly developed experimental tools. Here I review the recent progress in global studies of APA and the insights that have emerged from these and other studies that use more conventional methods.
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Affiliation(s)
- Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, California 92697, USA.
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31
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Yun EY, Kwon OY, Hwang JS, Goo TW. Molecular cloning and analysis of residues associated with iron binding of Spodoptera litura transferrin. Genes Genomics 2012. [DOI: 10.1007/s13258-012-0079-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Abstract
Polyadenylation [poly(A)] signals (PAS) are a defining feature of eukaryotic protein-coding genes. The central sequence motif AAUAAA was identified in the mid-1970s and subsequently shown to require flanking, auxiliary elements for both 3'-end cleavage and polyadenylation of premessenger RNA (pre-mRNA) as well as to promote downstream transcriptional termination. More recent genomic analysis has established the generality of the PAS for eukaryotic mRNA. Evidence for the mechanism of mRNA 3'-end formation is outlined, as is the way this RNA processing reaction communicates with RNA polymerase II to terminate transcription. The widespread phenomenon of alternative poly(A) site usage and how this interrelates with pre-mRNA splicing is then reviewed. This shows that gene expression can be drastically affected by how the message is ended. A central theme of this review is that while genomic analysis provides generality for the importance of PAS selection, detailed mechanistic understanding still requires the direct analysis of specific genes by genetic and biochemical approaches.
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Affiliation(s)
- Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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Tian B, Graber JH. Signals for pre-mRNA cleavage and polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:385-96. [PMID: 22012871 DOI: 10.1002/wrna.116] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pre-mRNA cleavage and polyadenylation is an essential step for 3' end formation of almost all protein-coding transcripts in eukaryotes. The reaction, involving cleavage of nascent mRNA followed by addition of a polyadenylate or poly(A) tail, is controlled by cis-acting elements in the pre-mRNA surrounding the cleavage site. Experimental and bioinformatic studies in the past three decades have elucidated conserved and divergent elements across eukaryotes, from yeast to human. Here we review histories and current models of these elements in a broad range of species.
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Affiliation(s)
- Bin Tian
- UMDNJ-New Jersey Medical School, Newark, NJ, USA.
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34
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Nakamichi N, Ito M, Maeda T, Matsumura T. Detection and cDNA cloning of H-strand mitochondrial regulatory region RNAs in cultured human cells and human tissues. Cytotechnology 2011; 33:175-88. [PMID: 19002825 DOI: 10.1023/a:1008154027997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the mitochondrion, essential genetic elements for replication and transcription are mostly housed within a shortsegment of its DNA located between tRNA(Phe) and tRNA(Pro) genes, which is called mitochondrial regulatoryregion (mrr). RNAs are known to be transcribed from mrr, thestructures and the functions of which are yet to be fullycharacterized.We detected ca. 1.3 kb H-strand transcripts of mrr (mrrH-RNAs),and 0.2 kb L-strand transcripts of mrr (mrrL-RNAs) in varioushuman cultured cells and tissues using double stranded mrrDNAprobes. The steady state levels of mrrL-RNAs were generally highin cultured cells, while they varied among tissues. On the otherhand, the levels of mrrH-RNAs varied among tissues and amongcultured cells. A tendency was observed in these cells andtissues that a high level of mrrL-RNA is associated with cellproliferation, and a high level of mrrH-RNA withdifferentiation. Several cDNA clones to 1.3 kb mrrH-RNA were obtained from humanskeletal muscle polyadenylated RNAs. The 5' terminus of the 1.3 kb RNA was determined to be at nucleotide position 15953 whichis immediately downstream of tRNA(Thr) sequence.Polyadenylation site for most of the clones was demonstrated tobe at nucleotide position 576 which is immediately upstream oftRNA(Phe) sequence. The longest cDNA insert obtained was 1177 bps long spanning from nucleotide positions 15969 to 576 which could code for a peptide of 76 amino acids. The cDNAs isolatedhere are the first cDNA clones reported to human mrrH-RNAs.These results, together with previous results, furthersubstantiate that polyadenylated mrrH- and mrrL-RNAs are commonly present at varying levels among human tissues andcells. The 3' end sequences of the cloned mrrH-cDNA provideswith insights into the mechanisms of transcription termination.The cDNA clones will provide tools to further the study of thefunction of mrr RNAs.
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Affiliation(s)
- N Nakamichi
- Cell Technology Center, Meiji Institute of Health Sciences and RITE Meinyu Branch Laboratory, Meiji Milk Products Co., Odawara, Japan, 250-0862
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35
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Yang Q, Doublié S. Structural biology of poly(A) site definition. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:732-47. [PMID: 21823232 DOI: 10.1002/wrna.88] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
3' processing is an essential step in the maturation of all messenger RNAs (mRNAs) and is a tightly coupled two-step reaction: endonucleolytic cleavage at the poly(A) site is followed by the addition of a poly(A) tail, except for metazoan histone mRNAs, which are cleaved but not polyadenylated. The recognition of a poly(A) site is coordinated by the sequence elements in the mRNA 3' UTR and associated protein factors. In mammalian cells, three well-studied sequence elements, UGUA, AAUAAA, and GU-rich, are recognized by three multisubunit factors: cleavage factor I(m) (CFI(m) ), cleavage and polyadenylation specificity factor (CPSF), and cleavage stimulation factor (CstF), respectively. In the yeast Saccharomyces cerevisiae, UA repeats and A-rich sequence elements are recognized by Hrp1p and cleavage factor IA. Structural studies of protein-RNA complexes have helped decipher the mechanisms underlying sequence recognition and shed light on the role of protein factors in poly(A) site selection and 3' processing machinery assembly. In this review we focus on the interactions between the mRNA cis-elements and the protein factors (CFI(m) , CPSF, CstF, and homologous factors from yeast and other eukaryotes) that define the poly(A) site. WIREs RNA 2011 2 732-747 DOI: 10.1002/wrna.88 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Qin Yang
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, USA
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36
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37
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Lagrimini LM, Burkhart W, Moyer M, Rothstein S. Molecular cloning of complementary DNA encoding the lignin-forming peroxidase from tobacco: Molecular analysis and tissue-specific expression. Proc Natl Acad Sci U S A 2010; 84:7542-6. [PMID: 16593885 PMCID: PMC299335 DOI: 10.1073/pnas.84.21.7542] [Citation(s) in RCA: 236] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant peroxidases play a major role in lignin formation and wound healing and are believed to be involved in auxin catabolism and defense to pathogen attack. The function of the anionic peroxidase isozymes is best understood in tobacco. These isozymes catalyze the formation of the lignin polymer and form rigid cross-links between lignin, cellulose, and extensin in the secondary plant cell wall. We report the purification of the anionic peroxidase isozymes from tobacco and their partial amino acid sequence. An oligonucleotide probe deduced from the amino acid sequence was used to screen a tobacco leaf cDNA library and a 1200-base-pair cDNA clone was isolated and sequenced in its entirety. The predicted amino acid sequence revealed a 22-amino acid signal peptide and a 302-amino acid mature protein (M(r), 32,311). The amino acid sequence was compared to that of the cationic peroxidases from horseradish and turnip and was found to be 52% and 46% homologous, respectively. By RNA blot analysis, the messenger for the tobacco isozyme was found to be abundant in stem tissue while expressed at very low levels in leaf and root tissue. Four distinguishable copies of the gene were found on genomic DNA blots. The gene copy number may reflect the allotetraploid nature of Nicotiana tabacum.
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Affiliation(s)
- L M Lagrimini
- Ciba-Geigy Agricultural Biotechnology Unit, P.O. Box 12257, Research Triangle Park, NC 27705
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38
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Kuchino Y, Nishimura S, Smith RE, Furuichi Y. Homologous Terminal Sequences in the Double-Stranded RNA Genome Segments of Cytoplasmic Polyhedrosis Virus of the Silkworm Bombyx mori. J Virol 2010; 44:538-43. [PMID: 16789232 PMCID: PMC256297 DOI: 10.1128/jvi.44.2.538-543.1982] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 3'-terminal regions (20 to 32 residues) of the genome double-stranded RNA (dsRNA) segments of cytoplasmic polyhedrosis virus were sequenced. The dsRNAs, which were labeled at their 3' termini by incubation with [5'-(32)P]pCp and T4 RNA ligase, were denatured and resolved into the plus and minus strands by agarose-urea gel electrophoresis. Ten single-stranded RNAs thus obtained from the five dsRNA segments IV, V, VIII, IX, and X were sequenced by postlabeling methods. Common 3'-terminal sequences, -GUUAGCC and -UUACU, were found in the plus and minus strands, respectively, of all five dsRNA segments. However, adjacent sequences diverged and were considerably variable. The homologous sequences found in the 3' end may be important recognition signals for viral RNA polymerases and for assembly of the genome segments.
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Affiliation(s)
- Y Kuchino
- National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo, Japan
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39
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Abstract
RNA genomes are vulnerable to corruption by a range of activities, including inaccurate replication by the error-prone replicase, damage from environmental factors, and attack by nucleases and other RNA-modifying enzymes that comprise the cellular intrinsic or innate immune response. Damage to coding regions and loss of critical cis-acting signals inevitably impair genome fitness; as a consequence, RNA viruses have evolved a variety of mechanisms to protect their genome integrity. These include mechanisms to promote replicase fidelity, recombination activities that allow exchange of sequences between different RNA templates, and mechanisms to repair the genome termini. In this article, we review examples of these processes from a range of RNA viruses to showcase the diverse approaches that viruses have evolved to maintain their genome sequence integrity, focusing first on mechanisms that viruses use to protect their entire genome, and then concentrating on mechanisms that allow protection of the genome termini, which are especially vulnerable. In addition, we discuss examples in which it might be beneficial for a virus to 'lose' its genomic termini and reduce its replication efficiency.
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Affiliation(s)
- John N Barr
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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40
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Neilson JR, Sandberg R. Heterogeneity in mammalian RNA 3' end formation. Exp Cell Res 2010; 316:1357-64. [PMID: 20211174 DOI: 10.1016/j.yexcr.2010.02.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 02/28/2010] [Indexed: 11/19/2022]
Abstract
Precisely directed cleavage and polyadenylation of mRNA is a fundamental part of eukaryotic gene expression. Yet, 3' end heterogeneity has been documented for thousands of mammalian genes, and usage of one cleavage and polyadenylation signal over another has been shown to impact gene expression in many cases. Building upon the rich biochemical and genetic understanding of the 3' end formation, recent genomic studies have begun to suggest that widespread changes in mRNA cleavage and polyadenylation may be a part of large, dynamic gene regulatory programs. In this review, we begin with a modest overview of the studies that defined the mechanisms of mammalian 3' end formation, and then discuss how recent genomic studies intersect with these more traditional approaches, showing that both will be crucial for expanding our understanding of this facet of gene regulation.
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Affiliation(s)
- Joel R Neilson
- Department of Molecular Physiology and Biophysics and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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41
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Abstract
Viruses enter host cells in order to complete their life cycles and have evolved to exploit host cell structures, regulatory factors and mechanisms. The virus and host cell interactions have consequences at multiple levels, spanning from evolution through disease to models and tools for scientific discovery and treatment. Virus-induced human cancers arise after a long duration of time and are monoclonal or oligoclonal in origin. Cancer is therefore a side effect rather than an essential part of viral infections in humans. Still, 15-20% of all human cancers are caused by viruses. A review of tumour virology shows its close integration in cancer research. Viral tools and experimental models have been indispensible for the progress of molecular biology. In particular, retroviruses and DNA tumour viruses have played major roles in our present understanding of the molecular biology of both viruses and the host. Recently, additional complex relationships due to virus and host co-evolution have appeared and may lead to a further understanding of the overall regulation of gene expression programmes in cancer.
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42
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Yuan W, Xie J, Long C, Erdjument-Bromage H, Ding X, Zheng Y, Tempst P, Chen S, Zhu B, Reinberg D. Heterogeneous nuclear ribonucleoprotein L Is a subunit of human KMT3a/Set2 complex required for H3 Lys-36 trimethylation activity in vivo. J Biol Chem 2009; 284:15701-7. [PMID: 19332550 PMCID: PMC2708867 DOI: 10.1074/jbc.m808431200] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The presence of histone H3 lysine 36 methylation (H3K36me) correlates with actively transcribed genes. In yeast, histone H3K36me mediated by KMT3 (also known as Set2) recruits a histone deacetylase complex, Rpd3s, to ensure the fidelity of transcription initiation. We report the purification of human KMT3a (also known as HYPB or hSet2) complex and the identification of a novel, higher eukaryotic specific subunit, heterogeneous nuclear ribonucleoprotein L (HnRNP-L). Interestingly, although KMT3a has intrinsic activity in vitro, HnRNP-L is essential in vivo. Moreover, KMT3a generates mono-, di-, and trimethylated products in vitro, but RNA interference against KMT3a or HnRNP-L down-regulates exclusively the H3K36me3 mark in vivo.
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Affiliation(s)
- Wen Yuan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100094, China
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43
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Kiefer H, Mizutani A, Iemura SI, Natsume T, Ando H, Kuroda Y, Mikoshiba K. Inositol 1,4,5-triphosphate receptor-binding protein released with inositol 1,4,5-triphosphate (IRBIT) associates with components of the mRNA 3' processing machinery in a phosphorylation-dependent manner and inhibits polyadenylation. J Biol Chem 2009; 284:10694-705. [PMID: 19224921 DOI: 10.1074/jbc.m807136200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IRBIT is a recently identified protein that modulates the activities of both inositol 1,4,5-triphosphate receptor and pancreas-type Na(+)/HCO(3)(-) cotransporter 1, and the multisite phosphorylation of IRBIT is required for achieving this modulatory action. Here, we report the identification of the cleavage and polyadenylation specificity factor (CPSF), which is a multi-protein complex involved in 3' processing of mRNA precursors, as an additional binding partner for IRBIT. We found that IRBIT interacted with CPSF and was recruited to an exogenous polyadenylation signal-containing RNA. The main target for IRBIT in CPSF was Fip1 subunit, and the phosphorylation of the serine-rich region of IRBIT was required both for direct association with Fip1 in vitro and for redistribution of Fip1 into the cytoplasm of intact cells. Furthermore, tert-butylhydroquinone (tBHQ), an agent that induces oxidative stress, increased the phosphorylation level of IRBIT in vivo and in parallel enhanced the interaction between IRBIT and CPSF and promoted the cytoplasmic distribution of endogenous Fip1. In addition to CPSF, IRBIT interacted in vitro with poly(A) polymerase (PAP), which is the enzyme recruited by CPSF to elongate the poly(A) tail, and inhibited PAP activity in a phosphorylation-dependent manner. These findings raise the possibility that IRBIT modulates the polyadenylation state of specific mRNAs, both by controlling the cytoplasmic/nuclear partitioning of Fip1 and by inhibiting PAP activity, in response to a stimulus that alters its phosphorylation state.
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Affiliation(s)
- Hélène Kiefer
- Laboratory for Developmental Neurobiology, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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44
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Howley PM, Livingston DM. Small DNA tumor viruses: large contributors to biomedical sciences. Virology 2009; 384:256-9. [PMID: 19136134 DOI: 10.1016/j.virol.2008.12.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 12/08/2008] [Indexed: 11/29/2022]
Abstract
Studies of the small DNA tumor viruses (the polyomaviruses, the adenoviruses and the papillomaviruses) have led to fundamental discoveries that have advanced our understanding of basic mammalian cell molecular biology processes such as transcription and DNA replication, uncovered pathways and genes often perturbed in human cancer, and identified bona fide human cancer viruses. In this article we examine the many contributions that have come from the small DNA tumor virus field and provide a recounting of some of the major landmark discoveries.
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Affiliation(s)
- Peter M Howley
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA.
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45
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Shan T, Wang Y, Wu T, Liu C, Guo J, Zhang Y, Liu J, Xu Z. Porcine sirtuin 1 gene clone, expression pattern, and regulation by resveratrol. J Anim Sci 2008; 87:895-904. [PMID: 18997065 DOI: 10.2527/jas.2008-1344] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Sirtuin1 (Sirt1) is a NAD-dependent deacetylase that plays important roles in a variety of biological processes. In the current study, we examined tissue-specific and different expression pattern of porcine Sirt1 and the effect of resveratrol (RES) on expression of Sirt1 in porcine adipocytes. The full-length complementary DNA sequence of porcine Sirt1 was 4,024 bp (GenBank accession no: EU030283), with a 2,226-bp open reading frame encoding a 742-AA protein (a predicted molecular mass of 80.9 kDa; GenBank accession no. ABS29571). Comparison of the deduced AA sequence with the corresponding sequences of human, dog, cattle, and mouse Sirt1 showed 82 to 92% similarity. Furthermore, the porcine Sirt1 was highly expressed in porcine brain, to a lesser degree in spleen and white adipose tissue, and had low but detectable expression in liver. In subcutaneous adipose tissue and omental adipose tissue, expression of the porcine Sirt1 mRNA was greater in adult pigs than in young pigs (P < 0.01). In vitro, exposure of cultured adipocytes to 40 and 80 micro M RES for 24 h increased mRNA levels of porcine Sirt1 by 47.86% (P < 0.01) and 91.04% (P < 0.01), respectively. Accordingly, lipid accumulation and NEFA release were decreased (P < 0.05), respectively. After cultures were treated with RES for 48 h, the mRNA level of porcine Sirt1 was increased by 103.84% (P < 0.01) and 148.79% (P < 0.01), respectively. Lipid accumulation was decreased and NEFA release was increased (P < 0.05), respectively. These results provide information needed for manipulating Sirt1 expression in regulating fat deposition in pigs.
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Affiliation(s)
- T Shan
- Institute of Feed Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, PR China
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46
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Chen L, Li M, Li Q, Yang X, An X, Chen Y. Characterization of the bovine immunoglobulin lambda light chain constant IGLC genes. Vet Immunol Immunopathol 2008; 124:284-94. [PMID: 18538861 DOI: 10.1016/j.vetimm.2008.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 03/27/2008] [Accepted: 04/09/2008] [Indexed: 11/24/2022]
Abstract
To characterize the bovine immunoglobulin lambda light chain constant region (IGLC) genes, we have isolated a bacterial artificial chromosome (BAC) clone by a PCR based approach from a bovine genomic DNA library, constructed using a genital ridge cell line derived from a male Holstein fetus. The positive BAC clone, containing the bovine IGLC genes, was fully sequenced and had a 138 kb insert. Sequence analysis revealed that the bovine immunoglobulin lambda light chain locus consisted of four joining-constant gene recombination units spanning approximately 20 kb DNA in length. A detailed examination of the recombination signal sequences, RNA splicing sites and coding sequences of the four joining-constant gene recombination units suggested that only two IGLC genes (IGLC2 and IGLC3) were functional while the IGLC1 and IGLC4 appeared to be pseudogenes. This conclusion was further confirmed by a series of RT-PCR amplifications, which also showed that among these four genes the IGLC3 was preferentially expressed in cattle. Phylogenetic analysis indicated that the bovine IGLC genes were more closely related to their equivalents in sheep and goats than that to other mammals.
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Affiliation(s)
- Limei Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, China
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47
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Abstract
Most eukaryotic mRNA precursors (premRNAs) must undergo extensive processing, including cleavage and polyadenylation at the 3'-end. Processing at the 3'-end is controlled by sequence elements in the pre-mRNA (cis elements) as well as protein factors. Despite the seeming biochemical simplicity of the processing reactions, more than 14 proteins have been identified for the mammalian complex, and more than 20 proteins have been identified for the yeast complex. The 3'-end processing machinery also has important roles in transcription and splicing. The mammalian machinery contains several sub-complexes, including cleavage and polyadenylation specificity factor, cleavage stimulation factor, cleavage factor I, and cleavage factor II. Additional protein factors include poly(A) polymerase, poly(A)-binding protein, symplekin, and the C-terminal domain of RNA polymerase II largest subunit. The yeast machinery includes cleavage factor IA, cleavage factor IB, and cleavage and polyadenylation factor.
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Affiliation(s)
- C. R. Mandel
- Department of Biological Sciences, Columbia University, New York, NY 10027 USA
| | - Y. Bai
- Department of Biological Sciences, Columbia University, New York, NY 10027 USA
| | - L. Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027 USA
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48
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Characterization of Smoc-1 uncovers two transcript variants showing differential tissue and age specific expression in Bubalus bubalis. BMC Genomics 2007; 8:436. [PMID: 18042303 PMCID: PMC2235864 DOI: 10.1186/1471-2164-8-436] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 11/28/2007] [Indexed: 01/06/2023] Open
Abstract
Background Secreted modular calcium binding protein-1 (Smoc-1) belongs to the BM-40 family which has been implicated with tissue remodeling, angiogenesis and bone mineralization. Besides its anticipated role in embryogenesis, Smoc-1 has been characterized only in a few mammalian species. We made use of the consensus sequence (5' CACCTCTCCACCTGCC 3') of 33.15 repeat loci to explore the buffalo transcriptome and uncovered the Smoc-1 transcript tagged with this repeat. The main objective of this study was to gain an insight into its structural and functional organization, and expressional status of Smoc-1 in water buffalo, Bubalus bubalis. Results We cloned and characterized the buffalo Smoc-1, including its copy number status, in-vitro protein expression, tissue & age specific transcription/translation, chromosomal mapping and localization to the basement membrane zone. Buffalo Smoc-1 was found to encode a secreted matricellular glycoprotein containing two EF-hand calcium binding motifs homologous to that of BM-40/SPARC family. In buffalo, this single copy gene consisted of 12 exons and was mapped onto the acrocentric chromosome 11. Though this gene was found to be evolutionarily conserved, the buffalo Smoc-1 showed conspicuous nucleotide/amino acid changes altering its secondary structure compared to that in other mammals. In silico analysis of the Smoc-1 proposed its glycoprotein nature with a calcium dependent conformation. Further, we unveiled two transcript variants of this gene, varying in their 3'UTR lengths but both coding for identical protein(s). Smoc-1 evinced highest expression of both the variants in liver and modest to negligible in other tissues. The relative expression of variant-02 was markedly higher compared to that of variant-01 in all the tissues examined. Moreover, expression of Smoc-1, though modest during the early ages, was conspicuously enhanced after 1 year and remained consistently higher during the entire life span of buffalo with gradual increment in expression of variant-02. Immunohistochemically, Smoc-1 was localized in the basement membrane zones and extracellular matrices of various tissues. Conclusion These data added to our understandings about the tissue, age and species specific functions of the Smoc-1. It also enabled us to demonstrate varying expression of the two transcript variants of Smoc-1 amongst different somatic tissues/gonads and ages, in spite of their identical coding frames. Pursuance of these variants for their roles in various disease phenotypes such as hepatocellular carcinoma and angiogenesis is envisaged to establish broader biological significance of this gene.
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49
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Zhu Y, Ding Q, Yang F. Characterization of a homologous-region-binding protein from white spot syndrome virus by phage display. Virus Res 2007; 125:145-52. [PMID: 17240469 DOI: 10.1016/j.virusres.2006.12.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 12/14/2006] [Accepted: 12/20/2006] [Indexed: 01/24/2023]
Abstract
Homologous regions (hrs) of white spot syndrome virus (WSSV) might serve as origins of DNA replication or be involved in transcriptional regulation. To characterize the interaction between hrs of WSSV and the viral proteins, in this investigation, phage display technology was used. WSSV genomic DNA was sheared by sonication to generate fragments in lengths between 0.5 and 2.0 kb. Then these fragments were blunt-ended with T4 DNA polymerase and cloned into the EcoRV site of rebuilt vector pCANTAB 5 EE to obtain WSSV genome phage display library. Using a 210 bp DNA from the b minifragment of WSSV hr2 as the bait, biopanning of WSSV genome phage display library for five rounds resulted in the isolation of a recombinant phage clone containing an exogenous DNA fragment of 306 bp. This DNA fragment was identified to be the 5' terminus of the wsv021 open reading frame in WSSV genome. Temporal transcription analysis revealed that the wsv021 gene was transcribed at the early stage of WSSV infection. The gene was expressed as a fusion protein in Escherichia coli XL1-Blue. The electrophoretic mobility shift assay indicated that the recombinant WSV021 protein (rWSV021) could bind specifically to the 210 bp DNA from the b minifragment of WSSV hr2. The wsv021 gene might be a functional gene involved in WSSV replication and transcriptional regulation.
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Affiliation(s)
- Yanbing Zhu
- School of Biotechnology, Jimei University, Xiamen 361005, People's Republic of China
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50
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Wang HJ, Shao JZ, Xiang LX, Shen J. Molecular Cloning, Characterization and Expression Analysis of an ILF2 Homologue from Tetraodon nigroviridis. BMB Rep 2006; 39:686-95. [PMID: 17129403 DOI: 10.5483/bmbrep.2006.39.6.686] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Interleukin-2 enhancer binding factor 2 (ILF2) was reported to regulate transcription of interleukin-2 (IL-2), a central cytokine in the regulation of T-cell responses. This property of ILF2 was well characterized in human and mammals, but little is known in bony fish. In this paper, an ILF2 homologue was cloned and well characterized from Tetraodon nigrovirid is for the further investigation of the function of ILF2 in bony fish. The full-length Tetraodon ILF2 cDNA was 1380 bp in size and contained an open reading frame (ORF) of 1164 bp that translates into a 387 amino-acid peptide with a molecular weight of 42.9 kDa, a 5' untranslated region (UTR) of 57 bp, and a 3' UTR of 159 bp containing a poly A tail. The deduced peptide of Tetraodon ILF2 shared an overall identity of 58%~93% with other known ILF2 sequences, and contained two Nglycosylation sites, two N-myristoylation sites, one RGD cell attachment sequence, six protein kinase C phosphorylation sites, one amino-terminal RGG-rich single-stranded RNAbinding domain, and a DZF zinc-finger nucleic acid binding domain, most of which were highly conserved through species compared. Constitutive expression of Tetraodon ILF2 was observed in all tissues examined, including gill, gut, head kidney, spleen, liver, brain and heart. The highest expression was detected in heart, followed by liver, head kidney and brain. Stimulation with LPS did not significantly alter the expression of Tetraodon ILF2. Gene organization analysis showed that the Tetraodon ILF2 gene have fifteen exons, one more than other known ILF2 genes in human and mouse. Genes upand down-stream from the Tetraodon ILF2 were Rpa12, Peroxin-11b, Smad4, Snapap and Txnip homologue, which were different from that in human and mouse.
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Affiliation(s)
- Hui-Ju Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310012, People's Republic of China
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