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Eftekhari Z, Zohrabi H, Oghalaie A, Ebrahimi T, Shariati FS, Behdani M, Kazemi-Lomedasht F. Advancements and challenges in mRNA and ribonucleoprotein-based therapies: From delivery systems to clinical applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102313. [PMID: 39281702 PMCID: PMC11402252 DOI: 10.1016/j.omtn.2024.102313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
The use of mRNA and ribonucleoproteins (RNPs) as therapeutic agents is a promising strategy for treating diseases such as cancer and infectious diseases. This review provides recent advancements and challenges in mRNA- and RNP-based therapies, focusing on delivery systems such as lipid nanoparticles (LNPs), which ensure efficient delivery to target cells. Strategies such as microfluidic devices are employed to prepare LNPs loaded with mRNA and RNPs, demonstrating effective genome editing and protein expression in vitro and in vivo. These applications extend to cancer treatment and infectious disease management, with promising results in genome editing for cancer therapy using LNPs encapsulating Cas9 mRNA and single-guide RNA. In addition, tissue-specific targeting strategies offer potential for improved therapeutic outcomes and reduced off-target effects. Despite progress, challenges such as optimizing delivery efficiency and targeting remain. Future research should enhance delivery efficiency, explore tissue-specific targeting, investigate combination therapies, and advance clinical translation. In conclusion, mRNA- and RNP-based therapies offer a promising avenue for treating various diseases and have the potential to revolutionize medicine, providing new hope for patients worldwide.
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Affiliation(s)
- Zohre Eftekhari
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Horieh Zohrabi
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Akbar Oghalaie
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Tahereh Ebrahimi
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Sadat Shariati
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Mahdi Behdani
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Kazemi-Lomedasht
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
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Di Grandi D, Dayeh DM, Kaur K, Chen Y, Henderson S, Moon Y, Bhowmick A, Ihnat PM, Fu Y, Muthusamy K, Palackal N, Pyles EA. A single-nucleotide resolution capillary gel electrophoresis workflow for poly(A) tail characterization in the development of mRNA therapeutics and vaccines. J Pharm Biomed Anal 2023; 236:115692. [PMID: 37696189 DOI: 10.1016/j.jpba.2023.115692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023]
Abstract
The 3' poly(A) tail is an important component of messenger RNA (mRNA). The length of the poly(A) tail has direct impact on the stability and translation efficiency of the mRNA molecule and is therefore considered to be a critical quality attribute (CQA) of mRNA-based therapeutics and vaccines. Various analytical methods have been developed to monitor this CQA. Methods like ion-pair reversed-phase liquid chromatography (IPRP-LC) can be used to quantify the percentage of mRNA with poly(A) tail but fail to provide further information on the actual length of poly(A). High-resolution methods such as liquid chromatography coupled with mass spectrometry (LC-MS) or next generation sequencing (NGS) can separate poly(A) tail length by one nucleotide (n/n + 1 resolution) but are complicated to implement for release testing of manufactured mRNA. In this study, a workflow utilizing capillary gel electrophoresis (CGE) for characterizing the poly(A) tail length of mRNA was developed. The CGE method demonstrated resolution comparable with the LC-MS method. With UV detection and the addition of poly(A) length markers, this method can provide poly(A) tail length information and can also provide quantitation of each poly(A) length, making it a suitable release method to monitor the CQA of poly(A) tail length.
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Affiliation(s)
- Deanna Di Grandi
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Daniel M Dayeh
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Keerat Kaur
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Yizhuo Chen
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Steven Henderson
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Youmi Moon
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Arijit Bhowmick
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Peter M Ihnat
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Yue Fu
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA.
| | - Kathir Muthusamy
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA.
| | - Nisha Palackal
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Erica A Pyles
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
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Kang DD, Li H, Dong Y. Advancements of in vitro transcribed mRNA (IVT mRNA) to enable translation into the clinics. Adv Drug Deliv Rev 2023; 199:114961. [PMID: 37321375 PMCID: PMC10264168 DOI: 10.1016/j.addr.2023.114961] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
The accelerated progress and approval of two mRNA-based vaccines to address the SARS-CoV-2 virus were unprecedented. This record-setting feat was made possible through the solid foundation of research on in vitro transcribed mRNA (IVT mRNA) which could be utilized as a therapeutic modality. Through decades of thorough research to overcome barriers to implementation, mRNA-based vaccines or therapeutics offer many advantages to rapidly address a broad range of applications including infectious diseases, cancers, and gene editing. Here, we describe the advances that have supported the adoption of IVT mRNA in the clinics, including optimization of the IVT mRNA structural components, synthesis, and lastly concluding with different classes of IVT RNA. Continuing interest in driving IVT mRNA technology will enable a safer and more efficacious therapeutic modality to address emerging and existing diseases.
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Affiliation(s)
- Diana D Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Haoyuan Li
- Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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de Felippes FF, Waterhouse PM. Plant terminators: the unsung heroes of gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2239-2250. [PMID: 36477559 PMCID: PMC10082929 DOI: 10.1093/jxb/erac467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/25/2022] [Indexed: 06/06/2023]
Abstract
To be properly expressed, genes need to be accompanied by a terminator, a region downstream of the coding sequence that contains the information necessary for the maturation of the mRNA 3' end. The main event in this process is the addition of a poly(A) tail at the 3' end of the new transcript, a critical step in mRNA biology that has important consequences for the expression of genes. Here, we review the mechanism leading to cleavage and polyadenylation of newly transcribed mRNAs and how this process can affect the final levels of gene expression. We give special attention to an aspect often overlooked, the effect that different terminators can have on the expression of genes. We also discuss some exciting findings connecting the choice of terminator to the biogenesis of small RNAs, which are a central part of one of the most important mechanisms of regulation of gene expression in plants.
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Affiliation(s)
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, QUT, Brisbane, QLD, Australia
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Infection of Trichinella spiralis Affects the Reproductive Capacity of ICR/CD-1 Male Mice by Reducing the Urine Pheromone Contents and Sperm Quality. Int J Mol Sci 2023; 24:ijms24065731. [PMID: 36982803 PMCID: PMC10058773 DOI: 10.3390/ijms24065731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Female mice can discriminate the urinary odors of male mice due to their olfactory acuity. Parasitic infection or subclinical infection can decrease the odor attractiveness of male mice and finally lead to aversion or avoidance responses in odor selection for female mice. Trichinella spiralis is a kind of tissue-parasitizing nematode that causes trichinellosis, a zoonotic parasitic disease that spreads throughout the world. However, the reproductive injury caused by Trichinella spiralis infection was not fully revealed. In this study, we explored the effect of Trichinella spiralis infection on the reproductive capacity in ICR/CD-1 male mice. We identified eight volatile compounds in urine by GC-MS analysis, and the results indicated that the contents of dimethyl sulfone, Z-7-tetradecen-1-ol, 6-Hydroxy-6-methyl-3-heptanone and (S)-2-sec-butyl-4,5-dihydrothiazole were significantly downregulated after parasitic infection, which might lead to the reduction of attractiveness of male mice urine to females. On the other hand, parasitic infection decreased sperm quality and downregulated the expression levels of Herc4, Ipo11, and Mrto4, and these genes were strongly related to spermatogenesis. In summary, this study revealed that the reproductive injury caused by Trichinella spiralis infection in ICR/CD-1 male mice could be associated with a decrease in urine pheromone content and sperm quality.
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Sun H, Zhang Y, Wang G, Yang W, Xu Y. mRNA-Based Therapeutics in Cancer Treatment. Pharmaceutics 2023; 15:pharmaceutics15020622. [PMID: 36839944 PMCID: PMC9964383 DOI: 10.3390/pharmaceutics15020622] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/28/2023] [Accepted: 01/28/2023] [Indexed: 02/15/2023] Open
Abstract
Over the past two decades, significant technological innovations have led to messenger RNA (mRNA) becoming a promising option for developing prophylactic and therapeutic vaccines, protein replacement therapies, and genome engineering. The success of the two COVID-19 mRNA vaccines has sparked new enthusiasm for other medical applications, particularly in cancer treatment. In vitro-transcribed (IVT) mRNAs are structurally designed to resemble naturally occurring mature mRNA. Delivery of IVT mRNA via delivery platforms such as lipid nanoparticles allows host cells to produce many copies of encoded proteins, which can serve as antigens to stimulate immune responses or as additional beneficial proteins for supplements. mRNA-based cancer therapeutics include mRNA cancer vaccines, mRNA encoding cytokines, chimeric antigen receptors, tumor suppressors, and other combination therapies. To better understand the current development and research status of mRNA therapies for cancer treatment, this review focused on the molecular design, delivery systems, and clinical indications of mRNA therapies in cancer.
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Affiliation(s)
- Han Sun
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ge Wang
- Department of Oral Maxillofacial & Head and Neck Oncology, National Center of Stomatology, National Clinical Research Center for Oral Disease, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Wen Yang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yingjie Xu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Correspondence:
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Brouze A, Krawczyk PS, Dziembowski A, Mroczek S. Measuring the tail: Methods for poly(A) tail profiling. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1737. [PMID: 35617484 PMCID: PMC10078590 DOI: 10.1002/wrna.1737] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/31/2023]
Abstract
The 3'-end poly(A) tail is an important and potent feature of most mRNA molecules that affects mRNA fate and translation efficiency. Polyadenylation is a posttranscriptional process that occurs in the nucleus by canonical poly(A) polymerases (PAPs). In some specific instances, the poly(A) tail can also be extended in the cytoplasm by noncanonical poly(A) polymerases (ncPAPs). This epitranscriptomic regulation of mRNA recently became one of the most interesting aspects in the field. Advances in RNA sequencing technologies and software development have allowed the precise measurement of poly(A) tails, identification of new ncPAPs, expansion of the function of known enzymes, discovery and a better understanding of the physiological role of tail heterogeneity, and recognition of a correlation between tail length and RNA translatability. Here, we summarize the development of polyadenylation research methods, including classic low-throughput approaches, Illumina-based genome-wide analysis, and advanced state-of-art techniques that utilize long-read third-generation sequencing with Pacific Biosciences and Oxford Nanopore Technologies platforms. A boost in technical opportunities over recent decades has allowed a better understanding of the regulation of gene expression at the mRNA level. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Aleksandra Brouze
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Szczepan Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Seweryn Mroczek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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Viscardi MJ, Arribere JA. Poly(a) selection introduces bias and undue noise in direct RNA-sequencing. BMC Genomics 2022; 23:530. [PMID: 35869428 PMCID: PMC9306060 DOI: 10.1186/s12864-022-08762-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/11/2022] [Indexed: 12/14/2022] Open
Abstract
Background Genome-wide RNA-sequencing technologies are increasingly critical to a wide variety of diagnostic and research applications. RNA-seq users often first enrich for mRNA, with the most popular enrichment method being poly(A) selection. In many applications it is well-known that poly(A) selection biases the view of the transcriptome by selecting for longer tailed mRNA species. Results Here, we show that poly(A) selection biases Oxford Nanopore direct RNA sequencing. As expected, poly(A) selection skews sequenced mRNAs toward longer poly(A) tail lengths. Interestingly, we identify a population of mRNAs (> 10% of genes’ mRNAs) that are inconsistently captured by poly(A) selection due to highly variable poly(A) tails, and demonstrate this phenomenon in our hands and in published data. Importantly, we show poly(A) selection is dispensable for Oxford Nanopore’s direct RNA-seq technique, and demonstrate successful library construction without poly(A) selection, with decreased input, and without loss of quality. Conclusions Our work expands the utility of direct RNA-seq by validating the use of total RNA as input, and demonstrates important technical artifacts from poly(A) selection that inconsistently skew mRNA expression and poly(A) tail length measurements. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08762-8.
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Li X, Yu K, Li F, Lu W, Wang Y, Zhang W, Bai Y. Novel Method of Full-Length RNA-seq That Expands the Identification of Non-Polyadenylated RNAs Using Nanopore Sequencing. Anal Chem 2022; 94:12342-12351. [PMID: 36018770 DOI: 10.1021/acs.analchem.2c01128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The occurrence of diseases displayed transcriptome alteration, including both coding and non-coding transcripts. The third-generation sequencing (TGS) technologies allow for intensive and comprehensive research of the transcriptome. However, the present standard TGS RNA sequencing method is unable to detect many of the non-polyadenylated [non-poly(A)] RNAs. To obtain more complete transcriptome information, we presented a new comprehensive sequencing approach by performing conventional poly(A) RNA-sequencing combined with the sequencing of non-poly(A) RNA fraction which was tailed by poly(U) on HepG2 and HL-7702 cell lines, enabling the detection of multiple categories of non-poly(A) RNAs excluded by the existing standard approach. Moreover, the length distribution of the full-splice match transcripts was longer than that assembled by short-reads, which contributed to characterizing alternative splicing events and provided a comprehensive portrait of transcriptional complexity. Besides the detection of genes with differential expression patterns in the poly(A) library between HepG2 and HL-7702, we also found a cancer-related non-coding gene in the poly(U) data, that is, growth arrest special 5 (GAS5). Collectively, our results suggested that the novel method effectively captured both poly(A) and non-poly(A) transcripts in the tested cell lines and allowed a deeper exploration of the transcriptome.
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Affiliation(s)
- Xiaohan Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Kequan Yu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Fuyu Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wenxiang Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Ying Wang
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Weizhong Zhang
- Department of Ophthalmology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yunfei Bai
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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Singh M, Ye B, Kim JH. Dual Leucine Zipper Kinase Regulates Dscam Expression through a Noncanonical Function of the Cytoplasmic Poly(A)-Binding Protein. J Neurosci 2022; 42:6007-6019. [PMID: 35764381 PMCID: PMC9351639 DOI: 10.1523/jneurosci.0543-21.2022] [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: 03/15/2021] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Dual leucine zipper kinase (DLK) plays a pivotal role in the development, degeneration, and regeneration of neurons. DLK can regulate gene expression post-transcriptionally, but the underlying mechanism remains poorly understood. The Drosophila DLK, Wallenda (Wnd), regulates the expression of Down syndrome cell adhesion molecule (Dscam) to control presynaptic arbor growth. This regulation is mediated by the 3' untranslated region (3'UTR) of Dscam mRNA, which suggests that RNA binding proteins (RBPs) mediate DLK function. We performed a genome-wide cell-based RNAi screen of RBPs and identified the cytoplasmic poly(A)-binding protein, pAbp, as an RBP that mediates Wnd-induced increase in Dscam expression. Genetic analysis shows that Wnd requires pAbp for promoting presynaptic arbor growth and for enhancing Dscam expression. Our analysis revealed that Dscam mRNAs harbor short poly(A) tails. We identified a region in Dscam 3'UTR that specifically interacts with pAbp. Removing this region significantly reduced Wnd-induced increase in Dscam expression. These suggest that a noncanonical interaction of PABP with the 3'UTR of target transcripts is essential for DLK functions.SIGNIFICANCE STATEMENT The kinase DLK plays key roles in a multitude of neuronal responses, including axon development, neurodegeneration, and nerve injury. Previous studies show that DLK acts via mRNAs to regulate protein synthesis, but how DLK does so is poorly understood. This study demonstrates that DLK regulates the synthesis of Dscam through the poly(A)-binding protein PABP-C. Whereas PABP-C is known as a general translational activator, our study shows that DLK-mediated Dscam expression involves a noncanonical interaction between PABP-C and the Dscam mRNA, which leads to a selective regulation of Dscam translation by PABP-C. Thus, our study provides novel insights into the mechanisms that underlie the function of DLK and regulation of gene expression of PABP-C.
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Affiliation(s)
- Monika Singh
- Department of Biology, University of Nevada, Reno, Nevada 89557
| | - Bing Ye
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Jung Hwan Kim
- Department of Biology, University of Nevada, Reno, Nevada 89557,
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Qin S, Tang X, Chen Y, Chen K, Fan N, Xiao W, Zheng Q, Li G, Teng Y, Wu M, Song X. mRNA-based therapeutics: powerful and versatile tools to combat diseases. Signal Transduct Target Ther 2022; 7:166. [PMID: 35597779 PMCID: PMC9123296 DOI: 10.1038/s41392-022-01007-w] [Citation(s) in RCA: 206] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 02/06/2023] Open
Abstract
The therapeutic use of messenger RNA (mRNA) has fueled great hope to combat a wide range of incurable diseases. Recent rapid advances in biotechnology and molecular medicine have enabled the production of almost any functional protein/peptide in the human body by introducing mRNA as a vaccine or therapeutic agent. This represents a rising precision medicine field with great promise for preventing and treating many intractable or genetic diseases. In addition, in vitro transcribed mRNA has achieved programmed production, which is more effective, faster in design and production, as well as more flexible and cost-effective than conventional approaches that may offer. Based on these extraordinary advantages, mRNA vaccines have the characteristics of the swiftest response to large-scale outbreaks of infectious diseases, such as the currently devastating pandemic COVID-19. It has always been the scientists’ desire to improve the stability, immunogenicity, translation efficiency, and delivery system to achieve efficient and safe delivery of mRNA. Excitingly, these scientific dreams have gradually been realized with the rapid, amazing achievements of molecular biology, RNA technology, vaccinology, and nanotechnology. In this review, we comprehensively describe mRNA-based therapeutics, including their principles, manufacture, application, effects, and shortcomings. We also highlight the importance of mRNA optimization and delivery systems in successful mRNA therapeutics and discuss the key challenges and opportunities in developing these tools into powerful and versatile tools to combat many genetic, infectious, cancer, and other refractory diseases.
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Affiliation(s)
- Shugang Qin
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoshan Tang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuting Chen
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Kepan Chen
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Na Fan
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wen Xiao
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qian Zheng
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Guohong Li
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuqing Teng
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58203, USA
| | - Xiangrong Song
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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12
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Enhanced Prodigiosin Production in Serratia marcescens JNB5-1 by Introduction of a Polynucleotide Fragment into the pigN 3' Untranslated Region and Disulfide Bonds into O-Methyl Transferase (PigF). Appl Environ Microbiol 2021; 87:e0054321. [PMID: 34232745 DOI: 10.1128/aem.00543-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In Serratia marcescens JNB5-1, prodigiosin was highly produced at 30°C, but it was noticeably repressed at ≥37°C. Our initial results demonstrated that both the production and the stability of the O-methyl transferase (PigF) and oxidoreductase (PigN) involved in the prodigiosin pathway in S. marcescens JNB5-1 sharply decreased at ≥37°C. Therefore, in this study, we improved mRNA stability and protein production using de novo polynucleotide fragments (PNFs) and the introduction of disulfide bonds, respectively, and observed their effects on prodigiosin production. Our results demonstrate that adding PNFs at the 3' untranslated regions of pigF and pigN significantly improved the mRNA half-lives of these genes, leading to an increase in the transcript and expression levels. Subsequently, the introduction of disulfide bonds in pigF improved the thermal stability, pH stability, and copper ion resistance of PigF. Finally, shake flask fermentation showed that the prodigiosin titer with the engineered S. marcescens was increased by 61.38% from 5.36 to 8.65 g/liter compared to the JNB5-1 strain at 30°C and, significantly, the prodigiosin yield increased 2.05-fold from 0.38 to 0.78 g/liter at 37°C. In this study, we revealed that the introduction of PNFs and disulfide bonds greatly improved the expression and stability of pigF and pigN, hence efficiently enhancing prodigiosin production with S. marcescens at 30 and 37°C. IMPORTANCE This study highlights a promising strategy to improve mRNA/enzyme stability and to increase production using de novo PNF libraries and the introduction of disulfide bonds into the protein. PNFs could increase the half-life of target gene mRNA and effectively prevent its degradation. Moreover, PNFs could increase the relative intensity of target genes without affecting the expression of other genes; as a result, it could alleviate the cellular burden compared to other regulatory elements such as promoters. In addition, we obtained a PigF variant with improved activity and stability by the introduction of disulfide bonds into PigF. Collectively, we demonstrate here a novel approach for improving mRNA/enzyme stability using PNFs, which results in enhanced prodigiosin production in S. marcescens at 30°C.
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Weber GM, Birkett J, Martin K, Dixon D, Gao G, Leeds TD, Vallejo RL, Ma H. Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability. BMC Genomics 2021; 22:448. [PMID: 34130620 PMCID: PMC8207762 DOI: 10.1186/s12864-021-07773-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Background Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage of the embryo. The transcriptome of the unfertilized egg, therefore, has potential to provide markers for predictors of egg quality and diagnosing problems with embryo production encountered by fish hatcheries. Although levels of specific transcripts have been shown to associate with measures of egg quality, these differentially expressed genes (DEGs) have not been consistent among studies. The present study compares differences in select transcripts among unfertilized rainbow trout eggs of different quality based on eyeing rate, among 2 year classes of the same line (A1, A2) and a population from a different hatchery (B). The study compared 65 transcripts previously reported to be differentially expressed with egg quality in rainbow trout. Results There were 32 transcripts identified as DEGs among the three groups by regression analysis. Group A1 had the most DEGs, 26; A2 had 15, 14 of which were shared with A1; and B had 12, 7 of which overlapped with A1 or A2. Six transcripts were found in all three groups, dcaf11, impa2, mrpl39_like, senp7, tfip11 and uchl1. Conclusions Our results confirmed maternal transcripts found to be differentially expressed between low- and high-quality eggs in one population of rainbow trout can often be found to overlap with DEGs in other populations. The transcripts differentially expressed with egg quality remain consistent among year classes of the same line. Greater similarity in dysregulated transcripts within year classes of the same line than among lines suggests patterns of transcriptome dysregulation may provide insight into causes of decreased viability within a hatchery population. Although many DEGs were identified, for each of the genes there is considerable variability in transcript abundance among eggs of similar quality and low correlations between transcript abundance and eyeing rate, making it highly improbable to predict the quality of a single batch of eggs based on transcript abundance of just a few genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07773-1.
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Affiliation(s)
- Gregory M Weber
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA.
| | - Jill Birkett
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | | | | | - Guangtu Gao
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | - Timothy D Leeds
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | - Roger L Vallejo
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | - Hao Ma
- USDA/ARS Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Ames, IA, USA
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Zheng M, Chen X, Cui Y, Li W, Dai H, Yue Q, Zhang H, Zheng Y, Guo X, Zhu H. TULP2, a New RNA-Binding Protein, Is Required for Mouse Spermatid Differentiation and Male Fertility. Front Cell Dev Biol 2021; 9:623738. [PMID: 33763418 PMCID: PMC7982829 DOI: 10.3389/fcell.2021.623738] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/27/2021] [Indexed: 11/13/2022] Open
Abstract
Spermatogenesis requires a large number of proteins to be properly expressed at certain stages, during which post-transcriptional regulation plays an important role. RNA-binding proteins (RBPs) are key players in post-transcriptional regulation, but only a few RBPs have been recognized and preliminary explored their function in spermatogenesis at present. Here we identified a new RBP tubby-like protein 2 (TULP2) and found three potential deleterious missense mutations of Tulp2 gene in dyszoospermia patients. Therefore, we explored the function and mechanism of TULP2 in male reproduction. TULP2 was specifically expressed in the testis and localized to spermatids. Studies on Tulp2 knockout mice demonstrated that the loss of TULP2 led to male sterility; on the one hand, increases in elongated spermatid apoptosis and restricted spermatid release resulted in a decreased sperm count; on the other hand, the abnormal differentiation of spermatids induced defective sperm tail structures and reduced ATP contents, influencing sperm motility. Transcriptome sequencing of mouse testis revealed the potential target molecular network of TULP2, which played its role in spermatogenesis by regulating specific transcripts related to the cytoskeleton, apoptosis, RNA metabolism and biosynthesis, and energy metabolism. We also explored the potential regulator of TULP2 protein function by using immunoprecipitation and mass spectrometry analysis, indicating that TUPL2 might be recognized by CCT8 and correctly folded by the CCT complex to play a role in spermiogenesis. Our results demonstrated the important role of TULP2 in spermatid differentiation and male fertility, which could provide an effective target for the clinical diagnosis and treatment of patients with oligo-astheno-teratozoospermia, and enrich the biological theory of the role of RBPs in male reproduction.
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Affiliation(s)
- Meimei Zheng
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.,Reproductive Medicine Center of No. 960 Hospital of PLA, Jinan, China
| | - Xu Chen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Wen Li
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Haiqian Dai
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Qiuling Yue
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Hao Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Ying Zheng
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Hui Zhu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
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15
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Czajkowska K, Walewska A, Ishikawa T, Szczepańska K, Ajduk A. Age-related alterations in fertilization-induced Ca2+ oscillations depend on the genetic background of mouse oocytes†. Biol Reprod 2020; 103:986-999. [PMID: 32761132 PMCID: PMC7609943 DOI: 10.1093/biolre/ioaa139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 06/05/2020] [Accepted: 08/08/2020] [Indexed: 12/21/2022] Open
Abstract
Maternal aging affects various aspects of oocytes' physiology, including the functionality of their nuclear apparatus and mitochondria. In the present paper, we wished to investigate whether advanced reproductive age impacts oocytes' ability to generate proper Ca2+ oscillations in response to monospermic fertilization. We examined three different mouse strains/crosses: inbred C57BL/6Tar, outbred Tar:SWISS, and hybrid F1 (C57BL/6Tar × CBA/Tar). The females were either 2-4 months old (young) or 13-16 months old (aged). We observed that the Ca2+ oscillatory pattern is altered in a strain-dependent manner and changes were more profound in aged C57BL/6Tar and F1 than in aged Tar:SWISS oocytes. We also showed that maternal aging differently affects the size of Ca2+ store and expression of Itpr1, Atp2a2, Erp44, and Pdia3 genes involved in Ca2+ homeostasis in oocytes of C57BL/6Tar, Tar:SWISS, and F1 genetic background, which may explain partially the differences in the extent of age-dependent changes in the Ca2+ oscillations in those oocytes. Maternal aging did not have any visible impact on the distribution of the ER cisterns in oocytes of all three genetic types. Finally, we showed that maternal aging alters the timing of the first embryonic interphase onset and that this timing correlates in C57BL/6Tar and Tar:SWISS oocytes with the frequency of fertilization-induced Ca2+ oscillations. Our results indicate that extreme caution is required when conclusions about oocyte/embryo physiological response to aging are made and complement an increasing amount of evidence that mammalian (including human) susceptibility to aging differs greatly depending on the genetic background of the individual.
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Affiliation(s)
- Katarzyna Czajkowska
- Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Walewska
- Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Takao Ishikawa
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Anna Ajduk
- Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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16
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Weng Y, Li C, Yang T, Hu B, Zhang M, Guo S, Xiao H, Liang XJ, Huang Y. The challenge and prospect of mRNA therapeutics landscape. Biotechnol Adv 2020; 40:107534. [PMID: 32088327 DOI: 10.1016/j.biotechadv.2020.107534] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 02/05/2020] [Accepted: 02/15/2020] [Indexed: 12/13/2022]
Abstract
Messenger RNA (mRNA)-based therapeutics hold the potential to cause a major revolution in the pharmaceutical industry because they can be used for precise and individualized therapy, and enable patients to produce therapeutic proteins in their own bodies without struggling with the comprehensive manufacturing issues associated with recombinant proteins. Compared with the current therapeutics, the production of mRNA is much cost-effective, faster and more flexible because it can be easily produced by in vitro transcription, and the process is independent of mRNA sequence. Moreover, mRNA vaccines allow people to develop personalized medications based on sequencing results and/or personalized conditions rapidly. Along with the great potential from bench to bedside, technical obstacles facing mRNA pharmaceuticals are also obvious. The stability, immunogenicity, translation efficiency, and delivery are all pivotal issues need to be addressed. In the recently published research results, these issues are gradually being overcome by state-of-the-art development technologies. In this review, we describe the structural properties and modification technologies of mRNA, summarize the latest advances in developing mRNA delivery systems, review the preclinical and clinical applications, and put forward our views on the prospect and challenges of developing mRNA into a new class of drug.
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Affiliation(s)
- Yuhua Weng
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Chunhui Li
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Tongren Yang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Bo Hu
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Mengjie Zhang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Shuai Guo
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Xing-Jie Liang
- Chinese Academy of Sciences (CAS), Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, PR China
| | - Yuanyu Huang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China.
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17
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Woo YM, Kwak Y, Namkoong S, Kristjánsdóttir K, Lee SH, Lee JH, Kwak H. TED-Seq Identifies the Dynamics of Poly(A) Length during ER Stress. Cell Rep 2019; 24:3630-3641.e7. [PMID: 30257221 DOI: 10.1016/j.celrep.2018.08.084] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 07/02/2018] [Accepted: 08/28/2018] [Indexed: 12/31/2022] Open
Abstract
Post-transcriptional RNA processing is a core mechanism of gene expression control in cell stress response. The poly(A) tail influences mRNA translation and stability, but it is unclear whether there are global roles of poly(A)-tail lengths in cell stress. To address this, we developed tail-end displacement sequencing (TED-seq) for an efficient transcriptome-wide profiling of poly(A) lengths and applied it to endoplasmic reticulum (ER) stress in human cells. ER stress induced increases in the poly(A) lengths of certain mRNAs, including known ER stress regulators, XBP1, DDIT3, and HSPA5. Importantly, the mRNAs with increased poly(A) lengths are both translationally de-repressed and stabilized. Furthermore, mRNAs in stress-induced RNA granules have shorter poly(A) tails than in the cytoplasm, supporting the view that RNA processing is compartmentalized. In conclusion, TED-seq reveals that poly(A) length is dynamically regulated upon ER stress, with potential consequences for both translation and mRNA turnover.
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Affiliation(s)
- Yu Mi Woo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sim Namkoong
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katla Kristjánsdóttir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seung Ha Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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18
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Kondo S, Kato H, Suzuki Y, Takada T, Eitoku M, Shiroishi T, Suganuma N, Sugano S, Kiyosawa H. Monoallelic, antisense and total RNA transcription in an in vitro neural differentiation system based on F1 hybrid mice. J Cell Sci 2019; 132:jcs.228973. [PMID: 31409693 DOI: 10.1242/jcs.228973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/04/2019] [Indexed: 11/20/2022] Open
Abstract
We developed an in vitro system to differentiate embryonic stem cells (ESCs) derived from reciprocally crossed F1 hybrid mice into neurons, and used it to investigate poly(A)+ and total RNA transcription at different stages of cell differentiation. By comparing expression profiles of transcripts assembled from 20 RNA sequencing datasets [2 alleles×(2 cell lines×4 time-points+2 mouse brains)], the relative influence of strain, cell and parent specificities to overall expression could be assessed. Divergent expression profiles of ESCs converged tightly at neural progenitor stage. Patterns of temporal variation of monoallelically expressed transcripts and antisense transcripts were quantified. Comparison of sense and antisense transcript pairs within the poly(A)+ sample, within the total RNA sample, and across poly(A)+ and total RNA samples revealed distinct rates of pairs showing anti-correlated expression variation. Unique patterns of sharing of poly(A)+ and poly(A)- transcription were identified in distinct RNA species. Regulation and functionality of monoallelic expression, antisense transcripts and poly(A)- transcription remain elusive. We demonstrated the effectiveness of our approach to capture these transcriptional activities, and provided new resources to elucidate the mammalian developmental transcriptome.
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Affiliation(s)
- Shinji Kondo
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan
| | - Hidemasa Kato
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Toyoyuki Takada
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan.,Mammalian Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Masamitsu Eitoku
- Department of Environmental Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Toshihiko Shiroishi
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan.,Mammalian Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Narufumi Suganuma
- Department of Environmental Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hidenori Kiyosawa
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan .,Department of Environmental Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
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19
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Jiménez-González V, Ogalla-García E, García-Quintanilla M, García-Quintanilla A. Deciphering GRINA/Lifeguard1: Nuclear Location, Ca 2+ Homeostasis and Vesicle Transport. Int J Mol Sci 2019; 20:ijms20164005. [PMID: 31426446 PMCID: PMC6719933 DOI: 10.3390/ijms20164005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 01/31/2023] Open
Abstract
The Glutamate Receptor Ionotropic NMDA-Associated Protein 1 (GRINA) belongs to the Lifeguard family and is involved in calcium homeostasis, which governs key processes, such as cell survival or the release of neurotransmitters. GRINA is mainly associated with membranes of the endoplasmic reticulum, Golgi, endosome, and the cell surface, but its presence in the nucleus has not been explained yet. Here we dissect, with the help of different software tools, the potential roles of GRINA in the cell and how they may be altered in diseases, such as schizophrenia or celiac disease. We describe for the first time that the cytoplasmic N-terminal half of GRINA (which spans a Proline-rich domain) contains a potential DNA-binding sequence, in addition to cleavage target sites and probable PY-nuclear localization sequences, that may enable it to be released from the rest of the protein and enter the nucleus under suitable conditions, where it could participate in the transcription, alternative splicing, and mRNA export of a subset of genes likely involved in lipid and sterol synthesis, ribosome biogenesis, or cell cycle progression. To support these findings, we include additional evidence based on an exhaustive review of the literature and our preliminary data of the protein–protein interaction network of GRINA.
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Affiliation(s)
| | - Elena Ogalla-García
- Department of Pharmacology, School of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Meritxell García-Quintanilla
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Albert García-Quintanilla
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Seville, 41012 Seville, Spain.
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20
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Ma H, Martin K, Dixon D, Hernandez AG, Weber GM. Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss. BMC Genomics 2019; 20:319. [PMID: 31029084 PMCID: PMC6486991 DOI: 10.1186/s12864-019-5690-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/11/2019] [Indexed: 12/31/2022] Open
Abstract
Background Maternal transcripts are accumulated in the oocyte during oogenesis to provide for protein synthesis from oocyte maturation through early embryonic development, when nuclear transcription is silenced. The maternal mRNAs have short poly(A) tails after undergoing post-transcriptional processing necessary for stabilizing them for storage. The transcripts undergo cytoplasmic polyadenylation when they are to be translated. Transcriptome analyses comparing total mRNA and elongated poly(A) mRNA content among eggs of different quality can provide insight into molecular mechanisms affecting egg developmental competence in rainbow trout. The present study used RNA-seq to compare transcriptomes of unfertilized eggs of rainbow trout females yielding different eyeing rates, following rRNA removal and poly(A) retention for construction of the libraries. Results The percentage of embryos to reach the 32-cell stage at 24 h post fertilization was significantly correlated to family eyeing rate, indicating that inviable embryos were developmentally compromised before zygotic genome activation. RNA sequencing identified 2 differentially expressed transcripts (DETs) from total mRNA sequencing comparing females with low-quality (< 5% eyeing), medium-quality (30–50% eyeing), and high-quality (> 80% eyeing) eggs. In contrast, RNA sequencing from poly(A) captured transcripts identified 945 DETs between low- and high-quality eggs, 1012 between low- and medium-quality eggs, and only 2 between medium- and high-quality eggs. The transcripts of mitochondrial genes were enriched with polyadenylated transcript sequencing and they were significantly reduced in low-quality eggs. Similarly, mitochondrial DNA was reduced in low-quality eggs compared with medium- and high-quality eggs. The functional gene analysis classified the 945 DETs between low- and high-quality eggs into 31 functional modules, many of which were related to ribosomal and mitochondrial functions. Other modules involved transcription, translation, cell division, apoptosis, and immune responses. Conclusions Our results indicate that differences in egg quality may be derived from differences in maternal nuclear transcript activation and cytoplasmic polyadenylation before ovulation, as opposed to accumulation and storage of maternal nuclear transcripts during oogenesis. Transcriptome comparisons suggest low-quality eggs suffered from impaired oxidative phosphorylation and translation. The DETs identified in this study provide insight into developmental competence in rainbow trout eggs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5690-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Ma
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | | | | | | | - Gregory M Weber
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA.
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21
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Nicholson AL, Pasquinelli AE. Tales of Detailed Poly(A) Tails. Trends Cell Biol 2018; 29:191-200. [PMID: 30503240 DOI: 10.1016/j.tcb.2018.11.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 11/18/2022]
Abstract
Poly(A) tails are non-templated additions of adenosines at the 3' ends of most eukaryotic mRNAs. In the nucleus, these RNAs are co-transcriptionally cleaved at a poly(A) site and then polyadenylated before being exported to the cytoplasm. In the cytoplasm, poly(A) tails play pivotal roles in the translation and stability of the mRNA. One challenge in studying poly(A) tails is that they are difficult to sequence and accurately measure. However, recent advances in sequencing technology, computational algorithms, and other assays have enabled a more detailed look at poly(A) tail length genome-wide throughout many developmental stages and organisms. With the help of these advances, our understanding of poly(A) tail length has evolved over the past 5 years with the recognition that highly expressed genes can have short poly(A) tails and the elucidation of the seemingly contradictory roles for poly(A)-binding protein (PABP) in facilitating both protection and deadenylation.
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Affiliation(s)
- Angela L Nicholson
- Division of Biology, University of California, San Diego (USCD), La Jolla, CA 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego (USCD), La Jolla, CA 92093-0349, USA.
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22
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Krause HM. New and Prospective Roles for lncRNAs in Organelle Formation and Function. Trends Genet 2018; 34:736-745. [PMID: 30017312 DOI: 10.1016/j.tig.2018.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023]
Abstract
The observation that long noncoding RNAs (lncRNAs) represent the majority of transcripts in humans has led to a rapid increase in interest and study. Most of this interest has focused on their roles in the nucleus. However, increasing evidence is beginning to reveal even more functions outside the nucleus, and even outside cells. Many of these roles are mediated by newly discovered properties, including the ability of lncRNAs to interact with lipids, membranes, and disordered protein domains, and to form differentially soluble RNA-protein sub-organelles. This review explores the possibilities enabled by these new properties and abilities, such as likely roles in exosome formation and function.
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Affiliation(s)
- Henry M Krause
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
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23
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Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. Sci Rep 2018; 8:4847. [PMID: 29555914 PMCID: PMC5859009 DOI: 10.1038/s41598-018-22297-7] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/19/2018] [Indexed: 12/12/2022] Open
Abstract
As an image-based single-cell transcriptomics approach, multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows hundreds to thousands of RNA species to be identified, counted and localized in individual cells while preserving the native spatial context of RNAs. In MERFISH, RNAs are identified via a combinatorial labeling approach that encodes RNA species with error-robust barcodes followed by sequential rounds of single-molecule FISH (smFISH) to read out these barcodes. The accuracy of RNA identification relies on spatially separated signals from individual RNA molecules, which limits the density of RNAs that can be measured and makes the multiplexed imaging of a large number of high-abundance RNAs challenging. Here we report an approach that combines MERFISH and expansion microscopy to substantially increase the total density of RNAs that can be measured. Using this approach, we demonstrate accurate identification and counting of RNAs, with a near 100% detection efficiency, in a ~130-RNA library composed of many high-abundance RNAs, the total density of which is more than 10 fold higher than previously reported. In parallel, we demonstrate the combination of MERFISH with immunofluorescence in expanded samples. These advances increase the versatility of MERFISH and will facilitate its application to a wide range of biological problems.
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Beverly M, Hagen C, Slack O. Poly A tail length analysis of in vitro transcribed mRNA by LC-MS. Anal Bioanal Chem 2018; 410:1667-1677. [PMID: 29313076 DOI: 10.1007/s00216-017-0840-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/03/2017] [Accepted: 11/17/2017] [Indexed: 11/29/2022]
Abstract
The 3'-polyadenosine (poly A) tail of in vitro transcribed (IVT) mRNA was studied using liquid chromatography coupled to mass spectrometry (LC-MS). Poly A tails were cleaved from the mRNA using ribonuclease T1 followed by isolation with dT magnetic beads. Extracted tails were then analyzed by LC-MS which provided tail length information at single-nucleotide resolution. A 2100-nt mRNA with plasmid-encoded poly A tail lengths of either 27, 64, 100, or 117 nucleotides was used for these studies as enzymatically added poly A tails showed significant length heterogeneity. The number of As observed in the tails closely matched Sanger sequencing results of the DNA template, and even minor plasmid populations with sequence variations were detected. When the plasmid sequence contained a discreet number of poly As in the tail, analysis revealed a distribution that included tails longer than the encoded tail lengths. These observations were consistent with transcriptional slippage of T7 RNAP taking place within a poly A sequence. The type of RNAP did not alter the observed tail distribution, and comparison of T3, T7, and SP6 showed all three RNAPs produced equivalent tail length distributions. The addition of a sequence at the 3' end of the poly A tail did, however, produce narrower tail length distributions which supports a previously described model of slippage where the 3' end can be locked in place by having a G or C after the poly nucleotide region. Graphical abstract Determination of mRNA poly A tail length using magnetic beads and LC-MS.
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Affiliation(s)
- Michael Beverly
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA.
| | - Caitlin Hagen
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA
| | - Olga Slack
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA
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25
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Afik S, Bartok O, Artyomov MN, Shishkin AA, Kadri S, Hanan M, Zhu X, Garber M, Kadener S. Defining the 5΄ and 3΄ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq. Nucleic Acids Res 2017; 45:e95. [PMID: 28335028 PMCID: PMC5499799 DOI: 10.1093/nar/gkx133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 02/15/2017] [Indexed: 01/19/2023] Open
Abstract
Cells regulate biological responses in part through changes in transcription start sites (TSS) or cleavage and polyadenylation sites (PAS). To fully understand gene regulatory networks, it is therefore critical to accurately annotate cell type-specific TSS and PAS. Here we present a simple and straightforward approach for genome-wide annotation of 5΄- and 3΄-RNA ends. Our approach reliably discerns bona fide PAS from false PAS that arise due to internal poly(A) tracts, a common problem with current PAS annotation methods. We applied our methodology to study the impact of temperature on the Drosophila melanogaster head transcriptome. We found hundreds of previously unidentified TSS and PAS which revealed two interesting phenomena: first, genes with multiple PASs tend to harbor a motif near the most proximal PAS, which likely represents a new cleavage and polyadenylation signal. Second, motif analysis of promoters of genes affected by temperature suggested that boundary element association factor of 32 kDa (BEAF-32) and DREF mediates a transcriptional program at warm temperatures, a result we validated in a fly line where beaf-32 is downregulated. These results demonstrate the utility of a high-throughput platform for complete experimental and computational analysis of mRNA-ends to improve gene annotation.
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Affiliation(s)
- Shaked Afik
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Osnat Bartok
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alexander A Shishkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sabah Kadri
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Mor Hanan
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Xiaopeng Zhu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
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26
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The non-canonical poly(A) polymerase FAM46C acts as an onco-suppressor in multiple myeloma. Nat Commun 2017; 8:619. [PMID: 28931820 PMCID: PMC5606997 DOI: 10.1038/s41467-017-00578-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/11/2017] [Indexed: 12/17/2022] Open
Abstract
FAM46C is one of the most frequently mutated genes in multiple myeloma. Here, using a combination of in vitro and in vivo approaches, we demonstrate that FAM46C encodes an active non-canonical poly(A) polymerase which enhances mRNA stability and gene expression. Reintroduction of active FAM46C into multiple myeloma cell lines, but not its catalytically-inactive mutant, leads to broad polyadenylation and stabilization of mRNAs strongly enriched with those encoding endoplasmic reticulum-targeted proteins and induces cell death. Moreover, silencing of FAM46C in multiple myeloma cells expressing WT protein enhance cell proliferation. Finally, using a FAM46C-FLAG knock-in mouse strain, we show that the FAM46C protein is strongly induced during activation of primary splenocytes and that B lymphocytes isolated from newly generated FAM46C KO mice proliferate faster than those isolated from their WT littermates. Concluding, our data clearly indicate that FAM46C works as an onco-suppressor, with the specificity for B-lymphocyte lineage from which multiple myeloma originates. FAM46C is one of the most frequently mutated genes in multiple myeloma (MM), but its molecular function remains unknown. Here the authors show that FAM46C is a poly(A) polymerase and that loss of function of FAM46C drives multiple myeloma through the destabilisation of ER response transcripts.
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27
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Park JE, Yi H, Kim Y, Chang H, Kim VN. Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. Mol Cell 2017; 62:462-471. [PMID: 27153541 DOI: 10.1016/j.molcel.2016.04.007] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/07/2016] [Accepted: 04/04/2016] [Indexed: 12/15/2022]
Abstract
Poly(A) tails are critical for mRNA stability and translation. However, recent studies have challenged this view, showing that poly(A) tail length and translation efficiency are decoupled in non-embryonic cells. Using TAIL-seq and ribosome profiling, we investigate poly(A) tail dynamics and translational control in the somatic cell cycle. We find dramatic changes in poly(A) tail lengths of cell-cycle regulatory genes like CDK1, TOP2A, and FBXO5, explaining their translational repression in M phase. We also find that poly(A) tail length is coupled to translation when the poly(A) tail is <20 nucleotides. However, as most genes have >20 nucleotide poly(A) tails, their translation is regulated mainly via poly(A) tail length-independent mechanisms during the cell cycle. Specifically, we find that terminal oligopyrimidine (TOP) tract-containing transcripts escape global translational suppression in M phase and are actively translated. Our quantitative and comprehensive data provide a revised view of translational control in the somatic cell cycle.
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Affiliation(s)
- Jong-Eun Park
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyerim Yi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yoosik Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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28
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Gudde AEEG, van Kessel IDG, André LM, Wieringa B, Wansink DG. Trinucleotide-repeat expanded and normal DMPK transcripts contain unusually long poly(A) tails despite differential nuclear residence. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:740-749. [PMID: 28435090 DOI: 10.1016/j.bbagrm.2017.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/26/2017] [Accepted: 04/14/2017] [Indexed: 12/29/2022]
Abstract
In yeast and higher eukaryotes nuclear retention of transcripts may serve in control over RNA decay, nucleocytoplasmic transport and premature cytoplasmic appearance of mRNAs. Hyperadenylation of RNA is known to be associated with nuclear retention, but the cause-consequence relationship between hyperadenylation and regulation of RNA nuclear export is still unclear. We compared polyadenylation status between normal and expanded DMPK transcripts in muscle cells and tissues derived from unaffected individuals and patients with myotonic dystrophy type 1 (DM1). DM1 is an autosomal dominant disorder caused by (CTG)n repeat expansion in the DMPK gene. DM1 etiology is characterized by an almost complete block of nuclear export of DMPK transcripts carrying a long (CUG)n repeat, including aberrant sequestration of RNA-binding proteins. We show here by use of cell fractionation, RNA size separation and analysis of poly(A) tail length that a considerable fraction of transcripts from the normal DMPK allele is also retained in the nucleus (~30%). They carry poly(A) tails with an unusually broad length distribution, ranging between a few dozen to >500 adenosine residues. Remarkably, expanded DMPK (CUG)n transcripts from the mutant allele, almost exclusively nuclear, carry equally long poly(A) tails. Our findings thus suggest that nuclear retention may be a common feature of regulation of DMPK RNA expression. The typical forced nuclear residence of expanded DMPK transcripts affects this regulation in tissues of DM1 patients, but not through hyperadenylation.
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Affiliation(s)
- Anke E E G Gudde
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Ingeborg D G van Kessel
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Laurène M André
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Bé Wieringa
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Derick G Wansink
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands.
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29
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Characterization of the Role of Hexamer AGUAAA and Poly(A) Tail in Coronavirus Polyadenylation. PLoS One 2016; 11:e0165077. [PMID: 27760233 PMCID: PMC5070815 DOI: 10.1371/journal.pone.0165077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/05/2016] [Indexed: 01/21/2023] Open
Abstract
Similar to eukaryotic mRNA, the positive-strand coronavirus genome of ~30 kilobases is 5’-capped and 3’-polyadenylated. It has been demonstrated that the length of the coronaviral poly(A) tail is not static but regulated during infection; however, little is known regarding the factors involved in coronaviral polyadenylation and its regulation. Here, we show that during infection, the level of coronavirus poly(A) tail lengthening depends on the initial length upon infection and that the minimum length to initiate lengthening may lie between 5 and 9 nucleotides. By mutagenesis analysis, it was found that (i) the hexamer AGUAAA and poly(A) tail are two important elements responsible for synthesis of the coronavirus poly(A) tail and may function in concert to accomplish polyadenylation and (ii) the function of the hexamer AGUAAA in coronaviral polyadenylation is position dependent. Based on these findings, we propose a process for how the coronaviral poly(A) tail is synthesized and undergoes variation. Our results provide the first genetic evidence to gain insight into coronaviral polyadenylation.
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30
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Lim J, Lee M, Son A, Chang H, Kim VN. mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development. Genes Dev 2016; 30:1671-82. [PMID: 27445395 PMCID: PMC4973296 DOI: 10.1101/gad.284802.116] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/28/2016] [Indexed: 12/04/2022]
Abstract
Here, Lim et al. report a new version of TAIL-seq (mRNA TAIL-seq [mTAIL-seq]) with enhanced sequencing depth for mRNAs (by ∼1000-fold compared with the previous version). Using their new methodology, the authors investigated mRNA tailing in Drosophila oocytes and embryos and demonstrated a relationship between poly(A) tail length and translational efficiency during egg activation. Eukaryotic mRNAs are subject to multiple types of tailing that critically influence mRNA stability and translatability. To investigate RNA tails at the genomic scale, we previously developed TAIL-seq, but its low sensitivity precluded its application to biological materials of minute quantity. In this study, we report a new version of TAIL-seq (mRNA TAIL-seq [mTAIL-seq]) with enhanced sequencing depth for mRNAs (by ∼1000-fold compared with the previous version). The improved method allows us to investigate the regulation of poly(A) tails in Drosophila oocytes and embryos. We found that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and that further modulation occurs upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates the vast majority of maternal mRNAs, with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAIL-seq data with ribosome profiling data, we found a strong coupling between poly(A) tail length and translational efficiency during egg activation. Our data suggest that regulation of poly(A) tails in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing in diverse biological systems.
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Affiliation(s)
- Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ahyeon Son
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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31
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Istomine R, Pavey N, Piccirillo CA. Posttranscriptional and Translational Control of Gene Regulation in CD4+ T Cell Subsets. THE JOURNAL OF IMMUNOLOGY 2016; 196:533-40. [PMID: 26747571 DOI: 10.4049/jimmunol.1501337] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The immune system is under strict regulatory control to ensure homeostasis of inflammatory responses, lying dormant when not needed but quick to act when called upon. Small changes in gene expression can lead to drastic changes in lineage commitment, cellular function, and immunity. Conventional assessment of these changes centered on the analysis of mRNA levels through a variety of methodologies, including microarrays. However, mRNA synthesis does not always correlate directly to protein synthesis and downstream functional activity. Work conducted in recent years has begun to shed light on the various posttranscriptional changes that occur in response to a dynamic external environment that a given cell type encounters. We provide a critical review of key posttranscriptional mechanisms (i.e., microRNA) and translational mechanisms of regulation of gene expression in the immune system, with a particular emphasis on these regulatory processes in various CD4(+) T cell subsets.
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Affiliation(s)
- Roman Istomine
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada;Translational Immunology Unit, Program in Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Center, Montreal, Quebec H4A 3J1, Canada; andFederation of Clinical Immunology Societies Center of Excellence, McGill University and the Research Institute of the McGill University Health Center, Montreal, Quebec H3H 2R9, Canada
| | - Nils Pavey
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada;Translational Immunology Unit, Program in Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Center, Montreal, Quebec H4A 3J1, Canada; andFederation of Clinical Immunology Societies Center of Excellence, McGill University and the Research Institute of the McGill University Health Center, Montreal, Quebec H3H 2R9, Canada
| | - Ciriaco A Piccirillo
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada;Translational Immunology Unit, Program in Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Center, Montreal, Quebec H4A 3J1, Canada; andFederation of Clinical Immunology Societies Center of Excellence, McGill University and the Research Institute of the McGill University Health Center, Montreal, Quebec H3H 2R9, Canada
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32
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Rauwerda H, Wackers P, Pagano JFB, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink HP, Jonker M, Breit TM. Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs. PLoS One 2016; 11:e0147151. [PMID: 26799215 PMCID: PMC4723340 DOI: 10.1371/journal.pone.0147151] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/28/2015] [Indexed: 12/19/2022] Open
Abstract
Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize technical interference, we used mature, unfertilized eggs from siblings. About half of the number of analyzed genes was found to be expressed as maternal RNA. The expressed and non-expressed genes showed that maternal mRNA accumulation is a non-random process, as it is related to specific biological pathways and processes relevant in early embryogenesis. Moreover, it turned out that overall the composition of the maternal transcriptome is tightly regulated as about half of the expressed genes display a less than twofold expression range between the observed minimum and maximum expression values of a gene in the experiment. Even more, the maximum gene-expression difference within clutches is for 88% of the expressed genes lower than twofold. This means that expression differences observed in maternally expressed genes are primarily caused by differences between mothers, with only limited variability between eggs from the same mother. This was underlined by the fact that 99% of the expressed genes were found to be differentially expressed between any of the mothers in an ANOVA test. Furthermore, linking chromosome location, transcription factor binding sites, and miRNA target sites of the genes in clusters of distinct and unique mother-specific gene-expression, suggest biological relevance of the mother-specific signatures in the maternal transcriptome composition. Altogether, the maternal transcriptome composition of mature zebrafish oocytes seems to be tightly regulated with a distinct mother-specific signature.
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Affiliation(s)
- Han Rauwerda
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Paul Wackers
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Johanna F. B. Pagano
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Mark de Jong
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Wim Ensink
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Rob Dekker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Ulrike Nehrdich
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Herman P. Spaink
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Martijs Jonker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Timo M. Breit
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
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Kojima S, Gendreau KL, Sher-Chen EL, Gao P, Green CB. Changes in poly(A) tail length dynamics from the loss of the circadian deadenylase Nocturnin. Sci Rep 2015; 5:17059. [PMID: 26586468 PMCID: PMC4653638 DOI: 10.1038/srep17059] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 10/21/2015] [Indexed: 12/15/2022] Open
Abstract
mRNA poly(A) tails are important for mRNA stability and translation, and enzymes that regulate the poly(A) tail length significantly impact protein profiles. There are eleven putative deadenylases in mammals, and it is thought that each targets specific transcripts, although this has not been clearly demonstrated. Nocturnin (NOC) is a unique deadenylase with robustly rhythmic expression and loss of Noc in mice (Noc KO) results in resistance to diet-induced obesity. In an attempt to identify target transcripts of NOC, we performed “poly(A)denylome” analysis, a method that measures poly(A) tail length of transcripts in a global manner, and identified 213 transcripts that have extended poly(A) tails in Noc KO liver. These transcripts share unexpected characteristics: they are short in length, have long half-lives, are actively translated, and gene ontology analyses revealed that they are enriched in functions in ribosome and oxidative phosphorylation pathways. However, most of these transcripts do not exhibit rhythmicity in poly(A) tail length or steady-state mRNA level, despite Noc’s robust rhythmicity. Therefore, even though the poly(A) tail length dynamics seen between genotypes may not result from direct NOC deadenylase activity, these data suggest that NOC exerts strong effects on physiology through direct and indirect control of target mRNAs.
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Affiliation(s)
- Shihoko Kojima
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390-9111.,Department of Biological Sciences, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA, 24061
| | - Kerry L Gendreau
- Department of Biological Sciences, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA, 24061
| | - Elaine L Sher-Chen
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390-9111
| | - Peng Gao
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390-9111
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390-9111
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Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana. PLoS Genet 2015; 11:e1005474. [PMID: 26305463 PMCID: PMC4549238 DOI: 10.1371/journal.pgen.1005474] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/28/2015] [Indexed: 11/29/2022] Open
Abstract
The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. The poly(A) tail of eukaryotic mRNAs promotes export from the nucleus, translation in the cytoplasm and stability of the mRNA, and changes in poly(A)-tail length can strongly impact on gene expression. The Arabidopsis thaliana genome encodes three nuclear canonical poly(A) polymerases (PAPS1, PAPS2, PAPS4) that fulfill different functions, presumably by preferentially polyadenylating certain subpopulations of pre-mRNAs. Here, we use a fractionation-based technique to assess the transcriptome-wide impact of reduced PAPS1 activity and identify functional classes of transcripts that are particularly sensitive to reduced PAPS1 activity. Analysis of these transcripts identifies two novel biological functions for PAPS1 in ribosome biogenesis and in redox homeostasis that we confirm experimentally. By overlaying our results with information about genome-wide co-expression, we demonstrate that genes co-expressed with PAPS1 are the most strongly affected in terms of poly(A)-tail length and total-abundance changes in the paps1 mutants. This provides strong evidence that the co-expression of these genes with PAPS1 that is seen across thousands of microarrays is at least partly caused by altered activity of the PAPS1 isoform, suggesting that the plant indeed uses modulation of the balance of isoform activities to coordinately regulate the expression of groups of genes.
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35
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Yartseva V, Giraldez AJ. The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming. Curr Top Dev Biol 2015; 113:191-232. [PMID: 26358874 DOI: 10.1016/bs.ctdb.2015.07.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cellular transitions occur at all stages of organismal life from conception to adult regeneration. Changing cellular state involves three main features: activating gene expression necessary to install the new cellular state, modifying the chromatin status to stabilize the new gene expression program, and removing existing gene products to clear out the previous cellular program. The maternal-to-zygotic transition (MZT) is one of the most profound changes in the life of an organism. It involves gene expression remodeling at all levels, including the active clearance of the maternal oocyte program to adopt the embryonic totipotency. In this chapter, we provide an overview of molecular mechanisms driving maternal mRNA clearance during the MZT, describe the developmental consequences of losing components of this gene regulation, and illustrate how remodeling of gene expression during the MZT is common to other cellular transitions with parallels to cellular reprogramming.
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Affiliation(s)
- Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.
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36
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Weiss B, Curran JA. CAP(+) selection: A combined chemical-enzymatic strategy for efficient eukaryotic messenger RNA enrichment via the 5' cap. Anal Biochem 2015; 484:72-4. [PMID: 25963893 DOI: 10.1016/j.ab.2015.04.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
Abstract
Eukaryotic messenger RNAs (mRNAs) are generally enriched using oligo(dT) selection. However, a significant fraction of mRNAs contain either short or no poly(A). Our technique permits the isolation of mRNAs via their unique biochemical feature, the 5' cap. It involves RNA extraction, blocking of the 3' ribose cis-diol by cordycepin, oxidation of the 5' cis-diol of the CAP to a dialdehyde, coupling to a biotinylated linker, and enrichment on a streptavidin affinity matrix. We demonstrate that it efficiently pulls out a synthetic capped and non-polyadenylated transcript used to spike total cell RNA as well as endogenous histone 3c mRNA reported to be poly(A) negative.
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Affiliation(s)
- Benjamin Weiss
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Joseph A Curran
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CH-1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, CH-1211 Geneva, Switzerland.
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Abe KI, Yamamoto R, Franke V, Cao M, Suzuki Y, Suzuki MG, Vlahovicek K, Svoboda P, Schultz RM, Aoki F. The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3' processing. EMBO J 2015; 34:1523-37. [PMID: 25896510 DOI: 10.15252/embj.201490648] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/19/2015] [Indexed: 12/18/2022] Open
Abstract
Initiation of zygotic transcription in mammals is poorly understood. In mice, zygotic transcription is first detected shortly after pronucleus formation in 1-cell embryos, but the identity of the transcribed loci and mechanisms regulating their expression are not known. Using total RNA-Seq, we have found that transcription in 1-cell embryos is highly promiscuous, such that intergenic regions are extensively expressed and thousands of genes are transcribed at comparably low levels. Striking is that transcription can occur in the absence of defined core-promoter elements. Furthermore, accumulation of translatable zygotic mRNAs is minimal in 1-cell embryos because of inefficient splicing and 3' processing of nascent transcripts. These findings provide novel insights into regulation of gene expression in 1-cell mouse embryos that may confer a protective mechanism against precocious gene expression that is the product of a relaxed chromatin structure present in 1-cell embryos. The results also suggest that the first zygotic transcription itself is an active component of chromatin remodeling in 1-cell embryos.
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Affiliation(s)
- Ken-Ichiro Abe
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Ryoma Yamamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Vedran Franke
- Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia
| | - Minjun Cao
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan The University of Tokyo, Tokyo, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia Department of Informatics, University of Oslo, Oslo, Norway
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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38
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Hajjawi OS. Ribonucleic acid (RNA) biosynthesis in human cancer. Cancer Cell Int 2015; 15:22. [PMID: 25717284 PMCID: PMC4339644 DOI: 10.1186/s12935-015-0167-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/20/2015] [Indexed: 12/28/2022] Open
Abstract
In many respects, the most remarkable chemical substances within the genome of eukaryotic cells are remarkable proteins which are the critical structural and functional units of living cells. The specifications for everything that goes in the cell are natural digital-to-digital decoding process in an archive sequence by deoxyribonucleic acid (DNA) and an articulate construction by ribonucleic acid (RNA). The products of DNA transcription are long polymers of ribonucleotides rather than deoxyribonucleotides and are termed ribonucleic acids. Certain deoxyribonucleotide sequences, or genes, give rise to transfer RNA (tRNA) and other ribosomal RNA (rRNA) when transcribed. The ribonucleotide sequences fold extensively and rRNA is associated with specific proteins to yield the essential cell components, ribosomes. Transcription of other special sequences yields messenger RNAs (mRNAs) that contain ribonucleotide sequences that will be ultimately translated into new types of amino acid sequences of functional cellular protein molecules. This switch to a different variety of cellular molecular sequences is complex, but each sequence of the three ribonucleotides specifies the insertion of one particular amino acid into the polypeptide chain under production. Whilst mRNA is considered the vehicle by which genetic information is transmitted from the genome and allocated in the appropriate cytoplasmic sites for translation into protein via cap-dependent mechanism, the actual translation depends also on the presence of other so-called household and luxury protein molecules. Recent evidence suggests RNA species are required at initiation, because treatment of cells with antibiotics or drugs that inhibit RNA synthesis cause a decrease in protein synthesis. The rRNA is necessary as a structural constituent of the ribosomes upon which translation takes place, whereas tRNA is necessary as an adaptor in amino acid activation and elongation protein chains to ribosomes. In this article, we review malignant tumor, with stem like properties, and recent technical advances into the phenomenon of micro-particles and micro-vesicles containing cell-free nucleic acids that circulate plasma. New areas of research have been opened into screening tumor telomerase progression, prognosis of aptamers targeting cell surface, monitoring the efficacy of anticancer therapies, oncogenic transformation of host cell, and RNA polymerases role in the cell cycle progression and differentiation.
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Affiliation(s)
- Omar S Hajjawi
- Department of Biology, Arab American University, P. O. Box 240, Jenin, Israeli Occupied Territories of Palestine
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Grabek KR, Diniz Behn C, Barsh GS, Hesselberth JR, Martin SL. Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator. eLife 2015; 4. [PMID: 25626169 PMCID: PMC4383249 DOI: 10.7554/elife.04517] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 12/23/2014] [Indexed: 12/21/2022] Open
Abstract
During hibernation, animals cycle between torpor and arousal. These cycles involve
dramatic but poorly understood mechanisms of dynamic physiological regulation at the
level of gene expression. Each cycle, Brown Adipose Tissue (BAT) drives periodic
arousal from torpor by generating essential heat. We applied digital transcriptome
analysis to precisely timed samples to identify molecular pathways that underlie the
intense activity cycles of hibernator BAT. A cohort of transcripts increased during
torpor, paradoxical because transcription effectively ceases at these low
temperatures. We show that this increase occurs not by elevated transcription but
rather by enhanced stabilization associated with maintenance and/or extension of long
poly(A) tails. Mathematical modeling further supports a temperature-sensitive
mechanism to protect a subset of transcripts from ongoing bulk degradation instead of
increased transcription. This subset was enriched in a C-rich motif and genes
required for BAT activation, suggesting a model and mechanism to prioritize
translation of key proteins for thermogenesis. DOI:http://dx.doi.org/10.7554/eLife.04517.001 Many mammals hibernate to avoid food scarcity and harsh conditions during winter.
Hibernation involves entering a state called torpor, which drastically reduces the
amount of energy used by the body. During torpor, body temperature also decreases.
This is particularly exemplified in ground squirrels, whose body temperature can
hover at just above or even below the point of freezing. However, hibernating mammals
cannot remain in this state continuously over the months of hibernation but instead
cycle between bouts of torpor lasting for 1–3 weeks and brief periods of
‘arousal’ lasting between 12–24 hr, during which their body
rapidly warms up. The heat required to start warming up the hibernator is generated from a specialized
form of fat called brown adipose tissue. Normally, the bursts of metabolic activity
that are required to create this heat depend on certain proteins being produced.
Making a protein involves ‘translating’ its sequence from template
molecules called messenger RNA (mRNA), which are ‘transcribed’ from the
gene that encodes the protein. During the low body temperatures experienced during
torpor, both of these processes stop. So how is the hibernator able to quickly and
efficiently heat itself up during the arousal periods of hibernation? Grabek et al. investigated this by analyzing the relative levels of mRNA in the brown
adipose tissue of hibernating 13-lined ground squirrels. Using a special technique to
sample and sequence small fragments of mRNA taken from brown adipose tissue, Grabek
et al. compiled a profile of the mRNA molecules present at different points in the
torpor–arousal cycle and compared this with a similar profile taken from
squirrels that were not hibernating. From this analysis, Grabek et al. detected that a particular group of mRNA molecules
that are required for producing heat increase in abundance during torpor, even though
body temperature is low enough to stop gene transcription. This increased abundance
does not occur because more of the mRNA molecules are made; instead, the mRNA
molecules are modified to become more stable and long lasting. Once the animal warms
up during arousal, gene transcription is reactivated and more new mRNA molecules are
made. Grabek et al. suggest that the key mRNAs required for brown adipose tissue function
are selectively stabilized during torpor through a temperature-dependent protective
mechanism. These mRNAs are then preferentially translated into proteins during
arousal to rapidly and efficiently heat the hibernator. Most other mRNA molecules
degrade throughout torpor, and so their numbers decline as replacements are not
transcribed until body temperature briefly recovers during arousal. Whether this
protective mechanism is also used in other tissues during torpor remains a question
for future work. DOI:http://dx.doi.org/10.7554/eLife.04517.002
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Affiliation(s)
- Katharine R Grabek
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Cecilia Diniz Behn
- Department of Applied Math and Statistics, Colorado School of Mines, Golden, United States
| | - Gregory S Barsh
- Department of Research, HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - Jay R Hesselberth
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Sandra L Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
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40
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Yin QF, Chen LL, Yang L. Fractionation of non-polyadenylated and ribosomal-free RNAs from mammalian cells. Methods Mol Biol 2015; 1206:69-80. [PMID: 25240887 DOI: 10.1007/978-1-4939-1369-5_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Most of mRNAs and well-characterized long noncoding RNAs are shaped with 5' cap and 3' poly(A) tail. Thereby, conventional transcriptome analysis typically involved the enrichment of poly(A)+ RNAs by oligo(dT) selection. However, accumulated lines of evidence suggest that there are many RNA transcripts processed in alternative ways, which largely failed to be detected by oligo(dT) purification. Here, we describe an enrichment strategy to purify non-polyadenylated (poly(A)-/ribo-) RNAs from total RNAs by removal of poly(A)+ RNA transcripts and ribosomal RNAs. In the combination with high-throughput sequencing methods, this strategy has been successfully applied to identify the rich repertoire of non-polyadenylated RNAs in vivo.
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Affiliation(s)
- Qing-Fei Yin
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
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41
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Abstract
The poly(A) tail is found on the 3'-end of most eukaryotic mRNAs, and its length significantly contributes to the mRNAs half-life and translational competence. Circadian regulation of poly(A)-tail length is a powerful mechanism to confer rhythmicity in gene expression posttranscriptionally and provides a means to regulate protein levels independent of rhythmic transcription in the nucleus. Therefore, analysis of circadian poly(A)-tail length regulation is important for a complete understanding of rhythmic physiology, since rhythmically expressed proteins are the ultimate mediators of rhythmic function. Nevertheless, it has previously been challenging to measure changes in poly(A)-tail length, especially at a global level, due to technical constraints. However, new methodology depending on differential fractionation of mRNAs depending on the length of their tails has recently been developed. In this chapter, we describe these methods as used for examining the circadian regulation of poly(A)-tail length and provide detailed experimental procedures to measure poly(A)-tail length both at a the single mRNA level and the global level. Although this chapter concentrates on methods we used for analyzing poly(A)-tail length in the mammalian circadian system, the methods described here can be applicable to any organisms and any biological processes.
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Affiliation(s)
- Shihoko Kojima
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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42
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Hrit J, Raynard N, Van Etten J, Sankar K, Petterson A, Goldstrohm AC. In vitro analysis of RNA degradation catalyzed by deadenylase enzymes. Methods Mol Biol 2014; 1125:325-39. [PMID: 24590800 DOI: 10.1007/978-1-62703-971-0_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this chapter, we describe a method for purification and analysis of the enzymatic activity of deadenylase enzymes. Nearly all eukaryotic messenger RNAs are modified at the 3' end by the addition of an adenosine polymer: the poly-adenosine tail. The poly(A) tail plays a central role in protein expression and mRNA fate. The poly(A) tail promotes translation of the mRNA. Shortening of the poly(A) tail, referred to as deadenylation, reduces protein synthesis and initiates destruction of the mRNA. A specialized class of exoribonucleases, called deadenylase enzymes, carries out this process. Deadenylases are found throughout eukarya, but their functions remain largely unexplored. We present a detailed protocol to analyze deadenylase activity in vitro. First, recombinant deadenylase enzyme is over-expressed and purified from bacteria. Next, labeled RNA substrate is prepared. Deadenylation reactions are performed, and reaction products are analyzed by denaturing gel electrophoresis. Reaction rates are then determined quantitatively. Crucial controls and experimental parameters are described along with practical tips that promote success.
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Affiliation(s)
- Joel Hrit
- Genetics Training Program, Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Dr., Room 5301 MSRB3, SPC 5606, Ann Arbor, MI, 48109, USA
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43
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Jalkanen AL, Coleman SJ, Wilusz J. Determinants and implications of mRNA poly(A) tail size--does this protein make my tail look big? Semin Cell Dev Biol 2014; 34:24-32. [PMID: 24910447 DOI: 10.1016/j.semcdb.2014.05.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 05/31/2014] [Indexed: 12/22/2022]
Abstract
While the phenomenon of polyadenylation has been well-studied, the dynamics of poly(A) tail size and its impact on transcript function and cell biology are less well-appreciated. The goal of this review is to encourage readers to view the poly(A) tail as a dynamic, changeable aspect of a transcript rather than a simple static entity that marks the 3' end of an mRNA. This could open up new angles of regulation in the post-transcriptional control of gene expression throughout development, differentiation and cancer.
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Affiliation(s)
- Aimee L Jalkanen
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Stephen J Coleman
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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44
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Simultaneous isolation of mRNA and native protein from minute samples of cells. Biotechniques 2014; 56:229-37. [PMID: 24806223 DOI: 10.2144/000114165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 03/04/2014] [Indexed: 11/23/2022] Open
Abstract
Precious biological samples often lack a sufficient number of cells for multiple procedures, such as extraction of mRNA while maintaining protein in a non-denatured state suitable for subsequent characterization. Here we present a new method for the simultaneous purification of mRNA and native proteins from samples containing small numbers of cells. Our approach utilizes oligodeoxythymidylate [oligo(dT)25]-coated paramagnetic beads in an optimized reaction buffer to isolate mRNA comparable in quantity and quality to mRNA isolated with existing methods, while maintaining the proteins in their native state for traditional protein assays. We validated the procedure using neonatal rat ovaries and small numbers of human granulosa cells, demonstrating the extraction of mRNA suitable for gene expression analysis with simultaneous isolation of native proteins suitable for downstream characterization using different protein assays.
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45
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Zheng D, Tian B. Sizing up the poly(A) tail: insights from deep sequencing. Trends Biochem Sci 2014; 39:255-7. [PMID: 24751511 DOI: 10.1016/j.tibs.2014.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 11/19/2022]
Abstract
Global investigation of poly(A) tails has been hindered by technical challenges. In a recent advance, two groups developed deep sequencing methods to globally interrogate poly(A) tail length and sequence with high precision, opening new avenues for investigation of poly(A) tail functions in mRNA metabolism. Initial applications of these methods reveal insights into the relationship between poly(A) tail length and translational efficiency, and identify widespread uridylation and guanylation at the 3' ends of transcripts.
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Affiliation(s)
- Dinghai Zheng
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Bin Tian
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ 07103.
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46
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Chang H, Lim J, Ha M, Kim VN. TAIL-seq: genome-wide determination of poly(A) tail length and 3' end modifications. Mol Cell 2014; 53:1044-52. [PMID: 24582499 DOI: 10.1016/j.molcel.2014.02.007] [Citation(s) in RCA: 318] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/23/2013] [Accepted: 02/03/2014] [Indexed: 01/05/2023]
Abstract
Global investigation of the 3' extremity of mRNA (3'-terminome), despite its importance in gene regulation, has not been feasible due to technical challenges associated with homopolymeric sequences and relative paucity of mRNA. We here develop a method, TAIL-seq, to sequence the very end of mRNA molecules. TAIL-seq allows us to measure poly(A) tail length at the genomic scale. Median poly(A) length is 50-100 nt in HeLa and NIH 3T3 cells. Poly(A) length correlates with mRNA half-life, but not with translational efficiency. Surprisingly, we discover widespread uridylation and guanylation at the downstream of poly(A) tail. The U tails are generally attached to short poly(A) tails (<25 nt), while the G tails are found mainly on longer poly(A) tails (>40 nt), implicating their generic roles in mRNA stability control. TAIL-seq is a potent tool to dissect dynamic control of mRNA turnover and translational control, and to discover unforeseen features of RNA cleavage and tailing.
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Affiliation(s)
- Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Minju Ha
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.
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47
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Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 2014; 508:66-71. [PMID: 24476825 PMCID: PMC4086860 DOI: 10.1038/nature13007] [Citation(s) in RCA: 446] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 12/23/2013] [Indexed: 12/16/2022]
Abstract
Poly(A) tails enhance the stability and translation of most eukaryotic
mRNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded
greater understanding of poly(A)-tail function. Here, we describe poly(A)-tail
length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of
millions of individual RNAs isolated from yeasts, cell lines,
Arabidopsis leaves, mouse liver, and zebrafish and frog
embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with
mRNAs encoding ribosomal proteins and other “housekeeping”
proteins tending to have shorter tails. As expected, tail lengths were coupled
to translational efficiency in early zebrafish and frog embryos. However, this
strong coupling diminished at gastrulation and was absent in non-embryonic
samples, indicating a rapid developmental switch in the nature of translational
control. This switch complements an earlier switch to zygotic transcriptional
control and explains why the predominant effect of microRNA-mediated
deadenylation concurrently shifts from translational repression to mRNA
destabilization.
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48
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Charlesworth A, Meijer HA, de Moor CH. Specificity factors in cytoplasmic polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:437-61. [PMID: 23776146 PMCID: PMC3736149 DOI: 10.1002/wrna.1171] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/12/2022]
Abstract
Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3' untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man.
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Affiliation(s)
- Amanda Charlesworth
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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49
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Abstract
Messenger RNA deadenylation is a process that allows rapid regulation of gene expression in response to different cellular conditions. The change of the mRNA poly(A) tail length by the activation of deadenylation might regulate gene expression by affecting mRNA stability, mRNA transport, or translation initiation. Activation of deadenylation processes are highly regulated and associated with different cellular conditions such as cancer, development, mRNA surveillance, DNA damage response, and cell differentiation. In the last few years, new technologies for studying deadenylation have been developed. Here we overview concepts related to deadenylation and its regulation in eukaryotic cells. We also describe some of the most commonly used protocols to study deadenylation in eukaryotic cells.
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Affiliation(s)
- Xiaokan Zhang
- Department of Chemistry, Hunter College and Graduate Center, City University of New York, 10065, New York, NY, USA
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50
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Mezan S, Ashwal-Fluss R, Shenhav R, Garber M, Kadener S. Genome-wide assessment of post-transcriptional control in the fly brain. Front Mol Neurosci 2013; 6:49. [PMID: 24367289 PMCID: PMC3856366 DOI: 10.3389/fnmol.2013.00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/20/2013] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional control of gene expression has central importance during development and adulthood and in physiology in general. However, little is known about the extent of post-transcriptional control of gene expression in the brain. Most post-transcriptional regulatory effectors (e.g., miRNAs) destabilize target mRNAs by shortening their polyA tails. Hence, the fraction of a given mRNA that it is fully polyadenylated should correlate with its stability and serves as a good measure of post-transcriptional control. Here, we compared RNA-seq datasets from fly brains that were generated either from total (rRNA-depleted) or polyA-selected RNA. By doing this comparison we were able to compute a coefficient that measures the extent of post-transcriptional control for each brain-expressed mRNA. In agreement with current knowledge, we found that mRNAs encoding ribosomal proteins, metabolic enzymes, and housekeeping genes are among the transcripts with least post-transcriptional control, whereas mRNAs that are known to be highly unstable, like circadian mRNAs and mRNAs expressing synaptic proteins and proteins with neuronal functions, are under strong post-transcriptional control. Surprisingly, the latter group included many specific groups of genes relevant to brain function and behavior. In order to determine the importance of miRNAs in this regulation, we profiled miRNAs from fly brains using oligonucleotide microarrays. Surprisingly, we did not find a strong correlation between the expression levels of miRNAs in the brain and the stability of their target mRNAs; however, genes identified as highly regulated post-transcriptionally were strongly enriched for miRNA targets. This demonstrates a central role of miRNAs for modulating the levels and turnover of brain-specific mRNAs in the fly.
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Affiliation(s)
- Shaul Mezan
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Reut Ashwal-Fluss
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Rom Shenhav
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School Worcester, MA, USA
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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