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Liu Q, Peng X, Shen M, Qian Q, Xing J, Li C, Gregory R. Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling. Nucleic Acids Res 2023; 51:D248-D261. [PMID: 36440758 PMCID: PMC9825487 DOI: 10.1093/nar/gkac1094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/27/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Upstream open reading frames (uORFs) are typically defined as translation sites located within the 5' untranslated region upstream of the main protein coding sequence (CDS) of messenger RNAs (mRNAs). Although uORFs are prevalent in eukaryotic mRNAs and modulate the translation of downstream CDSs, a comprehensive resource for uORFs is currently lacking. We developed Ribo-uORF (http://rnainformatics.org.cn/RiboUORF) to serve as a comprehensive functional resource for uORF analysis based on ribosome profiling (Ribo-seq) data. Ribo-uORF currently supports six species: human, mouse, rat, zebrafish, fruit fly, and worm. Ribo-uORF includes 501 554 actively translated uORFs and 107 914 upstream translation initiation sites (uTIS), which were identified from 1495 Ribo-seq and 77 quantitative translation initiation sequencing (QTI-seq) datasets, respectively. We also developed mRNAbrowse to visualize items such as uORFs, cis-regulatory elements, genetic variations, eQTLs, GWAS-based associations, RNA modifications, and RNA editing. Ribo-uORF provides a very intuitive web interface for conveniently browsing, searching, and visualizing uORF data. Finally, uORFscan and UTR5var were developed in Ribo-uORF to precisely identify uORFs and analyze the influence of genetic mutations on uORFs using user-uploaded datasets. Ribo-uORF should greatly facilitate studies of uORFs and their roles in mRNA translation and posttranscriptional control of gene expression.
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Affiliation(s)
- Qi Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Xin Peng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Mengyuan Shen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Qian Qian
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Junlian Xing
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou 510640, China
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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Wang L, Yang W, Li B, Yuan S, Wang F. Response to stress in biological disorders: Implications of stress granule assembly and function. Cell Prolif 2021; 54:e13086. [PMID: 34170048 PMCID: PMC8349659 DOI: 10.1111/cpr.13086] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
It is indispensable for cells to adapt and respond to environmental stresses, in order for organisms to survive. Stress granules (SGs) are condensed membrane‐less organelles dynamically formed in the cytoplasm of eukaryotes cells to cope with diverse intracellular or extracellular stress factors, with features of liquid‐liquid phase separation. They are composed of multiple constituents, including translationally stalled mRNAs, translation initiation factors, RNA‐binding proteins and also non‐RNA‐binding proteins. SG formation is triggered by stress stimuli, viral infection and signal transduction, while aberrant assembly of SGs may contribute to tissue degenerative diseases. Recently, a growing body of evidence has emerged on SG response mechanisms for cells facing high temperatures, oxidative stress and osmotic stress. In this review, we aim to summarize factors affecting SGs assembly, present the impact of SGs on germ cell development and other biological processes. We particularly emphasize the significance of recently reported RNA modifications in SG stress responses. In parallel, we also review all current perspectives on the roles of SGs in male germ cells, with a particular focus on the dynamics of SG assembly.
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Affiliation(s)
- Lingjuan Wang
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Weina Yang
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Bin Li
- Tianjin Medical University General Hospital, Tianjin, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shuiqiao Yuan
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Fengli Wang
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
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Wang J, Zhang J, Ma Y, Zeng Y, Lu C, Yang F, Jiang N, Zhang X, Wang Y, Xu Y, Hou H, Jiang S, Zhuang S. WTAP promotes myocardial ischemia/reperfusion injury by increasing endoplasmic reticulum stress via regulating m 6A modification of ATF4 mRNA. Aging (Albany NY) 2021; 13:11135-11149. [PMID: 33819187 PMCID: PMC8109143 DOI: 10.18632/aging.202770] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/03/2021] [Indexed: 12/19/2022]
Abstract
Myocardial infarction (MI) is one of the leading causes of death. Wilms' tumor 1-associating protein (WTAP), one of the components of the m6A methyltransferase complex, has been shown to affect gene expression via regulating mRNA modification. Although WTAP has been implicated in various diseases, its role in MI is unclear. In this study, we found that hypoxia/reoxygenation (H/R) time-dependently increased WTAP expression, which in turn promoted endoplasmic reticulum (ER) stress and apoptosis, in human cardiomyocytes (AC16). H/R effects on ER stress and apoptosis were all blocked by silencing of WTAP, promoted by WTAP overexpression, and ameliorated by administration of ER stress inhibitor, 4-PBA. We then investigated the underlying molecular mechanism and found that WTAP affected m6A methylation of ATF4 mRNA to regulate its expression, and that the inhibitory effects of WTAP on ER stress and apoptosis were ATF4 dependent. Finally, WTAP’s effects on myocardial I/R injury were confirmed in vivo. WTAP promoted myocardial I/R injury through promoting ER stress and cell apoptosis by regulating m6A modification of ATF4 mRNA. These findings highlight the importance of WTAP in I/R injury and provide new insights into therapeutic strategies for MI.
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Affiliation(s)
- Jiayi Wang
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Jiehan Zhang
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Yan Ma
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Yuxiao Zeng
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Cheng Lu
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Fenghua Yang
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Nianxin Jiang
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Xuan Zhang
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Yuhua Wang
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Yinghui Xu
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Hanjing Hou
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Shengyang Jiang
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Shaowei Zhuang
- Department of Cardiology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
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Chen HH, Tarn WY. uORF-mediated translational control: recently elucidated mechanisms and implications in cancer. RNA Biol 2019; 16:1327-1338. [PMID: 31234713 DOI: 10.1080/15476286.2019.1632634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Protein synthesis is tightly regulated, and its dysregulation can contribute to the pathology of various diseases, including cancer. Increased or selective translation of mRNAs can promote cancer cell proliferation, metastasis and tumor expansion. Translational control is one of the most important means for cells to quickly adapt to environmental stresses. Adaptive translation involves various alternative mechanisms of translation initiation. Upstream open reading frames (uORFs) serve as a major regulator of stress-responsive translational control. Since recent advances in omics technologies including ribo-seq have expanded our knowledge of translation, we discuss emerging mechanisms for uORF-mediated translation regulation and its impact on cancer cell biology. A better understanding of dysregulated translational control of uORFs in cancer would facilitate the development of new strategies for cancer therapy.
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Affiliation(s)
- Hung-Hsi Chen
- Institute of Biomedical Sciences, Academia Sinica , Taipei , Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica , Taipei , Taiwan
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Sriram A, Bohlen J, Teleman AA. Translation acrobatics: how cancer cells exploit alternate modes of translational initiation. EMBO Rep 2018; 19:embr.201845947. [PMID: 30224410 DOI: 10.15252/embr.201845947] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/09/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Recent work has brought to light many different mechanisms of translation initiation that function in cells in parallel to canonical cap-dependent initiation. This has important implications for cancer. Canonical cap-dependent translation initiation is inhibited by many stresses such as hypoxia, nutrient limitation, proteotoxic stress, or genotoxic stress. Since cancer cells are often exposed to these stresses, they rely on alternate modes of translation initiation for protein synthesis and cell growth. Cancer mutations are now being identified in components of the translation machinery and in cis-regulatory elements of mRNAs, which both control translation of cancer-relevant genes. In this review, we provide an overview on the various modes of non-canonical translation initiation, such as leaky scanning, translation re-initiation, ribosome shunting, IRES-dependent translation, and m6A-dependent translation, and then discuss the influence of stress on these different modes of translation. Finally, we present examples of how these modes of translation are dysregulated in cancer cells, allowing them to grow, to proliferate, and to survive, thereby highlighting the importance of translational control in cancer.
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Affiliation(s)
- Ashwin Sriram
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Jonathan Bohlen
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany .,Heidelberg University, Heidelberg, Germany
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