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Zhao Z, Chen Y, Zou X, Lin L, Zhou X, Cheng X, Yang G, Xu Q, Gong L, Li L, Ni T. Pan-cancer transcriptome analysis reveals widespread regulation through alternative tandem transcription initiation. SCIENCE ADVANCES 2024; 10:eadl5606. [PMID: 38985880 PMCID: PMC11235174 DOI: 10.1126/sciadv.adl5606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 06/05/2024] [Indexed: 07/12/2024]
Abstract
Abnormal transcription initiation from alternative first exon has been reported to promote tumorigenesis. However, the prevalence and impact of gene expression regulation mediated by alternative tandem transcription initiation were mostly unknown in cancer. Here, we developed a robust computational method to analyze alternative tandem transcription start site (TSS) usage from standard RNA sequencing data. Applying this method to pan-cancer RNA sequencing datasets, we observed widespread dysregulation of tandem TSS usage in tumors, many of which were independent of changes in overall expression level or alternative first exon usage. We showed that the dynamics of tandem TSS usage was associated with epigenomic modulation. We found that significant 5' untranslated region shortening of gene TIMM13 contributed to increased protein production, and up-regulation of TIMM13 by CRISPR-mediated transcriptional activation promoted proliferation and migration of lung cancer cells. Our findings suggest that dysregulated tandem TSS usage represents an addtional layer of cancer-associated transcriptome alterations.
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Affiliation(s)
- Zhaozhao Zhao
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu Chen
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xudong Zou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Limin Lin
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaolan Zhou
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaomeng Cheng
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Guangrui Yang
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiushi Xu
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lihai Gong
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Lei Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
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2
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Feng C, Xin K, Du Y, Zou J, Xing X, Xiu Q, Zhang Y, Zhang R, Huang W, Wang Q, Jiang C, Wang X, Kang Z, Xu JR, Liu H. Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi. Nat Commun 2024; 15:3934. [PMID: 38729938 PMCID: PMC11087585 DOI: 10.1038/s41467-024-48336-8] [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: 12/14/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
A-to-I mRNA editing in animals is mediated by ADARs, but the mechanism underlying sexual stage-specific A-to-I mRNA editing in fungi remains unknown. Here, we show that the eukaryotic tRNA-specific heterodimeric deaminase FgTad2-FgTad3 is responsible for A-to-I mRNA editing in Fusarium graminearum. This editing capacity relies on the interaction between FgTad3 and a sexual stage-specific protein called Ame1. Although Ame1 orthologs are widely distributed in fungi, the interaction originates in Sordariomycetes. We have identified key residues responsible for the FgTad3-Ame1 interaction. The expression and activity of FgTad2-FgTad3 are regulated through alternative promoters, alternative translation initiation, and post-translational modifications. Our study demonstrates that the FgTad2-FgTad3-Ame1 complex can efficiently edit mRNA in yeasts, bacteria, and human cells, with important implications for the development of base editors in therapy and agriculture. Overall, this study uncovers mechanisms, regulation, and evolution of RNA editing in fungi, highlighting the role of protein-protein interactions in modulating deaminase function.
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Affiliation(s)
- Chanjing Feng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Kaiyun Xin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanfei Du
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jingwen Zou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoxing Xing
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qi Xiu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yijie Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Rui Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weiwei Huang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qinhu Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cong Jiang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojie Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Huiquan Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Jin J, Nguyen LTG, Wassef A, Sadek R, Schmitt TM, Guo GL, Rasmussen TP, Zhong XB. Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction. Noncoding RNA 2024; 10:28. [PMID: 38668386 PMCID: PMC11053763 DOI: 10.3390/ncrna10020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
The long non-coding RNA (lncRNA) hepatocyte nuclear factor-1 alpha (HNF1A) antisense RNA 1 (HNF1A-AS1) is an important lncRNA for liver growth, development, cell differentiation, and drug metabolism. Like many lncRNAs, HNF1A-AS1 has multiple annotated alternative transcripts in the human genome. Several fundamental biological questions are still not solved: (1) How many transcripts really exist in biological samples, such as liver samples and liver cell lines? (2) What are the expression patterns of different alternative HNF1A-AS1 transcripts at different conditions, including during cell growth and development, after exposure to xenobiotics (such as drugs), and in disease conditions, such as metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD) cirrhosis, and obesity? (3) Does the siRNA used in previous studies knock down one or multiple transcripts? (4) Do different transcripts have the same or different functions for gene regulation? The presented data confirm the existence of several annotated HNF1A-AS1 transcripts in liver samples and cell lines, but also identify some new transcripts, which are not annotated in the Ensembl genome database. Expression patterns of the identified HNF1A-AS1 transcripts are highly correlated with the cell differentiation of matured hepatocyte-like cells from human embryonic stem cells (hESC), growth and differentiation of HepaRG cells, in response to rifampicin induction, and in various liver disease conditions. The expression levels of the HNF1A-AS1 transcripts are also highly correlated to the expression of cytochrome P450 enzymes, such as CYP3A4, during HepaRG growth, differentiation, and in response to rifampicin induction.
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Affiliation(s)
- Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Le Tra Giang Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Andrew Wassef
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
- Center of Excellence for Pharmaceutical Translational Research and Education, Rutgers University, Piscataway, NJ 08901, USA
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Ragui Sadek
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Timothy M. Schmitt
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Grace L. Guo
- Department of Pharmacology and Toxicology, Ernst Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
| | - Theodore P. Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
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Alfonso-Gonzalez C, Hilgers V. (Alternative) transcription start sites as regulators of RNA processing. Trends Cell Biol 2024:S0962-8924(24)00033-3. [PMID: 38531762 DOI: 10.1016/j.tcb.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/28/2024]
Abstract
Alternative transcription start site usage (ATSS) is a widespread regulatory strategy that enables genes to choose between multiple genomic loci for initiating transcription. This mechanism is tightly controlled during development and is often altered in disease states. In this review, we examine the growing evidence highlighting a role for transcription start sites (TSSs) in the regulation of mRNA isoform selection during and after transcription. We discuss how the choice of transcription initiation sites influences RNA processing and the importance of this crosstalk for cell identity and organism function. We also speculate on possible mechanisms underlying the integration of transcriptional and post-transcriptional processes.
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Affiliation(s)
- Carlos Alfonso-Gonzalez
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwigs University, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS- MCB), 79108 Freiburg, Germany
| | - Valérie Hilgers
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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5
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Wu S, Gao Y, Zhang Q, Liu F, Hu W. Application of Multi-Omics Technologies to the Study of Phytochromes in Plants. Antioxidants (Basel) 2024; 13:99. [PMID: 38247523 PMCID: PMC10812741 DOI: 10.3390/antiox13010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-depth analysis of phytochrome-mediated signaling pathways, integrated multi-omics (transcriptomics, proteomics, and metabolomics) approaches may provide the answer from a global perspective. This article comprehensively elaborates on applying multi-omics techniques in studying phytochromes. We describe the current research status and future directions on transcriptome-, proteome-, and metabolome-related network components mediated by phytochromes when cells are subjected to various stimulation. We emphasize the importance of multi-omics technologies in exploring the effects of phytochromes on cells and their molecular mechanisms. Additionally, we provide methods and ideas for future crop improvement.
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Affiliation(s)
- Shumei Wu
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Yue Gao
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Qi Zhang
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Weiming Hu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
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Reimão-Pinto MM, Castillo-Hair SM, Seelig G, Schier AF. The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.23.568470. [PMID: 38045294 PMCID: PMC10690280 DOI: 10.1101/2023.11.23.568470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The 5' UTRs of mRNAs are critical for translation regulation, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5' UTR is sufficient to confer temporal dynamics to translation initiation, and identified 86 motifs enriched in 5' UTRs with distinct ribosome recruitment capabilities. A quantitative deep learning model, DaniO5P, revealed a combined role for 5' UTR length, translation initiation site context, upstream AUGs and sequence motifs on in vivo ribosome recruitment. DaniO5P predicts the activities of 5' UTR isoforms and indicates that modulating 5' UTR length and motif grammar contributes to translation initiation dynamics. This study provides a first quantitative model of 5' UTR-based translation regulation in early vertebrate development and lays the foundation for identifying the underlying molecular effectors. Highlights In vivo MPRA systematically interrogates the regulatory potential of endogenous 5' UTRs The 5' UTR alone is sufficient to regulate the dynamics of ribosome recruitment during early embryogenesis The MPRA identifies 5' UTR cis -regulatory motifs for translation initiation control 5' UTR length, upstream AUGs and motif grammar contribute to the differential regulatory capability of 5' UTR switching isoforms.
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7
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Carrion SA, Michal JJ, Jiang Z. Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases. Genes (Basel) 2023; 14:2051. [PMID: 38002994 PMCID: PMC10671453 DOI: 10.3390/genes14112051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and APA site use has the highest impact on protein identity, with their ability to alter which first and last exons are utilized as well as impacting stability and translation efficiency. These RNA variants have been shown to be highly specific, both in tissue type and stage, with demonstrated importance to cell proliferation, differentiation and the transition from fetal to adult cells. While alternative exon splicing has a limited effect on protein identity, its ubiquity highlights the importance of these minor alterations, which can alter other features such as localization. The three processes are also highly interwoven, with overlapping, complementary, and competing factors, RNA polymerase II and its CTD (C-terminal domain) chief among them. Their role in development means dysregulation leads to a wide variety of disorders and cancers, with some forms of disease disproportionately affected by specific mechanisms (AES, ATS, or APA). Challenges associated with the genome-wide profiling of RNA variants and their potential solutions are also discussed in this review.
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Affiliation(s)
| | | | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620, USA; (S.A.C.); (J.J.M.)
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8
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Mao P, Shen Y, Mao X, Liu K, Zhong J. The single-cell landscape of alternative transcription start sites of diabetic retina. Exp Eye Res 2023; 233:109520. [PMID: 37236522 DOI: 10.1016/j.exer.2023.109520] [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: 12/31/2022] [Revised: 04/01/2023] [Accepted: 05/24/2023] [Indexed: 05/28/2023]
Abstract
More than half of mammalian protein-coding genes have multiple transcription start sites. Alternative transcription start site (TSS) modulate mRNA stability, localization, and translation efficiency on post-transcription level, and even generate novel protein isoforms. However, differential TSS usage among cell types in healthy and diabetic retina remains poorly characterized. In this study, by using 5'-tag-based single-cell RNA sequencing, we identified cell type-specific alternative TSS events and key transcription factors for each of retinal cell types. We observed that lengthening of 5'- UTRs in retinal cell types are enriched for multiple RNA binding protein binding sites, including splicing regulators Rbfox1/2/3 and Nova1. Furthermore, by comparing TSS expression between healthy and diabetic retina, we identified elevated apoptosis signal in Müller glia and microglia, which can be served as a putative early sign of diabetic retinopathy. By measuring 5'UTR isoforms in retinal single-cell dataset, our work provides a comprehensive panorama of alternative TSS and its potential consequence related to post-transcriptional regulation. We anticipate our assay can not only provide insights into cellular heterogeneity driven by transcriptional initiation, but also open up the perspectives for identification of novel diagnostic indexes for diabetic retinopathy.
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Affiliation(s)
- Peiyao Mao
- Department of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Yinchen Shen
- Department of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Xiying Mao
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kun Liu
- Department of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Jiawei Zhong
- Department of Medicine (H7), Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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Morse K, Swerdlow S, Ünal E. Swi/Snf Chromatin Remodeling Regulates Transcriptional Interference and Gene Repression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538572. [PMID: 37162931 PMCID: PMC10168381 DOI: 10.1101/2023.04.27.538572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Alternative transcription start sites can affect transcript isoform diversity and translation levels. In a recently described form of gene regulation, coordinated transcriptional and translational interference results in transcript isoform-dependent changes in protein expression. Specifically, a long undecoded transcript isoform (LUTI) is transcribed from a gene-distal promoter, interfering with expression of the gene-proximal promoter. While transcriptional and chromatin features associated with LUTI expression have been described, the mechanism underlying LUTI-based transcriptional interference is not well understood. Using an unbiased genetic approach followed by integrated genomic analysis, we uncovered that the Swi/Snf chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to LUTI-based repression. We identified genes with tandem promoters that rely on Swi/Snf function for transcriptional interference during protein folding stress, including LUTI-regulated genes. To our knowledge, this study is the first to observe Swi/Snf's direct involvement in gene repression via a cis transcriptional interference mechanism.
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Affiliation(s)
- Kaitlin Morse
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
| | - Sarah Swerdlow
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
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10
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Shen M, Goforth JB, Eisenstein RS. Iron-dependent post transcriptional control of mitochondrial aconitase expression. Metallomics 2023; 15:mfac099. [PMID: 36702557 PMCID: PMC9902864 DOI: 10.1093/mtomcs/mfac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/23/2022] [Indexed: 01/28/2023]
Abstract
Iron regulatory proteins (IRPs) control the translation of animal cell mRNAs encoding proteins with diverse roles. This includes the iron storage protein ferritin and the tricarboxylic cycle (TCA) enzyme mitochondrial aconitase (ACO2) through iron-dependent binding of IRP to the iron responsive element (IRE) in the 5' untranslated region (UTR). To further elucidate the mechanisms allowing IRPs to control translation of 5' IRE-containing mRNA differentially, we focused on Aco2 mRNA, which is weakly controlled versus the ferritins. Rat liver contains two classes of Aco2 mRNAs, with and without an IRE, due to alterations in the transcription start site. Structural analysis showed that the Aco2 IRE adopts the canonical IRE structure but lacks the dynamic internal loop/bulge five base pairs 5' of the CAGUG(U/C) terminal loop in the ferritin IREs. Unlike ferritin mRNAs, the Aco2 IRE lacks an extensive base-paired flanking region. Using a full-length Aco2 mRNA expression construct, iron controlled ACO2 expression in an IRE-dependent and IRE-independent manner, the latter of which was eliminated with the ACO23C3S mutant that cannot bind the FeS cluster. Iron regulation of ACO23C3S encoded by the full-length mRNA was completely IRE-dependent. Replacement of the Aco23C3S 5' UTR with the Fth1 IRE with base-paired flanking sequences substantially improved iron responsiveness, as did fusing of the Fth1 base-paired flanking sequences to the native IRE in the Aco3C3S construct. Our studies further define the mechanisms underlying the IRP-dependent translational regulatory hierarchy and reveal that Aco2 mRNA species lacking the IRE contribute to the expression of this TCA cycle enzyme.
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Affiliation(s)
- Macy Shen
- Department of Nutritional Sciences, University of Wisconsin-Madison, 1415 Linden Drive, Madison, WI 53706, USA
- Department of Chemistry and Biochemistry, California State University-Fullerton, Fullerton, CA 92834-6866, USA
| | - Jeremy B Goforth
- Department of Nutritional Sciences, University of Wisconsin-Madison, 1415 Linden Drive, Madison, WI 53706, USA
- Science Department, Lodi Middle School, 945 S. Ham Lane, Lodi, CA 95242, USA
| | - Richard S Eisenstein
- Department of Nutritional Sciences, University of Wisconsin-Madison, 1415 Linden Drive, Madison, WI 53706, USA
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11
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Su M, Pan T, Chen QZ, Zhou WW, Gong Y, Xu G, Yan HY, Li S, Shi QZ, Zhang Y, He X, Jiang CJ, Fan SC, Li X, Cairns MJ, Wang X, Li YS. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res 2022; 9:68. [PMID: 36461064 PMCID: PMC9716519 DOI: 10.1186/s40779-022-00434-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity for high-throughput scRNA-seq, including clinical samples, the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field. Here, we review the workflow for typical scRNA-seq data analysis, covering raw data processing and quality control, basic data analysis applicable for almost all scRNA-seq data sets, and advanced data analysis that should be tailored to specific scientific questions. While summarizing the current methods for each analysis step, we also provide an online repository of software and wrapped-up scripts to support the implementation. Recommendations and caveats are pointed out for some specific analysis tasks and approaches. We hope this resource will be helpful to researchers engaging with scRNA-seq, in particular for emerging clinical applications.
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Affiliation(s)
- Min Su
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Tao Pan
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Qiu-Zhen Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Wei-Wei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yi Gong
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.,Department of Immunology, Nanjing Medical University, Nanjing, 211166, China
| | - Gang Xu
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Huan-Yu Yan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Si Li
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Qiao-Zhen Shi
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Ya Zhang
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Xiao He
- Department of Laboratory Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401174, China
| | | | - Shi-Cai Fan
- Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China, Shenzhen, 518110, Guangdong, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, the University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia. .,Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia.
| | - Xi Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Yong-Sheng Li
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China.
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12
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Makhnovskii PA, Gusev OA, Bokov RO, Gazizova GR, Vepkhvadze TF, Lysenko EA, Vinogradova OL, Kolpakov FA, Popov DV. Alternative transcription start sites contribute to acute-stress-induced transcriptome response in human skeletal muscle. Hum Genomics 2022; 16:24. [PMID: 35869513 PMCID: PMC9308330 DOI: 10.1186/s40246-022-00399-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 07/14/2022] [Indexed: 11/18/2022] Open
Abstract
Background More than half of human protein-coding genes have an alternative transcription start site (TSS). We aimed to investigate the contribution of alternative TSSs to the acute-stress-induced transcriptome response in human tissue (skeletal muscle) using the cap analysis of gene expression approach. TSSs were examined at baseline and during recovery after acute stress (a cycling exercise). Results We identified 44,680 CAGE TSS clusters (including 3764 first defined) belonging to 12,268 genes and annotated for the first time 290 TSSs belonging to 163 genes. The transcriptome dynamically changes during the first hours after acute stress; the change in the expression of 10% of genes was associated with the activation of alternative TSSs, indicating differential TSSs usage. The majority of the alternative TSSs do not increase proteome complexity suggesting that the function of thousands of alternative TSSs is associated with the fine regulation of mRNA isoform expression from a gene due to the transcription factor-specific activation of various alternative TSSs. We identified individual muscle promoter regions for each TSS using muscle open chromatin data (ATAC-seq and DNase-seq). Then, using the positional weight matrix approach we predicted time course activation of “classic” transcription factors involved in response of skeletal muscle to contractile activity, as well as diversity of less/un-investigated factors. Conclusions Transcriptome response induced by acute stress related to activation of the alternative TSSs indicates that differential TSSs usage is an essential mechanism of fine regulation of gene response to stress stimulus. A comprehensive resource of accurate TSSs and individual promoter regions for each TSS in muscle was created. This resource together with the positional weight matrix approach can be used to accurate prediction of TFs in any gene(s) of interest involved in the response to various stimuli, interventions or pathological conditions in human skeletal muscle. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00399-8.
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13
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Sugimoto Y, Ratcliffe PJ. Isoform-resolved mRNA profiling of ribosome load defines interplay of HIF and mTOR dysregulation in kidney cancer. Nat Struct Mol Biol 2022; 29:871-880. [PMID: 36097292 PMCID: PMC9507966 DOI: 10.1038/s41594-022-00819-2] [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: 07/06/2021] [Accepted: 07/15/2022] [Indexed: 11/18/2022]
Abstract
Hypoxia inducible factor (HIF) and mammalian target of rapamycin (mTOR) pathways orchestrate responses to oxygen and nutrient availability. These pathways are frequently dysregulated in cancer, but their interplay is poorly understood, in part because of difficulties in simultaneous measurement of global and mRNA-specific translation. Here, we describe a workflow for measurement of ribosome load of mRNAs resolved by their transcription start sites (TSSs). Its application to kidney cancer cells reveals extensive translational reprogramming by mTOR, strongly affecting many metabolic enzymes and pathways. By contrast, global effects of HIF on translation are limited, and we do not observe reported translational activation by HIF2A. In contrast, HIF-dependent alterations in TSS usage are associated with robust changes in translational efficiency in a subset of genes. Analyses of the interplay of HIF and mTOR reveal that specific classes of HIF1A and HIF2A transcriptional target gene manifest different sensitivity to mTOR, in a manner that supports combined use of HIF2A and mTOR inhibitors in treatment of kidney cancer.
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Affiliation(s)
| | - Peter J Ratcliffe
- The Francis Crick Institute, London, UK.
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
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14
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Ogran A, Havkin-Solomon T, Becker-Herman S, David K, Shachar I, Dikstein R. Polysome-CAGE of TCL1-driven chronic lymphocytic leukemia revealed multiple N-terminally altered epigenetic regulators and a translation stress signature. eLife 2022; 11:77714. [PMID: 35939046 PMCID: PMC9359700 DOI: 10.7554/elife.77714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023] Open
Abstract
The transformation of normal to malignant cells is accompanied by substantial changes in gene expression programs through diverse mechanisms. Here, we examined the changes in the landscape of transcription start sites and alternative promoter (AP) usage and their impact on the translatome in TCL1-driven chronic lymphocytic leukemia (CLL). Our findings revealed a marked elevation of APs in CLL B cells from Eµ-Tcl1 transgenic mice, which are particularly enriched with intra-genic promoters that generate N-terminally truncated or modified proteins. Intra-genic promoter activation is mediated by (1) loss of function of ‘closed chromatin’ epigenetic regulators due to the generation of inactive N-terminally modified isoforms or reduced expression; (2) upregulation of transcription factors, including c-Myc, targeting the intra-genic promoters and their associated enhancers. Exogenous expression of Tcl1 in MEFs is sufficient to induce intra-genic promoters of epigenetic regulators and promote c-Myc expression. We further found a dramatic translation downregulation of transcripts bearing CNY cap-proximal trinucleotides, reminiscent of cells undergoing metabolic stress. These findings uncovered the role of Tcl1 oncogenic function in altering promoter usage and mRNA translation in leukemogenesis.
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Affiliation(s)
- Ariel Ogran
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Tal Havkin-Solomon
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Keren David
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Idit Shachar
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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15
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Lu P, Chen D, Qi Z, Wang H, Chen Y, Wang Q, Jiang C, Xu JR, Liu H. Landscape and regulation of alternative splicing and alternative polyadenylation in a plant pathogenic fungus. THE NEW PHYTOLOGIST 2022; 235:674-689. [PMID: 35451076 DOI: 10.1111/nph.18164] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) contribute significantly to the regulation of gene expression in higher eukaryotes. Their biological impact in filamentous fungi, however, is largely unknown. Here we combine PacBio Isoform-Sequencing and strand-specific RNA-sequencing of multiple tissues and mutant characterization to reveal the landscape and regulation of AS and APA in Fusarium graminearum. We generated a transcript annotation comprising 51 617 isoforms from 17 189 genes. In total, 4997 and 11 133 genes are alternatively spliced and polyadenylated, respectively. Majority of the AS events alter coding sequences. Unexpectedly, the AS transcripts containing premature-termination codons are not sensitive to nonsense-mediated messenger RNA decay. Unlike in yeasts and animals, distal APA sites have strong signals, but proximal APA isoforms are highly expressed in F. graminearum. The 3'-end processing factors FgRNA15, FgHRP1, and FgFIP1 play roles in promoting proximal APA site usage and intron splicing. A genome-wide increase in intron inclusion and distal APA site usage and downregulation of the spliceosomal and 3'-end processing factors were observed in older and quiescent tissues, indicating intron inclusion and 3'-untranslated region lengthening as novel mechanisms in regulating aging and dormancy in fungi. This study provides new insights into the complexity and regulation of AS and APA in filamentous fungi.
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Affiliation(s)
- Ping Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Daipeng Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Zhaomei Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yitong Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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16
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Niederer RO, Rojas-Duran MF, Zinshteyn B, Gilbert WV. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation. Cell Syst 2022; 13:256-264.e3. [PMID: 35041803 PMCID: PMC8930539 DOI: 10.1016/j.cels.2021.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/15/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022]
Abstract
Translational control shapes the proteome in normal and pathophysiological conditions. Current high-throughput approaches reveal large differences in mRNA-specific translation activity but cannot identify the causative mRNA features. We developed direct analysis of ribosome targeting (DART) and used it to dissect regulatory elements within 5' untranslated regions that confer 1,000-fold differences in ribosome recruitment in biochemically accessible cell lysates. Using DART, we determined a functional role for most alternative 5' UTR isoforms expressed in yeast, revealed a general mode of increased translation via direct binding to a core translation factor, and identified numerous translational control elements including C-rich silencers that are sufficient to repress translation both in vitro and in vivo. DART enables systematic assessment of the translational regulatory potential of 5' UTR variants, whether native or disease-associated, and will facilitate engineering of mRNAs for optimized protein production in various systems.
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Affiliation(s)
- Rachel O Niederer
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA
| | - Maria F Rojas-Duran
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA
| | - Boris Zinshteyn
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wendy V Gilbert
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA.
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17
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Li L, Waymack R, Gad M, Wunderlich Z. Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo. Genetics 2021; 219:6372693. [PMID: 34849867 DOI: 10.1093/genetics/iyab154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/12/2021] [Indexed: 11/13/2022] Open
Abstract
Proper development depends on precise spatiotemporal gene expression patterns. Most developmental genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical "sharp" developmental promoter, while the other resembles a "broad" promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter, indicating that promoters provide both redundancy and specificity. By analyzing the reporter dynamics, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the combination of promoter and enhancer. Using locus-sized reporters, we discovered that enhancers with no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is due both to enhancer preference and a need for redundancy and that "broad" promoters with dispersed transcription start sites are common among developmental genes. They also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where other variables shape a gene's overall expression pattern.
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Affiliation(s)
- Lily Li
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel Waymack
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mario Gad
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.,Department of Biology, Boston University, Boston, MA 02215, USA
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18
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Stephenson M, Nip KM, HafezQorani S, Gagalova KK, Yang C, Warren RL, Birol I. RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes. NAR Genom Bioinform 2021; 3:lqab105. [PMID: 34859209 PMCID: PMC8633890 DOI: 10.1093/nargab/lqab105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/21/2021] [Accepted: 11/26/2021] [Indexed: 11/12/2022] Open
Abstract
Recent advances in single-cell RNA sequencing technologies have made detection of transcripts in single cells possible. The level of resolution provided by these technologies can be used to study changes in transcript usage across cell populations and help investigate new biology. Here, we introduce RNA-Scoop, an interactive cell cluster and transcriptome visualization tool to analyze transcript usage across cell categories and clusters. The tool allows users to examine differential transcript expression across clusters and investigate how usage of specific transcript expression mechanisms varies across cell groups.
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Affiliation(s)
- Maria Stephenson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Computer Science Co-op Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
| | - Saber HafezQorani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
| | - Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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19
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Abstract
Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
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Affiliation(s)
| | - Gabriel E. Zentner
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
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20
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Naftaly AS, Pau S, White MA. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish. Genome Res 2021; 31:1486-1497. [PMID: 34131005 PMCID: PMC8327910 DOI: 10.1101/gr.274282.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
Alternate isoforms are important contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five organs in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly in which gene annotations are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq-predicted transcription start sites were more accurate and verified through ATAC-seq. We also detected many alternative splicing events between sexes and across organs. We found a substantial number of genes in both somatic and gonadal samples that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.
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Affiliation(s)
- Alice S Naftaly
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Shana Pau
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Biology, University of Texas Arlington, Arlington, Texas 76019, USA
| | - Michael A White
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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21
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Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon. PLoS Genet 2020; 16:e1009055. [PMID: 32997662 PMCID: PMC7549781 DOI: 10.1371/journal.pgen.1009055] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 10/12/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
A major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report a cis-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factor vestigial-like 3 (vgll3) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (Salmo salar). Using a common-garden experiment, we first show that vgll3 genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling of vgll3 expression in ten tissues across the first year of salmon development, we identify a pubertal transition in vgll3 expression where maturation coincided with a 66% reduction in testicular vgll3 expression. The late maturation allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform of vgll3 pre-puberty. By comparing absolute vgll3 mRNA copies in heterozygotes we show that the expression difference between the early and late maturity alleles is largely cis-regulatory. We propose a model whereby expression of a rare isoform from the late allele shifts the liability of its carriers towards delaying puberty. These results exemplify the potential importance of regulatory differences as a mechanism for the evolution of life history traits. Alternative life history strategies are an important source of diversity within populations and promote the maintenance of adaptive capacity and population resilience. However, in many cases the molecular basis of different life history strategies remains elusive. Age at maturity is a key adaptive life history trait in Atlantic salmon and has a relatively simple genetic basis. Using salmon age at maturity as a model, we report a mechanism whereby different transcript isoforms of the key age at maturity gene, vestigial-like 3 (vgll3), associate with variation in the timing of male puberty. Our results show how gene regulatory differences in conjunction with variation in gene transcript structure can encode for complex alternative life histories.
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22
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Hoang HD, Graber TE, Jia JJ, Vaidya N, Gilchrist VH, Xiang X, Li W, Cowan KN, Gkogkas CG, Jaramillo M, Jafarnejad SM, Alain T. Induction of an Alternative mRNA 5' Leader Enhances Translation of the Ciliopathy Gene Inpp5e and Resistance to Oncolytic Virus Infection. Cell Rep 2020; 29:4010-4023.e5. [PMID: 31851930 DOI: 10.1016/j.celrep.2019.11.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/16/2019] [Accepted: 11/15/2019] [Indexed: 01/10/2023] Open
Abstract
Residual cell-intrinsic innate immunity in cancer cells hampers infection with oncolytic viruses. Translational control of mRNA is an important feature of innate immunity, yet the identity of translationally regulated mRNAs functioning in host defense remains ill-defined. We report the translatomes of resistant murine "4T1" breast cancer cells infected with three of the most clinically advanced oncolytic viruses: herpes simplex virus 1, reovirus, and vaccinia virus. Common among all three infections are translationally de-repressed mRNAs, including Inpp5e, encoding an inositol 5-phosphatase that modifies lipid second messenger signaling. We find that viral infection induces the expression of an Inpp5e mRNA variant that lacks repressive upstream open reading frames (uORFs) within its 5' leader and is efficiently translated. Furthermore, we show that INPP5E contributes to antiviral immunity by altering virus attachment. These findings uncover a role for translational control through alternative 5' leader expression and assign an antiviral function to the ciliopathy gene Inpp5e.
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Affiliation(s)
- Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC H3A 1A3, Canada
| | - Jian-Jun Jia
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Nasana Vaidya
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Victoria H Gilchrist
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Xiao Xiang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Wencheng Li
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ 07101, USA
| | - Kyle N Cowan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Department of Surgery, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Christos G Gkogkas
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Maritza Jaramillo
- INRS Institut Armand-Frappier Research Centre, Laval, QC H7V 1B7, Canada
| | - Seyed Mehdi Jafarnejad
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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23
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Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
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24
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Hoang HD, Neault S, Pelin A, Alain T. Emerging translation strategies during virus-host interaction. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1619. [PMID: 32757266 PMCID: PMC7435527 DOI: 10.1002/wrna.1619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 01/02/2023]
Abstract
Translation control is crucial during virus-host interaction. On one hand, viruses completely rely on the protein synthesis machinery of host cells to propagate and have evolved various mechanisms to redirect the host's ribosomes toward their viral mRNAs. On the other hand, the host rewires its translation program in an attempt to contain and suppress the virus early on during infection; the antiviral program includes specific control on protein synthesis to translate several antiviral mRNAs involved in quenching the infection. As the infection progresses, host translation is in turn inhibited in order to limit viral propagation. We have learnt of very diverse strategies that both parties utilize to gain or retain control over the protein synthesis machinery. Yet novel strategies continue to be discovered, attesting for the importance of mRNA translation in virus-host interaction. This review focuses on recently described translation strategies employed by both hosts and viruses. These discoveries provide additional pieces in the understanding of the complex virus-host translation landscape. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation.
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Affiliation(s)
- Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Apoptosis Research Centre, Ottawa, Ontario, K1H8L1, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Serge Neault
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Adrian Pelin
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Apoptosis Research Centre, Ottawa, Ontario, K1H8L1, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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25
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Heterogeneity in mRNA Translation. Trends Cell Biol 2020; 30:606-618. [DOI: 10.1016/j.tcb.2020.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/23/2020] [Accepted: 04/30/2020] [Indexed: 11/18/2022]
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26
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Kanodia P, Prasanth KR, Roa-Linares VC, Bradrick SS, Garcia-Blanco MA, Miller WA. A rapid and simple quantitative method for specific detection of smaller coterminal RNA by PCR (DeSCo-PCR): application to the detection of viral subgenomic RNAs. RNA (NEW YORK, N.Y.) 2020; 26:888-901. [PMID: 32238481 PMCID: PMC7297113 DOI: 10.1261/rna.074963.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/26/2020] [Indexed: 05/10/2023]
Abstract
RNAs that are 5'-truncated versions of a longer RNA but share the same 3' terminus can be generated by alternative promoters in transcription of cellular mRNAs or by replicating RNA viruses. These truncated RNAs cannot be distinguished from the longer RNA by a simple two-primer RT-PCR because primers that anneal to the cDNA from the smaller RNA also anneal to-and amplify-the longer RNA-derived cDNA. Thus, laborious methods, such as northern blot hybridization, are used to distinguish shorter from longer RNAs. For rapid, low-cost, and specific detection of these truncated RNAs, we report detection of smaller coterminal RNA by PCR (DeSCo-PCR). DeSCo-PCR uses a nonextendable blocking primer (BP), which outcompetes a forward primer (FP) for annealing to longer RNA-derived cDNA, while FP outcompetes BP for annealing to shorter RNA-derived cDNA. In the presence of BP, FP, and the reverse primer, only cDNA from the shorter RNA is amplified in a single-tube reaction containing both RNAs. Many positive strand RNA viruses generate 5'-truncated forms of the genomic RNA (gRNA) called subgenomic RNAs (sgRNA), which play key roles in viral gene expression and pathogenicity. We demonstrate that DeSCo-PCR is easily optimized to selectively detect relative quantities of sgRNAs of red clover necrotic mosaic virus from plants and Zika virus from human cells, each infected with viral strains that generate different amounts of sgRNA. This technique should be readily adaptable to other sgRNA-producing viruses, and for quantitative detection of any truncated or alternatively spliced RNA.
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Affiliation(s)
- Pulkit Kanodia
- Interdepartmental Genetics and Genomics, Iowa State University, Ames, Iowa 50011, USA
- Plant Pathology and Microbiology Department, Iowa State University, Ames, Iowa 50011, USA
| | - K Reddisiva Prasanth
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Vicky C Roa-Linares
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
- Molecular and Translational Medicine Group, Institute of Medical Research, Faculty of Medicine University of Antioquia, Medellin 050010, Colombia
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
- Programme of Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - W Allen Miller
- Interdepartmental Genetics and Genomics, Iowa State University, Ames, Iowa 50011, USA
- Plant Pathology and Microbiology Department, Iowa State University, Ames, Iowa 50011, USA
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27
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Policastro RA, Raborn RT, Brendel VP, Zentner GE. Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Res 2020; 30:910-923. [PMID: 32660958 PMCID: PMC7370879 DOI: 10.1101/gr.261545.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
Abstract
Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
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Affiliation(s)
| | | | - Volker P Brendel
- Department of Biology
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Gabriel E Zentner
- Department of Biology
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, USA
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28
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AP-TSS: A New Method for the Analysis of RNA Expression from Particular and Challenging Transcription Start Sites. Biomolecules 2020; 10:biom10060827. [PMID: 32481529 PMCID: PMC7355800 DOI: 10.3390/biom10060827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 11/25/2022] Open
Abstract
Alternative promoter usage involved in the regulation of transcription, splicing, and translation contributes to proteome diversity and is involved in a large number of diseases, in particular, cancer. Epigenetic mechanisms and cis regulatory elements are involved in alternative promoter activity. Multiple transcript isoforms can be produced from a gene, due to the initiation of transcription at different transcription start sites (TSS). These transcripts may not have regions that allow discrimination during RT-qPCR, making quantification technically challenging. This study presents a general method for the relative quantification of a transcript synthesized from a particular TSS that we called AP-TSS (analysis of particular TSS). AP-TSS is based on the specific elongation of the cDNA of interest, followed by its quantification by qPCR. As proof of principle, AP-TSS was applied to two non-coding RNA: telomeric repeat-containing RNAs (TERRA) from a particular subtelomeric TSS, and Alu transcripts. The treatment of cells with a DNA methylation inhibitor was associated with a global increase of the total TERRA level, but the TERRA expression from the TSS of interest did not change in HT1080 cells, and only modestly increased in HeLa cells. This result suggests that TERRA upregulation induced by global demethylation of the genome is mainly due to activation from sites other than this particular TSS. For Alu RNA, the signal obtained by AP-TSS is specific for the RNA Polymerase III-dependent Alu transcript. In summary, our method provides a tool to study regulation of gene expression from a given transcription start site, in different conditions that could be applied to many genes. In particular, AP-TSS can be used to investigate the epigenetic regulation of alternative TSS usage that is of importance for the development of epigenetic-targeted therapies.
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29
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de la Fuente L, Arzalluz-Luque Á, Tardáguila M, Del Risco H, Martí C, Tarazona S, Salguero P, Scott R, Lerma A, Alastrue-Agudo A, Bonilla P, Newman JRB, Kosugi S, McIntyre LM, Moreno-Manzano V, Conesa A. tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing. Genome Biol 2020; 21:119. [PMID: 32423416 PMCID: PMC7236505 DOI: 10.1186/s13059-020-02028-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/23/2020] [Indexed: 12/26/2022] Open
Abstract
Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at https://app.tappas.org.
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Affiliation(s)
- Lorena de la Fuente
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
- Present Address: Bioinformatics Unit, IIS Fundación Jiménez Díaz, Madrid, Spain
| | - Ángeles Arzalluz-Luque
- Department of Statistics and Operational Research, Polytechnical University of Valencia, Valencia, Spain
| | - Manuel Tardáguila
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
- Present Address: Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Héctor Del Risco
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Cristina Martí
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Sonia Tarazona
- Department of Statistics and Operational Research, Polytechnical University of Valencia, Valencia, Spain
| | - Pedro Salguero
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Raymond Scott
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Alberto Lerma
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Ana Alastrue-Agudo
- Present Address: Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Pablo Bonilla
- Present Address: Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jeremy R B Newman
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Shunichi Kosugi
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Wako, Japan
| | - Lauren M McIntyre
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | | | - Ana Conesa
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
- Genetics Institute, University of Florida, Gainesville, FL, USA.
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30
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Palavecino CE, Carrasco-Véliz N, Quest AFG, Garrido MP, Valenzuela-Valderrama M. The 5' untranslated region of the anti-apoptotic protein Survivin contains an inhibitory upstream AUG codon. Biochem Biophys Res Commun 2020; 526:898-905. [PMID: 32279998 DOI: 10.1016/j.bbrc.2020.03.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 03/28/2020] [Indexed: 12/20/2022]
Abstract
Survivin (BIRC5) is an anti-apoptotic protein that is important in cancer. Mechanisms responsible for controlling Survivin levels in cells include transcriptional regulation and modulation of protein stability via post-translational modifications; however to date, translational control has been poorly studied. Here, we focused particularly on the primary control elements present in the Survivin 5' untranslated region (5'UTR). Bioinformatic analysis of ribosome occupancy on the Survivin 5'UTR revealed the presence of elongating ribosomes upstream of the canonical initiator AUG, suggesting an alternative upstream initiator AUG (uAUG) might exist. This uAUG was found out-of-frame at position -71 and appeared as a conserved element in mammals. RACE analysis revealed different transcriptional start sites for BIRC5, which indicated that translational control by this uAUG is restricted to longer 5'UTR variants. We studied the activity of the uAUG in different cell types by cloning the Survivin 5'UTR DNA sequence (wild-type and mutated variants) upstream of renilla luciferase (RLuc) into a pcDNA3 plasmid. Changes in RLuc activity were determined by luminescence assays and Western blotting. Results showed that when this uAUG was mutated to AUU or AGG in the cloned Survivin 5'UTR, RLuc activity was significantly increased. Similar results were obtained when uAUG was positioned inframe with the RLuc initiator AUG. Immunodetection of Renilla (35 kDa) by Western blotting revealed the presence of a second band (37 kDa approximately) in cells transfected with the Inframe reporter constructs, indicating that the uAUG was functional in our experimental conditions. In conclusion, our experimental data demonstrate the presence of an alternative and inhibitory initiator uAUG in the Survivin 5' UTR. This inhibitory uAUG may help understanding how Survivin expression is downregulated under physiological or pathological conditions.
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Affiliation(s)
- Christian E Palavecino
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Santiago, 8320000, Chile
| | - Nicolás Carrasco-Véliz
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Santiago, 8320000, Chile
| | - Andrew F G Quest
- Centro de Estudios Avanzados en Enfermedades Crónicas (ACCDiS), Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile; Laboratorio de Comunicaciones Celulares, Centro de Estudios en Ejercicio, Metabolismo y Cáncer (CEMC), Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Avenida Independencia 1027, Independencia, 8380453, Chile
| | - Maritza P Garrido
- Laboratorio de Endocrinología y Biología de la Reproducción, Departamento de Obstetricia y Ginecología, Hospital Clínico Universidad de Chile, Avenida Santos Dumont 999, Independencia, 8380456, Chile
| | - Manuel Valenzuela-Valderrama
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Santiago, 8320000, Chile; Centro de Estudios Avanzados en Enfermedades Crónicas (ACCDiS), Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile.
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31
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Campla CK, Mast H, Dong L, Lei J, Halford S, Sekaran S, Swaroop A. Targeted deletion of an NRL- and CRX-regulated alternative promoter specifically silences FERM and PDZ domain containing 1 (Frmpd1) in rod photoreceptors. Hum Mol Genet 2020; 28:804-817. [PMID: 30445545 DOI: 10.1093/hmg/ddy388] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/15/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of cell type-specific gene expression is critical for generating neuronal diversity. Transcriptome analyses have unraveled extensive heterogeneity of transcribed sequences in retinal photoreceptors because of alternate splicing and/or promoter usage. Here we show that Frmpd1 (FERM and PDZ domain containing 1) is transcribed from an alternative promoter specifically in the retina. Electroporation of Frmpd1 promoter region, -505 to +382 bp, activated reporter gene expression in mouse retina in vivo. A proximal promoter sequence (-8 to +33 bp) of Frmpd1 binds to neural retina leucine zipper (NRL) and cone-rod homeobox protein (CRX), two rod-specific differentiation factors, and is necessary for activating reporter gene expression in vitro and in vivo. Clustered regularly interspaced short palindromic repeats/Cas9-mediated deletion of the genomic region, including NRL and CRX binding sites, in vivo completely eliminated Frmpd1 expression in rods and dramatically reduced expression in rod bipolar cells, thereby overcoming embryonic lethality caused by germline Frmpd1 deletion. Our studies demonstrate that a cell type-specific regulatory control region is a credible target for creating loss-of-function alleles of widely expressed genes.
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Affiliation(s)
- Christie K Campla
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.,Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Hannah Mast
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jingqi Lei
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Sumathi Sekaran
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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32
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Sikorski PJ, Warminski M, Kubacka D, Ratajczak T, Nowis D, Kowalska J, Jemielity J. The identity and methylation status of the first transcribed nucleotide in eukaryotic mRNA 5' cap modulates protein expression in living cells. Nucleic Acids Res 2020; 48:1607-1626. [PMID: 31984425 PMCID: PMC7038993 DOI: 10.1093/nar/gkaa032] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/21/2022] Open
Abstract
7-Methylguanosine 5' cap on mRNA is necessary for efficient protein expression in vitro and in vivo. Recent studies revealed structural diversity of endogenous mRNA caps, which carry different 5'-terminal nucleotides and additional methylations (2'-O-methylation and m6A). Currently available 5'-capping methods do not address this diversity. We report trinucleotide 5' cap analogs (m7GpppN(m)pG), which are utilized by RNA polymerase T7 to initiate transcription from templates carrying Φ6.5 promoter and enable production of mRNAs differing in the identity of the first transcribed nucleotide (N = A, m6A, G, C, U) and its methylation status (±2'-O-methylation). HPLC-purified mRNAs carrying these 5' caps were used to study protein expression in three mammalian cell lines (3T3-L1, HeLa and JAWS II). The highest expression was observed for mRNAs carrying 5'-terminal A/Am and m6Am, whereas the lowest was observed for G and Gm. The mRNAs carrying 2'-O-methyl at the first transcribed nucleotide (cap 1) had significantly higher expression than unmethylated counterparts (cap 0) only in JAWS II dendritic cells. Further experiments indicated that the mRNA expression characteristic does not correlate with affinity for translation initiation factor 4E or in vitro susceptibility to decapping, but instead depends on mRNA purity and the immune state of the cells.
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Affiliation(s)
- Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Dorota Kubacka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Tomasz Ratajczak
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Dominika Nowis
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
- Department of Genomic Medicine, Medical University of Warsaw, Nielubowicza 5, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
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33
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Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nat Commun 2020; 11:168. [PMID: 31924754 PMCID: PMC6954239 DOI: 10.1038/s41467-019-13687-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 11/19/2019] [Indexed: 12/26/2022] Open
Abstract
Variations in transcription start site (TSS) selection reflect diversity of preinitiation complexes and can impact on post-transcriptional RNA fates. Most metazoan polymerase II-transcribed genes carry canonical initiation with pyrimidine/purine (YR) dinucleotide, while translation machinery-associated genes carry polypyrimidine initiator (5’-TOP or TCT). By addressing the developmental regulation of TSS selection in zebrafish we uncovered a class of dual-initiation promoters in thousands of genes, including snoRNA host genes. 5’-TOP/TCT initiation is intertwined with canonical initiation and used divergently in hundreds of dual-initiation promoters during maternal to zygotic transition. Dual-initiation in snoRNA host genes selectively generates host and snoRNA with often different spatio-temporal expression. Dual-initiation promoters are pervasive in human and fruit fly, reflecting evolutionary conservation. We propose that dual-initiation on shared promoters represents a composite promoter architecture, which can function both coordinately and divergently to diversify RNAs. The functional significance of start site choice in promoter architectures is little understood. Here the authors identify in zebrafish development and mammalian cells a class of dual-initiation promoters, in which non-canonical YC dinucleotides reflecting 5’-TOP/TCT initiation are intertwined with canonical YR-initiation.
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34
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Monteuuis G, Miścicka A, Świrski M, Zenad L, Niemitalo O, Wrobel L, Alam J, Chacinska A, Kastaniotis AJ, Kufel J. Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins. Nucleic Acids Res 2019; 47:5777-5791. [PMID: 31216041 PMCID: PMC6582344 DOI: 10.1093/nar/gkz301] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/15/2022] Open
Abstract
Utilization of non-AUG alternative translation start sites is most common in bacteria and viruses, but it has been also reported in other organisms. This phenomenon increases proteome complexity by allowing expression of multiple protein isoforms from a single gene. In Saccharomyces cerevisiae, a few described cases concern proteins that are translated from upstream near-cognate start codons as N-terminally extended variants that localize to mitochondria. Using bioinformatics tools, we provide compelling evidence that in yeast the potential for producing alternative protein isoforms by non-AUG translation initiation is much more prevalent than previously anticipated and may apply to as many as a few thousand proteins. Several hundreds of candidates are predicted to gain a mitochondrial targeting signal (MTS), generating an unrecognized pool of mitochondrial proteins. We confirmed mitochondrial localization of a subset of proteins previously not identified as mitochondrial, whose standard forms do not carry an MTS. Our data highlight the potential of non-canonical translation initiation in expanding the capacity of the mitochondrial proteome and possibly also other cellular features.
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Affiliation(s)
- Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Anna Miścicka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Lounis Zenad
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Olli Niemitalo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Lidia Wrobel
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Jahangir Alam
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Agnieszka Chacinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
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35
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Wang X, You X, Langer JD, Hou J, Rupprecht F, Vlatkovic I, Quedenau C, Tushev G, Epstein I, Schaefke B, Sun W, Fang L, Li G, Hu Y, Schuman EM, Chen W. Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus. Nat Commun 2019; 10:5009. [PMID: 31676752 PMCID: PMC6825209 DOI: 10.1038/s41467-019-13037-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022] Open
Abstract
Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstruct a full-length transcriptome in the rat hippocampus, which is further validated using independent 5´ and 3´-end profiling approaches. In total, we detect 28,268 full-length transcripts (FLTs), covering 6,380 RefSeq genes and 849 unannotated loci. Based on these FLTs, we discover co-occurring alternative RNA processing events. Integrating with polysome profiling and ribosome footprinting data, we predict isoform-specific translational status and reconstruct an open reading frame (ORF)-eome. Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons. Collectively, our data advance our knowledge of RNA and protein isoform diversity in the rat brain and provide a rich resource for functional studies. It is challenging to characterize diverse transcript isoforms by short-read sequencing. Here the authors report full-length transcriptomes in rat hippocampus by hybrid-sequencing, predict isoform-specific translational status, and reconstruct open reading frames validated by mass spectrometry.
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Affiliation(s)
- Xi Wang
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany. .,German Cancer Research Center, 69120, Heidelberg, Germany.
| | - Xintian You
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany.,Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Jingyi Hou
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Fiona Rupprecht
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Irena Vlatkovic
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Claudia Quedenau
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Georgi Tushev
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Irina Epstein
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Bernhard Schaefke
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Wei Sun
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Liang Fang
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Guipeng Li
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Yuhui Hu
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China. .,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.
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36
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Sample PJ, Wang B, Reid DW, Presnyak V, McFadyen IJ, Morris DR, Seelig G. Human 5' UTR design and variant effect prediction from a massively parallel translation assay. Nat Biotechnol 2019; 37:803-809. [PMID: 31267113 PMCID: PMC7100133 DOI: 10.1038/s41587-019-0164-5] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
Abstract
The ability to predict the impact of cis-regulatory sequences on gene expression would facilitate discovery in fundamental and applied biology. Here we combine polysome profiling of a library of 280,000 randomized 5' untranslated regions (UTRs) with deep learning to build a predictive model that relates human 5' UTR sequence to translation. Together with a genetic algorithm, we use the model to engineer new 5' UTRs that accurately direct specified levels of ribosome loading, providing the ability to tune sequences for optimal protein expression. We show that the same approach can be extended to chemically modified RNA, an important feature for applications in mRNA therapeutics and synthetic biology. We test 35,212 truncated human 5' UTRs and 3,577 naturally occurring variants and show that the model predicts ribosome loading of these sequences. Finally, we provide evidence of 45 single-nucleotide variants (SNVs) associated with human diseases that substantially change ribosome loading and thus may represent a molecular basis for disease.
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Affiliation(s)
- Paul J Sample
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Ban Wang
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | | | | | | | - David R Morris
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
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37
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The landscape of transcription initiation across latent and lytic KSHV genomes. PLoS Pathog 2019; 15:e1007852. [PMID: 31188901 PMCID: PMC6590836 DOI: 10.1371/journal.ppat.1007852] [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: 01/23/2019] [Revised: 06/24/2019] [Accepted: 05/20/2019] [Indexed: 11/19/2022] Open
Abstract
Precise promoter annotation is required for understanding the mechanistic basis of transcription initiation. In the context of complex genomes, such as herpesviruses where there is extensive genic overlap, identification of transcription start sites (TSSs) is particularly problematic and cannot be comprehensively accessed by standard RNA sequencing approaches. Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic gammaherpesvirus and the etiological agent of Kaposi's sarcoma and the B cell lymphoma primary effusion lymphoma (PEL). Here, we leverage RNA annotation and mapping of promoters for analysis of gene expression (RAMPAGE) and define KSHV TSSs transcriptome-wide and at nucleotide resolution in two widely used models of KSHV infection, namely iSLK.219 cells and the PEL cell line TREx-BCBL1-RTA. By mapping TSSs over a 96 h time course of reactivation we confirm 48 of 50 previously identified TSSs. Moreover, we identify over 100 novel transcription start site clusters (TSCs) in each cell line. Our analyses identified cell-type specific differences in TSC positions as well as promoter strength, and defined motifs within viral core promoters. Collectively, by defining TSSs at high resolution we have greatly expanded the transcriptional landscape of the KSHV genome and identified transcriptional control mechanisms at play during KSHV lytic reactivation.
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38
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Boersma S, Khuperkar D, Verhagen BMP, Sonneveld S, Grimm JB, Lavis LD, Tanenbaum ME. Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding. Cell 2019; 178:458-472.e19. [PMID: 31178119 PMCID: PMC6630898 DOI: 10.1016/j.cell.2019.05.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/05/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2022]
Abstract
mRNA translation is a key step in decoding genetic information. Genetic decoding is surprisingly heterogeneous because multiple distinct polypeptides can be synthesized from a single mRNA sequence. To study translational heterogeneity, we developed the MoonTag, a fluorescence labeling system to visualize translation of single mRNAs. When combined with the orthogonal SunTag system, the MoonTag enables dual readouts of translation, greatly expanding the possibilities to interrogate complex translational heterogeneity. By placing MoonTag and SunTag sequences in different translation reading frames, each driven by distinct translation start sites, start site selection of individual ribosomes can be visualized in real time. We find that start site selection is largely stochastic but that the probability of using a particular start site differs among mRNA molecules and can be dynamically regulated over time. This study provides key insights into translation start site selection heterogeneity and provides a powerful toolbox to visualize complex translation dynamics. Development of MoonTag, a fluorescence labeling system to visualize translation Combining MoonTag and SunTag enables visualization of translational heterogeneity mRNAs from a single gene vary in initiation frequency at different start sites Ribosomes take many different “paths” along the 5′ UTR of a single mRNA molecule
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Affiliation(s)
- Sanne Boersma
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Deepak Khuperkar
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bram M P Verhagen
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stijn Sonneveld
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Marvin E Tanenbaum
- Oncode Institute, Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
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39
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Klein JC, Keith A, Rice SJ, Shepherd C, Agarwal V, Loughlin J, Shendure J. Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nat Commun 2019; 10:2434. [PMID: 31164647 PMCID: PMC6547687 DOI: 10.1038/s41467-019-10439-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and the mechanisms by which they contribute to disease risk have yet to be pinpointed. Here, we functionally test 1,605 single nucleotide variants associated with osteoarthritis for regulatory activity using a massively parallel reporter assay. We identify six single nucleotide polymorphisms (SNPs) with differential regulatory activity between the major and minor alleles. We show that the most significant SNP, rs4730222, exhibits differential nuclear protein binding in electrophoretic mobility shift assays and drives increased expression of an alternative isoform of HBP1 in a heterozygote chondrosarcoma cell line, in a CRISPR-edited osteosarcoma cell line, and in chondrocytes derived from osteoarthritis patients. This study provides a framework for prioritization of GWAS variants and highlights a role of HBP1 and Wnt signaling in osteoarthritis pathogenesis.
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Affiliation(s)
- Jason C Klein
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Aidan Keith
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Sarah J Rice
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Colin Shepherd
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - John Loughlin
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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40
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Connahs H, Tlili S, van Creij J, Loo TYJ, Banerjee TD, Saunders TE, Monteiro A. Activation of butterfly eyespots by Distal-less is consistent with a reaction-diffusion process. Development 2019; 146:dev169367. [PMID: 30992277 PMCID: PMC6526720 DOI: 10.1242/dev.169367] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 04/05/2019] [Indexed: 01/08/2023]
Abstract
Eyespots on the wings of nymphalid butterflies represent colorful examples of pattern formation, yet the developmental origins and mechanisms underlying eyespot center differentiation are still poorly understood. Using CRISPR-Cas9 we re-examine the function of Distal-less (Dll) as an activator or repressor of eyespots, a topic that remains controversial. We show that the phenotypic outcome of CRISPR mutations depends upon which specific exon is targeted. In Bicyclus anynana, exon 2 mutations are associated with both missing and ectopic eyespots, and also exon skipping. Exon 3 mutations, which do not lead to exon skipping, produce only null phenotypes, including missing eyespots, lighter wing coloration and loss of scales. Reaction-diffusion modeling of Dll function, using Wnt and Dpp as candidate morphogens, accurately replicates these complex crispant phenotypes. These results provide new insight into the function of Dll as a potential activator of eyespot development, scale growth and melanization, and suggest that the tuning of Dll expression levels can generate a diversity of eyespot phenotypes, including their appearance on the wing.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Heidi Connahs
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Sham Tlili
- Mechanobiology Institute, National University of Singapore, Singapore 117411
| | - Jelle van Creij
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Tricia Y J Loo
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Tirtha Das Banerjee
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Timothy E Saunders
- Department of Biological Sciences, National University of Singapore, Singapore 117558
- Mechanobiology Institute, National University of Singapore, Singapore 117411
- Institute of Molecular and Cell Biology, A*Star, Proteos, Singapore 138673
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117558
- Yale-NUS College, Singapore 138527
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41
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Shiau CK, Huang JH, Tsai HK. CATANA: a tool for generating comprehensive annotations of alternative transcript events. Bioinformatics 2019; 35:1414-1415. [PMID: 30202999 DOI: 10.1093/bioinformatics/bty795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/15/2018] [Accepted: 09/06/2018] [Indexed: 11/14/2022] Open
Abstract
SUMMARY In higher eukaryotes, the generation of transcript isoforms from a single gene through alternative splicing (AS) and alternative transcription (AT) mechanisms increases functional and regulatory diversities. Annotating these alternative transcript events is essential for genomic studies. However, there are no existing tools that generate comprehensive annotations of all these alternative transcript events including both AS and AT events. In the present study, we develop CATANA, with the encoded exon usage patterns based on the flattened gene model, to identify ten types of AS and AT events. We demonstrate the power and versatility of CATANA by showing greater depth of annotations of alternative transcript events according to either genome annotation or RNA-seq data. AVAILABILITY AND IMPLEMENTATION CATANA is available on https://github.com/shiauck/CATANA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Cheng-Kai Shiau
- Institute of Information Science Academia Sinica, Taipei, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Jia-Hsin Huang
- Institute of Information Science Academia Sinica, Taipei, Taiwan
| | - Huai-Kuang Tsai
- Institute of Information Science Academia Sinica, Taipei, Taiwan
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42
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Li H, Bai L, Li H, Li X, Kang Y, Zhang N, Sun J, Shao Z. Selective translational usage of TSS and core promoters revealed by translatome sequencing. BMC Genomics 2019; 20:282. [PMID: 30987607 PMCID: PMC6463679 DOI: 10.1186/s12864-019-5650-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/27/2019] [Indexed: 12/17/2022] Open
Abstract
Background In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive. Results In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. By comparing the two profiles, we identified the 5′ isoforms preferentially used in translatome and revealed a widespread selective usage of TSSs (32.0%) and core promoters (48.7%) by polysome. We discovered the transcription initiation patterns and the sequence characteristics that were highly correlated with polysome selection. We further identified 5804 genes significantly enriched or depleted in translatome and showed that polysome selection was an important contributing factor to the abundance of related gene products. Moreover, after comparison with public transcriptome CAGE data from 180 human tissues and primary cells, we raised a question on whether it is a widely adopted mechanism to regulate translation efficiency by changing the transcription initiation sites on the transcription level in cells of different conditions. Conclusions Using HEK293 cells as a model, we delineated an indirect selection toward TSSs and core promoters by the translation machinery. Our findings lend additional evidence for a much closer coordination between transcription and translation, warranting future translatome studies in more cell types and conditions to develop a more intricate regulatory model for gene expression. Electronic supplementary material The online version of this article (10.1186/s12864-019-5650-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hua Li
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Ling Bai
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Hongmei Li
- Instrumental Analysis Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xinhui Li
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yani Kang
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Ningbo Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jielin Sun
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhifeng Shao
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
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43
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Hollerer I, Barker JC, Jorgensen V, Tresenrider A, Dugast-Darzacq C, Chan LY, Darzacq X, Tjian R, Ünal E, Brar GA. Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells. G3 (BETHESDA, MD.) 2019; 9:1045-1053. [PMID: 30723103 PMCID: PMC6469420 DOI: 10.1534/g3.118.200802] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 01/25/2019] [Indexed: 11/18/2022]
Abstract
We recently described an unconventional mode of gene regulation in budding yeast by which transcriptional and translational interference collaborate to down-regulate protein expression. Developmentally timed transcriptional interference inhibited production of a well translated mRNA isoform and resulted in the production of an mRNA isoform containing inhibitory upstream open reading frames (uORFs) that prevented translation of the main ORF. Transcriptional interference and uORF-based translational repression are established mechanisms outside of yeast, but whether this type of integrated regulation was conserved was unknown. Here we find that, indeed, a similar type of regulation occurs at the locus for the human oncogene MDM2 We observe evidence of transcriptional interference between the two MDM2 promoters, which produce a poorly translated distal promoter-derived uORF-containing mRNA isoform and a well-translated proximal promoter-derived transcript. Down-regulation of distal promoter activity markedly up-regulates proximal promoter-driven expression and results in local reduction of histone H3K36 trimethylation. Moreover, we observe that this transcript toggling between the two MDM2 isoforms naturally occurs during human embryonic stem cell differentiation programs.
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Affiliation(s)
- Ina Hollerer
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Juliet C Barker
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Victoria Jorgensen
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Amy Tresenrider
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley, CA 94720
| | - Leon Y Chan
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley, CA 94720
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley, CA 94720
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Gloria A Brar
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
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44
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Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis. Cell 2019; 172:910-923.e16. [PMID: 29474919 DOI: 10.1016/j.cell.2018.01.035] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 12/22/2022]
Abstract
To better understand the gene regulatory mechanisms that program developmental processes, we carried out simultaneous genome-wide measurements of mRNA, translation, and protein through meiotic differentiation in budding yeast. Surprisingly, we observed that the levels of several hundred mRNAs are anti-correlated with their corresponding protein products. We show that rather than arising from canonical forms of gene regulatory control, the regulation of at least 380 such cases, or over 8% of all measured genes, involves temporally regulated switching between production of a canonical, translatable transcript and a 5' extended isoform that is not efficiently translated into protein. By this pervasive mechanism for the modulation of protein levels through a natural developmental program, a single transcription factor can coordinately activate and repress protein synthesis for distinct sets of genes. The distinction is not based on whether or not an mRNA is induced but rather on the type of transcript produced.
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45
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Li Z, Qi DL, Singh HP, Zou Y, Shen B, Cobrinik D. A novel thyroid hormone receptor isoform, TRβ2-46, promotes SKP2 expression and retinoblastoma cell proliferation. J Biol Chem 2019; 294:2961-2969. [PMID: 30643022 DOI: 10.1074/jbc.ac118.006041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/07/2019] [Indexed: 12/13/2022] Open
Abstract
Retinoblastoma is a childhood retinal tumor that develops from cone photoreceptor precursors in response to inactivating RB1 mutations and loss of functional RB protein. The cone precursor's response to RB loss involves cell type-specific signaling circuitry that helps to drive tumorigenesis. One component of the cone precursor circuitry, the thyroid hormone receptor β2 (TRβ2), enables the aberrant proliferation of diverse RB-deficient cells in part by opposing the down-regulation of S-phase kinase-associated protein 2 (SKP2) by the more widely expressed and tumor-suppressive TRβ1. However, it is unclear how TRβ2 opposes TRβ1 to enable SKP2 expression and cell proliferation. Here, we show that in human retinoblastoma cells TRβ2 mRNA encodes two TRβ2 protein isoforms: a predominantly cytoplasmic 54-kDa protein (TRβ2-54) corresponding to the well-characterized full-length murine Trβ2 and an N-terminally truncated and exclusively cytoplasmic 46-kDa protein (TRβ2-46) that starts at Met-79. Whereas TRβ2 knockdown decreased SKP2 expression and impaired retinoblastoma cell cycle progression, re-expression of TRβ2-46 but not TRβ2-54 stabilized SKP2 and restored proliferation to an extent similar to that of ectopic SKP2 restoration. We conclude that TRβ2-46 is an oncogenic thyroid hormone receptor isoform that promotes SKP2 expression and SKP2-dependent retinoblastoma cell proliferation.
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Affiliation(s)
- Zhengke Li
- From The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California 90027, .,Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010.,Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614, and
| | - Dong-Lai Qi
- From The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California 90027
| | - Hardeep P Singh
- From The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California 90027
| | - Yue Zou
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614, and
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010
| | - David Cobrinik
- From The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California 90027, .,Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, and USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
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46
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Zhao J, Qin B, Nikolay R, Spahn CMT, Zhang G. Translatomics: The Global View of Translation. Int J Mol Sci 2019; 20:ijms20010212. [PMID: 30626072 PMCID: PMC6337585 DOI: 10.3390/ijms20010212] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 01/01/2023] Open
Abstract
In all kingdoms of life, proteins are synthesized by ribosomes in a process referred to as translation. The amplitude of translational regulation exceeds the sum of transcription, mRNA degradation and protein degradation. Therefore, it is essential to investigate translation in a global scale. Like the other “omics”-methods, translatomics investigates the totality of the components in the translation process, including but not limited to translating mRNAs, ribosomes, tRNAs, regulatory RNAs and nascent polypeptide chains. Technical advances in recent years have brought breakthroughs in the investigation of these components at global scale, both for their composition and dynamics. These methods have been applied in a rapidly increasing number of studies to reveal multifaceted aspects of translation control. The process of translation is not restricted to the conversion of mRNA coding sequences into polypeptide chains, it also controls the composition of the proteome in a delicate and responsive way. Therefore, translatomics has extended its unique and innovative power to many fields including proteomics, cancer research, bacterial stress response, biological rhythmicity and plant biology. Rational design in translation can enhance recombinant protein production for thousands of times. This brief review summarizes the main state-of-the-art methods of translatomics, highlights recent discoveries made in this field and introduces applications of translatomics on basic biological and biomedical research.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Andreassi C, Crerar H, Riccio A. Post-transcriptional Processing of mRNA in Neurons: The Vestiges of the RNA World Drive Transcriptome Diversity. Front Mol Neurosci 2018; 11:304. [PMID: 30210293 PMCID: PMC6121099 DOI: 10.3389/fnmol.2018.00304] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022] Open
Abstract
Neurons are morphologically complex cells that rely on the compartmentalization of protein expression to develop and maintain their extraordinary cytoarchitecture. This formidable task is achieved, at least in part, by targeting mRNA to subcellular compartments where they are rapidly translated. mRNA transcripts are the conveyor of genetic information from DNA to the translational machinery, however, they are also endowed with additional functions linked to both the coding sequence (open reading frame, or ORF) and the flanking 5′ and 3′ untranslated regions (UTRs), that may harbor coding-independent functions. In this review, we will highlight recent evidences supporting new coding-dependent and -independent functions of mRNA and discuss how nuclear and cytoplasmic post-transcriptional modifications of mRNA contribute to localization and translation in mammalian cells with specific emphasis on neurons. We also describe recently developed techniques that can be employed to study RNA dynamics at subcellular level in eukaryotic cells in developing and regenerating neurons.
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Affiliation(s)
- Catia Andreassi
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Hamish Crerar
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Antonella Riccio
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
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48
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Qin Z, Stoilov P, Zhang X, Xing Y. SEASTAR: systematic evaluation of alternative transcription start sites in RNA. Nucleic Acids Res 2018; 46:e45. [PMID: 29546410 PMCID: PMC5934623 DOI: 10.1093/nar/gky053] [Citation(s) in RCA: 14] [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: 04/09/2017] [Revised: 12/30/2017] [Accepted: 03/12/2018] [Indexed: 12/23/2022] Open
Abstract
Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ends of transcripts. We developed a computational pipeline SEASTAR that identifies first exons from RNA-seq data alone then quantifies and compares alternative first exon usage across multiple biological conditions. The exons inferred by SEASTAR coincide with transcription start sites identified directly by CAGE experiments and bear epigenetic hallmarks of active promoters. To determine if differential usage of alternative first exons can yield insights into the mechanism controlling gene expression, we applied SEASTAR to an RNA-seq dataset that tracked the reprogramming of mouse fibroblasts into induced pluripotent stem cells. We observed dynamic temporal changes in the usage of alternative first exons, along with correlated changes in transcription factor expression. Using a combined sequence motif and gene set enrichment analysis we identified N-Myc as a regulator of alternative first exon usage in the pluripotent state. Our results demonstrate that SEASTAR can leverage the available RNA-seq data to gain insights into the control of gene expression and alternative transcript variation in eukaryotic transcriptomes.
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Affiliation(s)
- Zhiyi Qin
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Peter Stoilov
- Department of Biochemistry and Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China
- School of Life Sciences, and Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yi Xing
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Lin D, Hiron TK, O'Callaghan CA. Intragenic transcriptional interference regulates the human immune ligand MICA. EMBO J 2018; 37:embj.201797138. [PMID: 29643123 DOI: 10.15252/embj.201797138] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 02/08/2018] [Accepted: 02/09/2018] [Indexed: 12/27/2022] Open
Abstract
Many human genes have tandem promoters driving overlapping transcription, but the value of this distributed promoter configuration is generally unclear. Here we show that MICA, a gene encoding a ligand for the activating immune receptor NKG2D, contains a conserved upstream promoter that expresses a noncoding transcript. Transcription from the upstream promoter represses the downstream standard promoter activity in cis through transcriptional interference. The effect of transcriptional interference depends on the strength of transcription from the upstream promoter and can be described quantitatively by a simple reciprocal repressor function. Transcriptional interference coincides with recruitment at the standard downstream promoter of the FACT histone chaperone complex, which is involved in nucleosomal remodelling during transcription. The mechanism is invoked in the regulation of MICA expression by the physiological inputs interferon-γ and interleukin-4 that act on the upstream promoter. Genome-wide analysis indicates that transcriptional interference between tandem intragenic promoters may constitute a general mechanism with widespread importance in human transcriptional regulation.
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Affiliation(s)
- Da Lin
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas K Hiron
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christopher A O'Callaghan
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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50
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Im H, Rao V, Sridhar K, Bentley J, Mishra T, Chen R, Hall J, Graber A, Zhang Y, Li X, Mias GI, Snyder MP, Greenberg PL. Distinct transcriptomic and exomic abnormalities within myelodysplastic syndrome marrow cells. Leuk Lymphoma 2018; 59:2952-2962. [PMID: 29616851 DOI: 10.1080/10428194.2018.1452210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To provide biologic insights into mechanisms underlying myelodysplastic syndromes (MDS) we evaluated the CD34+ marrow cells transcriptome using high-throughput RNA sequencing (RNA-Seq). We demonstrated significant differential gene expression profiles (GEPs) between MDS and normal and identified 41 disease classifier genes. Additionally, two main clusters of GEPs distinguished patients based on their major clinical features, particularly between those whose disease remained stable versus patients who transformed into acute myeloid leukemia within 12 months. The genes whose expression was associated with disease outcome were involved in functional pathways and biologic processes highly relevant for MDS. Combined with exomic analysis we identified differential isoform usage of genes in MDS mutational subgroups, with consequent dysregulation of distinct biologic functions. This combination of clinical, transcriptomic and exomic findings provides valuable understanding of mechanisms underlying MDS and its progression to a more aggressive stage and also facilitates prognostic characterization of MDS patients.
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Affiliation(s)
- Hogune Im
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Varsha Rao
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Kunju Sridhar
- b Hematology Division , Stanford University School of Medicine, Stanford Cancer Institute , Stanford , CA , USA
| | - Jason Bentley
- c Quantitative Science Unit , Stanford University , Stanford , CA , USA
| | - Tejaswini Mishra
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Rui Chen
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Jeff Hall
- d Genoptix Inc. , Carlsbad , CA , USA
| | | | - Yan Zhang
- e Department of Hematology , Jiaotong University, 6th Hospital , Shanghai , China
| | - Xiao Li
- e Department of Hematology , Jiaotong University, 6th Hospital , Shanghai , China
| | - George I Mias
- f Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , MI , USA
| | - Michael P Snyder
- a Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Peter L Greenberg
- b Hematology Division , Stanford University School of Medicine, Stanford Cancer Institute , Stanford , CA , USA
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