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Pelletier OB, Brunori G, Wang Y, Robishaw JD. Post-transcriptional regulation and subcellular localization of G-protein γ7 subunit: implications for striatal function and behavioral responses to cocaine. Front Neuroanat 2024; 18:1394659. [PMID: 38764487 PMCID: PMC11100332 DOI: 10.3389/fnana.2024.1394659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/17/2024] [Indexed: 05/21/2024] Open
Abstract
The striatal D1 dopamine receptor (D1R) and A2a adenosine receptor (A2aR) signaling pathways play important roles in drug-related behaviors. These receptors activate the Golf protein comprised of a specific combination of αolfβ2γ7 subunits. During assembly, the γ7 subunit sets the cellular level of the Golf protein. In turn, the amount of Golf protein determines the collective output from both D1R and A2aR signaling pathways. This study shows the Gng7 gene encodes multiple γ7 transcripts differing only in their non-coding regions. In striatum, Transcript 1 is the predominant isoform. Preferentially expressed in the neuropil, Transcript 1 is localized in dendrites where it undergoes post-transcriptional regulation mediated by regulatory elements in its 3' untranslated region that contribute to translational suppression of the γ7 protein. Earlier studies on gene-targeted mice demonstrated loss of γ7 protein disrupts assembly of the Golf protein. In the current study, morphological analysis reveals the loss of the Golf protein is associated with altered dendritic morphology of medium spiny neurons. Finally, behavioral analysis of conditional knockout mice with cell-specific deletion of the γ7 protein in distinct populations of medium spiny neurons reveals differential roles of the Golf protein in mediating behavioral responses to cocaine. Altogether, these findings provide a better understanding of the regulation of γ7 protein expression, its impact on Golf function, and point to a new potential target and mechanisms for treating addiction and related disorders.
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Affiliation(s)
- Oliver B. Pelletier
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, United States
| | - Gloria Brunori
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, United States
| | - Yingcai Wang
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, United States
| | - Janet D. Robishaw
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, United States
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
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2
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Li B, Hu P, Liu K, Xu W, Wang J, Li Q, Chen B, Deng Y, Han C, Sun T, Liu X, Li M, Wang T, Liu J, Lin H, Rao K. MiRNA-100 ameliorates diabetes mellitus-induced erectile dysfunction by modulating autophagy, anti-inflammatory, and antifibrotic effects. Andrology 2024. [PMID: 38227138 DOI: 10.1111/andr.13586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/12/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Diabetes mellitus-induced erectile dysfunction (DMED) has become a common disease in adult men that can seriously reduce the quality of life of patients, and new therapies are urgently needed. miRNA-100 has many targets and can induce autophagy and reduce fibrosis by inhibiting the mTOR pathway and the TGF-β pathway. However, no research has been conducted with miR-100 in the field of DMED, and the specific mechanism of action is still unclear. OBJECTIVES To ascertain the effects of miR-100 on corpus cavernosum tissue of DMED rats and vascular endothelial cells in a high glucose environment and to elucidate the relevant mechanisms in autophagy, fibrosis and inflammation to find a new approach for the DMED therapy. METHODS Thirty rats were divided into three groups: the control group, the DMED group, and the DMED + miR-100 group. Using intraperitoneal injections of streptozotocin, all rats except the control group were modeled with diabetes mellitus, which was verified using the apomorphine (APO) test. For rats in the DMED + miR-100 group, rno-miR-100-5p agomir (50 nmol/kg, every 2 days, 6 times in total) was injected via the tail vein. After 13 weeks, the erectile function of each rat was assessed using cavernous manometry, and the corpus cavernosum tissue was harvested for subsequent experiments. For cellular experiments, human coronary microartery endothelial cells (HCMEC) were divided into four groups: the control group, the high-glucose (HG, 40 mM) group, the HG + mimic group, and the HG + inhibitor group. The cells were cultured for 6 days and collected for subsequent experiments 2 days after transfection. RESULTS Diabetic modeling impaired the erectile function in rats, and miR-100 reversed this effect. By measuring autophagy-related proteins such as mTOR/Raptor/Beclin1/p62/LC3B, we found that miR-100 could suppress the expression of mTOR and induce autophagy. The analysis of the eNOS/NO/cGMP axis function indicated that impaired endothelial function was improved by miR-100. By evaluating the TGF-β1/CTGF/Smad2/3 and NF-κB/TNF-α pathways, we found that miR-100 could lower the level of inflammation and fibrosis, which contributed to the improvement of the erectile function. Cellular experiments can be used as supporting evidence for these findings. CONCLUSION MiR-100 can improve the erectile function by inhibiting mTOR and thus inducing autophagy, improving the endothelial function through the eNOS/NO/cGMP axis, and exerting antifibrotic and anti-inflammatory effects, which may provide new ideas and directions for the treatment of DMED.
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Affiliation(s)
- Beining Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenchao Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaxin Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinyu Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bingliang Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxuan Deng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenglin Han
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Taotao Sun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinqi Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingchao Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huang Lin
- Department of Urology, Fujian Provincial Hospital, Fuzhou, China
- Department of Urology, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Ke Rao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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3
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Kozlov EN, Deev RV, Tokmatcheva EV, Tvorogova A, Kachaev ZM, Gilmutdinov RA, Zhukova M, Savvateeva-Popova EV, Schedl P, Shidlovskii YV. 3'UTR of mRNA Encoding CPEB Protein Orb2 Plays an Essential Role in Intracellular Transport in Neurons. Cells 2023; 12:1717. [PMID: 37443751 PMCID: PMC10340461 DOI: 10.3390/cells12131717] [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: 04/30/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Intracellular trafficking plays a critical role in the functioning of highly polarized cells, such as neurons. Transport of mRNAs, proteins, and other molecules to synaptic terminals maintains contact between neurons and ensures the transmission of nerve impulses. Cytoplasmic polyadenylation element binding (CPEB) proteins play an essential role in long-term memory (LTM) formation by regulating local translation in synapses. Here, we show that the 3'UTR of the Drosophila CPEB gene orb2 is required for targeting the orb2 mRNA and protein to synapses and that this localization is important for LTM formation. When the orb2 3'UTR is deleted, the orb2 mRNAs and proteins fail to localize in synaptic fractions, and pronounced LTM deficits arise. We found that the phenotypic effects of the orb2 3'UTR deletion were rescued by introducing the 3'UTR from the orb, another Drosophila CPEB gene. In contrast, the phenotypic effects of the 3'UTR deletion were not rescued by the 3'UTR from one of the Drosophila α-tubulin genes. Our results show that the orb2 mRNAs must be targeted to the correct locations in neurons and that proper targeting depends upon sequences in the 3'UTR.
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Affiliation(s)
- Eugene N. Kozlov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (E.N.K.); (R.V.D.); (Z.M.K.); (R.A.G.); (M.Z.); (P.S.)
| | - Roman V. Deev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (E.N.K.); (R.V.D.); (Z.M.K.); (R.A.G.); (M.Z.); (P.S.)
| | - Elena V. Tokmatcheva
- Institute of Physiology, Russian Academy of Sciences, 188680 St. Petersburg, Russia; (E.V.T.); (E.V.S.-P.)
| | - Anna Tvorogova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Zaur M. Kachaev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (E.N.K.); (R.V.D.); (Z.M.K.); (R.A.G.); (M.Z.); (P.S.)
| | - Rudolf A. Gilmutdinov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (E.N.K.); (R.V.D.); (Z.M.K.); (R.A.G.); (M.Z.); (P.S.)
| | - Mariya Zhukova
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (E.N.K.); (R.V.D.); (Z.M.K.); (R.A.G.); (M.Z.); (P.S.)
| | - Elena V. Savvateeva-Popova
- Institute of Physiology, Russian Academy of Sciences, 188680 St. Petersburg, Russia; (E.V.T.); (E.V.S.-P.)
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (E.N.K.); (R.V.D.); (Z.M.K.); (R.A.G.); (M.Z.); (P.S.)
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (E.N.K.); (R.V.D.); (Z.M.K.); (R.A.G.); (M.Z.); (P.S.)
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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4
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Vlasenok M, Margasyuk S, Pervouchine DD. Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation. NAR Genom Bioinform 2023; 5:lqad051. [PMID: 37260513 PMCID: PMC10227441 DOI: 10.1093/nargab/lqad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023] Open
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) are two crucial steps in the post-transcriptional regulation of eukaryotic gene expression. Protocols capturing and sequencing RNA 3'-ends have uncovered widespread intronic polyadenylation (IPA) in normal and disease conditions, where it is currently attributed to stochastic variations in the pre-mRNA processing. Here, we took advantage of the massive amount of RNA-seq data generated by the Genotype Tissue Expression project (GTEx) to simultaneously identify and match tissue-specific expression of intronic polyadenylation sites with tissue-specific splicing. A combination of computational methods including the analysis of short reads with non-templated adenines revealed that APA events are more abundant in introns than in exons. While the rate of IPA in composite terminal exons and skipped terminal exons expectedly correlates with splicing, we observed a considerable fraction of IPA events that lack AS support and attributed them to spliced polyadenylated introns (SPI). We hypothesize that SPIs represent transient byproducts of a dynamic coupling between APA and AS, in which the spliceosome removes the intron while it is being cleaved and polyadenylated. These findings indicate that cotranscriptional pre-mRNA splicing could serve as a rescue mechanism to suppress premature transcription termination at intronic polyadenylation sites.
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Affiliation(s)
- Maria Vlasenok
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar 30, Moscow 121205, Russia
| | - Sergey Margasyuk
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar 30, Moscow 121205, Russia
| | - Dmitri D Pervouchine
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar 30, Moscow 121205, Russia
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5
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Mattick JS. RNA out of the mist. Trends Genet 2023; 39:187-207. [PMID: 36528415 DOI: 10.1016/j.tig.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
Abstract
RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia; UNSW RNA Institute, UNSW, Sydney, NSW 2052, Australia.
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6
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Li B, Ding T, Chen H, Li C, Chen B, Xu X, Huang P, Hu F, Guo L. CircStrn3 targeting microRNA-9-5p is involved in the regulation of cartilage degeneration and subchondral bone remodelling in osteoarthritis. Bone Joint Res 2023; 12:33-45. [PMID: 36642417 PMCID: PMC9872037 DOI: 10.1302/2046-3758.121.bjr-2022-0231.r1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
AIMS Circular RNA (circRNA) is involved in the regulation of articular cartilage degeneration induced by inflammatory factors or oxidative stress. In a previous study, we found that the expression of circStrn3 was significantly reduced in chondrocytes of osteoarthritis (OA) patients and OA mice. Therefore, the aim of this paper was to explore the role and mechanism of circStrn3 in osteoarthritis. METHODS Minus RNA sequencing, fluorescence in situ hybridization, and quantitative real-time polymerase chain reaction (qRT-PCR) were used to detect the expression of circStrn3 in human and mouse OA cartilage tissues and chondrocytes. Chondrocytes were then stimulated to secrete exosomal miR-9-5p by cyclic tensile strain. Intra-articular injection of exosomal miR-9-5p into the model induced by destabilized medial meniscus (DMM) surgery was conducted to alleviate OA progression. RESULTS Tensile strain could decrease the expression of circStrn3 in chondrocytes. CircStrn3 expression was significantly decreased in human and mouse OA cartilage tissues and chondrocytes. CircStrn3 could inhibit matrix metabolism of chondrocytes through competitively 'sponging' miRNA-9-5p targeting Kruppel-like factor 5 (KLF5), indicating that the decrease in circStrn3 might be a protective factor in mechanical instability-induced OA. The tensile strain stimulated chondrocytes to secrete exosomal miR-9-5p. Exosomes with high miR-9-5p expression from chondrocytes could inhibit osteoblast differentiation by targeting KLF5. Intra-articular injection of exosomal miR-9-5p alleviated the progression of OA induced by destabilized medial meniscus surgery in mice. CONCLUSION Taken together, these results demonstrate that reduction of circStrn3 causes an increase in miR-9-5p, which acts as a protective factor in mechanical instability-induced OA, and provides a novel mechanism of communication among joint components and a potential application for the treatment of OA.Cite this article: Bone Joint Res 2023;12(1):33-45.
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Affiliation(s)
- Bin Li
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Ding
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoyi Chen
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changwei Li
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Chen
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing Xu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Huang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fangqiong Hu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Guo
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Lei Guo. E-mail:
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7
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Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential. Mol Cell 2022; 82:3840-3855.e8. [PMID: 36270248 PMCID: PMC9636002 DOI: 10.1016/j.molcel.2022.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/13/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
The use of alternative promoters, splicing, and cleavage and polyadenylation (APA) generates mRNA isoforms that expand the diversity and complexity of the transcriptome. Here, we uncovered thousands of previously undescribed 5' uncapped and polyadenylated transcripts (5' UPTs). We show that these transcripts resist exonucleases due to a highly structured RNA and N6-methyladenosine modification at their 5' termini. 5' UPTs appear downstream of APA sites within their host genes and are induced upon APA activation. Strong enrichment in polysomal RNA fractions indicates 5' UPT translational potential. Indeed, APA promotes downstream translation initiation, non-canonical protein output, and consistent changes to peptide presentation at the cell surface. Lastly, we demonstrate the biological importance of 5' UPTs using Bcl2, a prominent anti-apoptotic gene whose entire coding sequence is a 5' UPT generated from 5' UTR-embedded APA sites. Thus, APA is not only accountable for terminating transcripts, but also for generating downstream uncapped RNAs with translation potential and biological impact.
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8
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Ueno D, Yamasaki S, Sadakiyo Y, Teruyama T, Demura T, Kato K. Sequence features around cleavage sites are highly conserved among different species and a critical determinant for RNA cleavage position across eukaryotes. J Biosci Bioeng 2022; 134:450-461. [PMID: 36137896 DOI: 10.1016/j.jbiosc.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 10/14/2022]
Abstract
RNA degradation is one of the critical steps for control of gene expression, and endonucleolytic cleavage-dependent RNA degradation is conserved among eukaryotes. Some cleavage sites are secondarily capped in the cytoplasm and identified using the Cap analysis of gene expression (CAGE) method. Although uncapped cleavage sites are widespread in eukaryotes, comparatively little information has been obtained about these sites using CAGE-based degradome analysis. Previously, we developed the truncated RNA-end sequencing (TREseq) method in plant species and used it to acquire comprehensive information about uncapped cleavage sites; we observed G-rich sequences near cleavage sites. However, it remains unclear whether this finding is general to other eukaryotes. In this study, we conducted TREseq analyses in fruit flies (Drosophila melanogaster) and budding yeast (Saccharomyces cerevisiae). The results revealed specific sequence features related to RNA cleavage in D. melanogaster and S. cerevisiae that were similar to sequence patterns in Arabidopsis thaliana. Although previous studies suggest that ribosome movements are important for determining cleavage position, feature selection using a random forest classifier showed that sequences around cleavage sites were major determinant for cleaved or uncleaved sites. Together, our results suggest that sequence features around cleavage sites are critical for determining cleavage position, and that sequence-specific endonucleolytic cleavage-dependent RNA degradation is highly conserved across eukaryotes.
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Affiliation(s)
- Daishin Ueno
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shotaro Yamasaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yuta Sadakiyo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Takumi Teruyama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Ko Kato
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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9
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Chan JJ, Zhang B, Chew XH, Salhi A, Kwok ZH, Lim CY, Desi N, Subramaniam N, Siemens A, Kinanti T, Ong S, Sanchez-Mejias A, Ly PT, An O, Sundar R, Fan X, Wang S, Siew BE, Lee KC, Chong CS, Lieske B, Cheong WK, Goh Y, Fam WN, Ooi MG, Koh BTH, Iyer SG, Ling WH, Chen J, Yoong BK, Chanwat R, Bonney GK, Goh BKP, Zhai W, Fullwood MJ, Wang W, Tan KK, Chng WJ, Dan YY, Pitt JJ, Roca X, Guccione E, Vardy LA, Chen L, Gao X, Chow PKH, Yang H, Tay Y. Pan-cancer pervasive upregulation of 3' UTR splicing drives tumourigenesis. Nat Cell Biol 2022; 24:928-939. [PMID: 35618746 PMCID: PMC9203280 DOI: 10.1038/s41556-022-00913-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/07/2022] [Indexed: 11/15/2022]
Abstract
Most mammalian genes generate messenger RNAs with variable untranslated regions (UTRs) that are important post-transcriptional regulators. In cancer, shortening at 3′ UTR ends via alternative polyadenylation can activate oncogenes. However, internal 3′ UTR splicing remains poorly understood as splicing studies have traditionally focused on protein-coding alterations. Here we systematically map the pan-cancer landscape of 3′ UTR splicing and present this in SpUR (http://www.cbrc.kaust.edu.sa/spur/home/). 3′ UTR splicing is widespread, upregulated in cancers, correlated with poor prognosis and more prevalent in oncogenes. We show that antisense oligonucleotide-mediated inhibition of 3′ UTR splicing efficiently reduces oncogene expression and impedes tumour progression. Notably, CTNNB1 3′ UTR splicing is the most consistently dysregulated event across cancers. We validate its upregulation in hepatocellular carcinoma and colon adenocarcinoma, and show that the spliced 3′ UTR variant is the predominant contributor to its oncogenic functions. Overall, our study highlights the importance of 3′ UTR splicing in cancer and may launch new avenues for RNA-based anti-cancer therapeutics. Chan et al. report that 3′ UTR splicing is widespread and enhanced across different cancer types and is associated with more advanced tumour progression.
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Affiliation(s)
- Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xiao Hong Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Adil Salhi
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA, USA
| | - Chun You Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ng Desi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Nagavidya Subramaniam
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore, Singapore
| | - Angela Siemens
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,The University of British Columbia, Vancouver, British Columbia, Canada
| | - Tyas Kinanti
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shane Ong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Avencia Sanchez-Mejias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Integra Therapeutics S.L., Barcelona, Spain
| | - Phuong Thao Ly
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Raghav Sundar
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
| | - Xiaonan Fan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shi Wang
- Department of Pathology, National University Health System, Singapore, Singapore
| | - Bei En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kuok Chung Lee
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Choon Seng Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Bettina Lieske
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wai-Kit Cheong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Yufen Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wee Nih Fam
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Melissa G Ooi
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan T H Koh
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shridhar Ganpathi Iyer
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Hepatobiliary & Pancreatic Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wen Huan Ling
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Boon-Koon Yoong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Rawisak Chanwat
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | - Glenn Kunnath Bonney
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Hepatobiliary & Pancreatic Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Brian K P Goh
- Department of Hepatopancreatobiliary and Transplantation Surgery, Singapore General Hospital and National Cancer Center Singapore, Singapore, Singapore
| | - Weiwei Zhai
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Melissa J Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wilson Wang
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yock Young Dan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ernesto Guccione
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Leah A Vardy
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,BioMap, Beijing, China
| | - Pierce K H Chow
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore.,Department of Hepatopancreatobiliary and Transplantation Surgery, Singapore General Hospital and National Cancer Center Singapore, Singapore, Singapore.,Academic Clinical Programme for Surgery, SingHealth Duke-NUS Academic Medical Centre (AMC), Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. .,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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10
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Ghosh S, Ataman M, Bak M, Börsch A, Schmidt A, Buczak K, Martin G, Dimitriades B, Herrmann CJ, Kanitz A, Zavolan M. CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acids Res 2022; 50:3096-3114. [PMID: 35234914 PMCID: PMC8989530 DOI: 10.1093/nar/gkac114] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
The mammalian cleavage factor I (CFIm) has been implicated in alternative polyadenylation (APA) in a broad range of contexts, from cancers to learning deficits and parasite infections. To determine how the CFIm expression levels are translated into these diverse phenotypes, we carried out a multi-omics analysis of cell lines in which the CFIm25 (NUDT21) or CFIm68 (CPSF6) subunits were either repressed by siRNA-mediated knockdown or over-expressed from stably integrated constructs. We established that >800 genes undergo coherent APA in response to changes in CFIm levels, and they cluster in distinct functional classes related to protein metabolism. The activity of the ERK pathway traces the CFIm concentration, and explains some of the fluctuations in cell growth and metabolism that are observed upon CFIm perturbations. Furthermore, multiple transcripts encoding proteins from the miRNA pathway are targets of CFIm-dependent APA. This leads to an increased biogenesis and repressive activity of miRNAs at the same time as some 3′ UTRs become shorter and presumably less sensitive to miRNA-mediated repression. Our study provides a first systematic assessment of a core set of APA targets that respond coherently to changes in CFIm protein subunit levels (CFIm25/CFIm68). We describe the elicited signaling pathways downstream of CFIm, which improve our understanding of the key role of CFIm in integrating RNA processing with other cellular activities.
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Affiliation(s)
- Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Meric Ataman
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Maciej Bak
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Anastasiya Börsch
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Beatrice Dimitriades
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Christina J Herrmann
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Kanitz
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.,Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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11
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Yu D, Dai N, Wolf EJ, Corrêa IR, Zhou J, Wu T, Blumenthal RM, Zhang X, Cheng X. Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs. J Biol Chem 2022; 298:101751. [PMID: 35189146 PMCID: PMC8931429 DOI: 10.1016/j.jbc.2022.101751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 02/08/2023] Open
Abstract
The phosphorylated RNA polymerase II CTD interacting factor 1 (PCIF1) is a methyltransferase that adds a methyl group to the N6-position of 2′O-methyladenosine (Am), generating N6, 2′O-dimethyladenosine (m6Am) when Am is the cap-proximal nucleotide. In addition, PCIF1 has ancillary methylation activities on internal adenosines (both A and Am), although with much lower catalytic efficiency relative to that of its preferred cap substrate. The PCIF1 preference for 2′O-methylated Am over unmodified A nucleosides is due mainly to increased binding affinity for Am. Importantly, it was recently reported that PCIF1 can methylate viral RNA. Although some viral RNA can be translated in the absence of a cap, it is unclear what roles PCIF1 modifications may play in the functionality of viral RNAs. Here we show, using in vitro assays of binding and methyltransfer, that PCIF1 binds an uncapped 5′-Am oligonucleotide with approximately the same affinity as that of a cap analog (KM = 0.4 versus 0.3 μM). In addition, PCIF1 methylates the uncapped 5′-Am with activity decreased by only fivefold to sixfold compared with its preferred capped substrate. We finally discuss the relationship between PCIF1-catalyzed RNA methylation, shown here to have broader substrate specificity than previously appreciated, and that of the RNA demethylase fat mass and obesity-associated protein (FTO), which demonstrates PCIF1-opposing activities on capped RNAs.
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Affiliation(s)
- Dan Yu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nan Dai
- New England Biolabs, Inc, Ipswich, Massachusetts, USA
| | - Eric J Wolf
- New England Biolabs, Inc, Ipswich, Massachusetts, USA
| | - Ivan R Corrêa
- New England Biolabs, Inc, Ipswich, Massachusetts, USA
| | - Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tao Wu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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12
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Zhao Y, Zhong G, Du R, Zhao D, Li J, Li Y, Xing W, Jin X, Zhang W, Sun W, Liu C, Liu Z, Yuan X, Kan G, Han X, Li Q, Chang YZ, Li Y, Ling S. Ckip-1 3′-UTR Attenuates Simulated Microgravity-Induced Cardiac Atrophy. Front Cell Dev Biol 2022; 9:796902. [PMID: 35186951 PMCID: PMC8847737 DOI: 10.3389/fcell.2021.796902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 12/24/2022] Open
Abstract
Microgravity prominently affected cardiovascular health, which was the gravity-dependent physical factor. Deep space exploration had been increasing in frequency, but heart function was susceptible to conspicuous damage and cardiac mass declined in weightlessness. Understanding of the etiology of cardiac atrophy exposed to microgravity currently remains limited. The 3′-untranslated region (UTR) of casein kinase-2 interacting protein-1 (Ckip-1) was a pivotal mediator in pressure overload-induced cardiac remodeling. However, the role of Ckip-1 3′-UTR in the heart during microgravity was unknown. We analyzed Ckip-1 mRNA 3′-UTR and coding sequence (CDS) expression levels in ground-based analogs such as mice hindlimb unloading (HU) and rhesus monkey head-down bed rest model. Ckip-1 3′-UTR had transcribed levels in the opposite change trend with cognate CDS expression in the hearts. We then subjected wild-type (WT) mice and cardiac-specific Ckip-1 3′-UTR-overexpressing mice to hindlimb unloading for 28 days. Our results uncovered that Ckip-1 3′-UTR remarkably attenuated cardiac dysfunction and mass loss in simulated microgravity environments. Mechanistically, Ckip-1 3′-UTR inhibited lipid accumulation and elevated fatty acid oxidation-related gene expression in the hearts through targeting calcium/calmodulin-dependent kinase 2 (CaMKK2) and activation of the AMPK-PPARα-CPT1b signaling pathway. These findings demonstrated Ckip-1 3′-UTR was an important regulator in atrophic heart growth after simulated microgravity.
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Affiliation(s)
- Yinglong Zhao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Guohui Zhong
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- School of Aerospace Medicine, Fourth Military Medical University, Xi’an, China
| | - Ruikai Du
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Dingsheng Zhao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Jianwei Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Yuheng Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- School of Aerospace Medicine, Fourth Military Medical University, Xi’an, China
| | - Wenjuan Xing
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- School of Aerospace Medicine, Fourth Military Medical University, Xi’an, China
| | - Xiaoyan Jin
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Wenjuan Zhang
- State Key Laboratory of Proteomics, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Weijia Sun
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Caizhi Liu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Zizhong Liu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Xinxin Yuan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Guanghan Kan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Xuan Han
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Qi Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Yan-Zhong Chang
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, College of Life Science, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Yan-Zhong Chang, ; Yingxian Li, ; Shukuan Ling,
| | - Yingxian Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- *Correspondence: Yan-Zhong Chang, ; Yingxian Li, ; Shukuan Ling,
| | - Shukuan Ling
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- *Correspondence: Yan-Zhong Chang, ; Yingxian Li, ; Shukuan Ling,
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13
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Mars JC, Ghram M, Culjkovic-Kraljacic B, Borden KLB. The Cap-Binding Complex CBC and the Eukaryotic Translation Factor eIF4E: Co-Conspirators in Cap-Dependent RNA Maturation and Translation. Cancers (Basel) 2021; 13:6185. [PMID: 34944805 PMCID: PMC8699206 DOI: 10.3390/cancers13246185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/26/2022] Open
Abstract
The translation of RNA into protein is a dynamic process which is heavily regulated during normal cell physiology and can be dysregulated in human malignancies. Its dysregulation can impact selected groups of RNAs, modifying protein levels independently of transcription. Integral to their suitability for translation, RNAs undergo a series of maturation steps including the addition of the m7G cap on the 5' end of RNAs, splicing, as well as cleavage and polyadenylation (CPA). Importantly, each of these steps can be coopted to modify the transcript signal. Factors that bind the m7G cap escort these RNAs through different steps of maturation and thus govern the physical nature of the final transcript product presented to the translation machinery. Here, we describe these steps and how the major m7G cap-binding factors in mammalian cells, the cap binding complex (CBC) and the eukaryotic translation initiation factor eIF4E, are positioned to chaperone transcripts through RNA maturation, nuclear export, and translation in a transcript-specific manner. To conceptualize a framework for the flow and integration of this genetic information, we discuss RNA maturation models and how these integrate with translation. Finally, we discuss how these processes can be coopted by cancer cells and means to target these in malignancy.
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Affiliation(s)
- Jean-Clement Mars
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Mehdi Ghram
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
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14
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Dynamic Variations of 3'UTR Length Reprogram the mRNA Regulatory Landscape. Biomedicines 2021; 9:biomedicines9111560. [PMID: 34829789 PMCID: PMC8615635 DOI: 10.3390/biomedicines9111560] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/10/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022] Open
Abstract
This paper concerns 3′-untranslated regions (3′UTRs) of mRNAs, which are non-coding regulatory platforms that control stability, fate and the correct spatiotemporal translation of mRNAs. Many mRNAs have polymorphic 3′UTR regions. Controlling 3′UTR length and sequence facilitates the regulation of the accessibility of functional effectors (RNA binding proteins, miRNAs or other ncRNAs) to 3′UTR functional boxes and motifs and the establishment of different regulatory landscapes for mRNA function. In this context, shortening of 3′UTRs would loosen miRNA or protein-based mechanisms of mRNA degradation, while 3′UTR lengthening would strengthen accessibility to these effectors. Alterations in the mechanisms regulating 3′UTR length would result in widespread deregulation of gene expression that could eventually lead to diseases likely linked to the loss (or acquisition) of specific miRNA binding sites. Here, we will review the mechanisms that control 3′UTR length dynamics and their alterations in human disorders. We will discuss, from a mechanistic point of view centered on the molecular machineries involved, the generation of 3′UTR variability by the use of alternative polyadenylation and cleavage sites, of mutually exclusive terminal alternative exons (exon skipping) as well as by the process of exonization of Alu cassettes to generate new 3′UTRs with differential functional features.
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15
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Wang P, Zhou Y, Richards AM. Effective tools for RNA-derived therapeutics: siRNA interference or miRNA mimicry. Am J Cancer Res 2021; 11:8771-8796. [PMID: 34522211 PMCID: PMC8419061 DOI: 10.7150/thno.62642] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
The approval of the first small interfering RNA (siRNA) drug Patisiran by FDA in 2018 marks a new era of RNA interference (RNAi) therapeutics. MicroRNAs (miRNA), an important post-transcriptional gene regulator, are also the subject of both basic research and clinical trials. Both siRNA and miRNA mimics are ~21 nucleotides RNA duplexes inducing mRNA silencing. Given the well performance of siRNA, researchers ask whether miRNA mimics are unnecessary or developed siRNA technology can pave the way for the emergence of miRNA mimic drugs. Through comprehensive comparison of siRNA and miRNA, we focus on (1) the common features and lessons learnt from the success of siRNAs; (2) the unique characteristics of miRNA that potentially offer additional therapeutic advantages and opportunities; (3) key areas of ongoing research that will contribute to clinical application of miRNA mimics. In conclusion, miRNA mimics have unique properties and advantages which cannot be fully matched by siRNA in clinical applications. MiRNAs are endogenous molecules and the gene silencing effects of miRNA mimics can be regulated or buffered to ameliorate or eliminate off-target effects. An in-depth understanding of the differences between siRNA and miRNA mimics will facilitate the development of miRNA mimic drugs.
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16
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Zhao Y, Ling S, Li J, Zhong G, Du R, Li Y, Wang Y, Liu C, Jin X, Liu W, Liu T, Li Y, Zhao D, Sun W, Liu Z, Liu Z, Pan J, Yuan X, Gao X, Xing W, Chang YZ, Li Y. 3' untranslated region of Ckip-1 inhibits cardiac hypertrophy independently of its cognate protein. Eur Heart J 2021; 42:3786-3799. [PMID: 34347073 DOI: 10.1093/eurheartj/ehab503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/13/2021] [Accepted: 07/15/2021] [Indexed: 12/16/2022] Open
Abstract
AIMS 3' untranslated region (3' UTR) of mRNA is more conserved than other non-coding sequences in vertebrate genomes, and its sequence space has substantially expanded during the evolution of higher organisms, which substantiates their significance in biological regulation. However, the independent role of 3' UTR in cardiovascular disease was largely unknown. METHODS AND RESULTS Using bioinformatics, RNA fluorescent in situ hybridization and quantitative real-time polymerase chain reaction, we found that 3' UTR and coding sequence regions of Ckip-1 mRNA exhibited diverse expression and localization in cardiomyocytes. We generated cardiac-specific Ckip-1 3' UTR overexpression mice under wild type and casein kinase 2 interacting protein-1 (CKIP-1) knockout background. Cardiac remodelling was assessed by histological, echocardiography, and molecular analyses at 4 weeks after transverse aortic constriction (TAC) surgery. The results showed that cardiac Ckip-1 3' UTR significantly inhibited TAC-induced cardiac hypertrophy independent of CKIP-1 protein. To determine the mechanism of Ckip-1 3' UTR in cardiac hypertrophy, we performed transcriptome and metabolomics analyses, RNA immunoprecipitation, biotin-based RNA pull-down, and reporter gene assays. We found that Ckip-1 3' UTR promoted fatty acid metabolism through AMPK-PPARα-CPT1b axis, leading to its protection against pathological cardiac hypertrophy. Moreover, Ckip-1 3' UTR RNA therapy using adeno-associated virus obviously alleviates cardiac hypertrophy and improves heart function. CONCLUSIONS These findings disclose that Ckip-1 3' UTR inhibits cardiac hypertrophy independently of its cognate protein. Ckip-1 3' UTR is an effective RNA-based therapy tool for treating cardiac hypertrophy and heart failure.
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Affiliation(s)
- Yinlong Zhao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China.,Laboratory of Molecular Iron Metabolism, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, College of Life Science, Hebei Normal University, No.20 Road East 2nd Ring South, Yuhua District, Shijiazhuang 050200, China
| | - Shukuan Ling
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Jianwei Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Guohui Zhong
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Ruikai Du
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Youyou Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Yanqing Wang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Caizhi Liu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Xiaoyan Jin
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Wei Liu
- Department of Cardiology, Beijing AnZhen Hospital, Capital Medical University, No.2 Anzhen Road, Chaoyang District, Beijing 100029, China
| | - Tong Liu
- Department of Cardiology, Beijing AnZhen Hospital, Capital Medical University, No.2 Anzhen Road, Chaoyang District, Beijing 100029, China
| | - Yuheng Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Dingsheng Zhao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Weijia Sun
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Zizhong Liu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Zifan Liu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China.,Department of Cardiovascular Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, No.28 Fuxing Road, Haidian District, Beijing 100853, China
| | - Junjie Pan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China.,Department of Cardiology, Medical College of Soochow University, No.1 Shizi Road, Gusu District, Suzhou 215006, China
| | - Xinxin Yuan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Xingcheng Gao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Wenjuan Xing
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
| | - Yan-Zhong Chang
- Laboratory of Molecular Iron Metabolism, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, College of Life Science, Hebei Normal University, No.20 Road East 2nd Ring South, Yuhua District, Shijiazhuang 050200, China
| | - Yingxian Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No.26 Beiqing Road, Haidian District, Beijing 100094, China
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17
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Ji S, Yang Z, Gozali L, Kenney T, Kocabas A, Jinsook Park C, Hynes M. Distinct expression of select and transcriptome-wide isolated 3'UTRs suggests critical roles in development and transition states. PLoS One 2021; 16:e0250669. [PMID: 33951080 PMCID: PMC8099112 DOI: 10.1371/journal.pone.0250669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 04/08/2021] [Indexed: 01/06/2023] Open
Abstract
Mature mRNA molecules are expected to be comprised of a 5’UTR, a 3’UTR and a coding region (CDS). Unexpectedly, however, there have been multiple recent reports of widespread differential expression of mRNA 3’UTRs and their cognate coding regions (CDS), reflecting the expression of isolated 3’UTRs (i3’UTRs); these i3’UTRs can be highly expressed, often in reciprocal patterns to their cognate CDS. As with other long non-coding (lncRNAs), isolated 3’UTRs are likely to play an important role in gene regulation, but little is known about the contexts in which they are deployed. To illuminate the functions of i3’UTRs, here we carry out in vitro, in vivo and in silico analyses of differential 3’UTR/CDS mRNA ratio usage across tissues, development and cell state changes both for a select list of developmentally important genes as well as by unbiased transcriptome-wide analyses. Across two developmental paradigms we find a distinct switch from high i3’UTR expression for stem cell related genes in proliferating cells to high CDS for these genes in newly differentiated cells. Unbiased transcriptome analysis across multiple gene sets shows that regardless of tissue, genes with high 3’UTR to CDS ratios belong predominantly to gene ontology categories related to cell-type specific functions. In contrast, the gene ontology categories of genes with low 3’UTR to CDS ratios are similar across tissues and relate to common cellular functions. We further show that, at least for some genes, traditional transcriptional start site genomic elements correspond to identified RNAseq 3’UTR peak regions, suggesting that some i3’UTRs may be generated by de novo transcription. Our results provide critical information from which detailed hypotheses for individual i3’UTRs can be tested, with a common theme that i3’UTRs appear poised to regulate cell-specific gene expression and state.
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Affiliation(s)
- Shaoyi Ji
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
- * E-mail: (MH); (SJ); (ZY)
| | - Ze Yang
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
- * E-mail: (MH); (SJ); (ZY)
| | - Leonardi Gozali
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
| | - Thomas Kenney
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
| | - Arif Kocabas
- Rockefeller University, New York, NY, United States of America
| | | | - Mary Hynes
- Dept. of Biology, Stanford University, Stanford, CA, United States of America
- Rockefeller University, New York, NY, United States of America
- * E-mail: (MH); (SJ); (ZY)
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18
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Wang T, Li X, Zhang X, Wang Q, Liu W, Lu X, Gao S, Liu Z, Liu M, Gao L, Zhang W. RNA Motifs and Modification Involve in RNA Long-Distance Transport in Plants. Front Cell Dev Biol 2021; 9:651278. [PMID: 33869208 PMCID: PMC8047152 DOI: 10.3389/fcell.2021.651278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 02/22/2021] [Indexed: 01/31/2023] Open
Abstract
A large number of RNA molecules have been found in the phloem of higher plants, and they can be transported to distant organelles through the phloem. RNA signals are important cues to be evolving in fortification strategies by long-distance transportation when suffering from various physiological challenges. So far, the mechanism of RNA selectively transportation through phloem cells is still in progress. Up to now, evidence have shown that several RNA motifs including Polypyrimidine (poly-CU) sequence, transfer RNA (tRNA)-related sequence, Single Nucleotide Mutation bound with specific RNA binding proteins to form Ribonucleotide protein (RNP) complexes could facilitate RNA mobility in plants. Furthermore, some RNA secondary structure such as tRNA-like structure (TLS), untranslation region (UTR) of mRNA, stem-loop structure of pre-miRNA also contributed to the mobility of RNAs. Latest researchs found that RNA methylation such as methylated 5′ cytosine (m5C) played an important role in RNA transport and function. These studies lay a theoretical foundation to uncover the mechanism of RNA transport. We aim to provide ideas and clues to inspire future research on the function of RNA motifs in RNA long-distance transport, furthermore to explore the underlying mechanism of RNA systematic signaling.
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Affiliation(s)
- Tao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaojing Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Qing Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Wenqian Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaohong Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Shunli Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Zixi Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Mengshuang Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
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19
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Andreassi C, Luisier R, Crerar H, Darsinou M, Blokzijl-Franke S, Lenn T, Luscombe NM, Cuda G, Gaspari M, Saiardi A, Riccio A. Cytoplasmic cleavage of IMPA1 3' UTR is necessary for maintaining axon integrity. Cell Rep 2021; 34:108778. [PMID: 33626357 PMCID: PMC7918530 DOI: 10.1016/j.celrep.2021.108778] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 12/22/2020] [Accepted: 01/29/2021] [Indexed: 12/31/2022] Open
Abstract
The 3' untranslated regions (3' UTRs) of messenger RNAs (mRNAs) are non-coding sequences involved in many aspects of mRNA metabolism, including intracellular localization and translation. Incorrect processing and delivery of mRNA cause severe developmental defects and have been implicated in many neurological disorders. Here, we use deep sequencing to show that in sympathetic neuron axons, the 3' UTRs of many transcripts undergo cleavage, generating isoforms that express the coding sequence with a short 3' UTR and stable 3' UTR-derived fragments of unknown function. Cleavage of the long 3' UTR of Inositol Monophosphatase 1 (IMPA1) mediated by a protein complex containing the endonuclease argonaute 2 (Ago2) generates a translatable isoform that is necessary for maintaining the integrity of sympathetic neuron axons. Thus, our study provides a mechanism of mRNA metabolism that simultaneously regulates local protein synthesis and generates an additional class of 3' UTR-derived RNAs.
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Affiliation(s)
- Catia Andreassi
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | | | - Hamish Crerar
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Marousa Darsinou
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Sasja Blokzijl-Franke
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Tchern Lenn
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Nicholas M Luscombe
- Francis Crick Institute, London NW1 1AT, UK; UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Giovanni Cuda
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro 88100, Italy
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro 88100, Italy
| | - Adolfo Saiardi
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Antonella Riccio
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
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20
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De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives. Int J Mol Sci 2021; 22:ijms22020941. [PMID: 33477898 PMCID: PMC7833382 DOI: 10.3390/ijms22020941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
Microcystin-LR (MC-LR) is a potent hepatotoxin for which a substantial gap in knowledge persists regarding the underlying molecular mechanisms of liver toxicity and injury. Although long non-coding RNAs (lncRNAs) have been extensively studied in model organisms, our knowledge concerning the role of lncRNAs in liver injury is limited. Given that lncRNAs show low levels of sequence conservation, their role becomes even more unclear in non-model organisms without an annotated genome, like whitefish (Coregonus lavaretus). The objective of this study was to discover and profile aberrantly expressed polyadenylated lncRNAs that are involved in MC-LR-induced liver injury in whitefish. Using RNA sequencing (RNA-Seq) data, we de novo assembled a high-quality whitefish liver transcriptome. This enabled us to find 94 differentially expressed (DE) putative evolutionary conserved lncRNAs, such as MALAT1, HOTTIP, HOTAIR or HULC, and 4429 DE putative novel whitefish lncRNAs, which differed from annotated protein-coding transcripts (PCTs) in terms of minimum free energy, guanine-cytosine (GC) base-pair content and length. Additionally, we identified DE non-coding transcripts that might be 3′ autonomous untranslated regions (3′UTRs) of mRNAs. We found both evolutionary conserved lncRNAs as well as novel whitefish lncRNAs that could serve as biomarkers of liver injury.
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21
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Bae B, Gruner HN, Lynch M, Feng T, So K, Oliver D, Mastick GS, Yan W, Pieraut S, Miura P. Elimination of Calm1 long 3'-UTR mRNA isoform by CRISPR-Cas9 gene editing impairs dorsal root ganglion development and hippocampal neuron activation in mice. RNA (NEW YORK, N.Y.) 2020; 26:1414-1430. [PMID: 32522888 PMCID: PMC7491327 DOI: 10.1261/rna.076430.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/06/2020] [Indexed: 05/04/2023]
Abstract
The majority of mouse and human genes are subject to alternative cleavage and polyadenylation (APA), which most often leads to the expression of two or more alternative length 3' untranslated region (3'-UTR) mRNA isoforms. In neural tissues, there is enhanced expression of APA isoforms with longer 3'-UTRs on a global scale, but the physiological relevance of these alternative 3'-UTR isoforms is poorly understood. Calmodulin 1 (Calm1) is a key integrator of calcium signaling that generates short (Calm1-S) and long (Calm1-L) 3'-UTR mRNA isoforms via APA. We found Calm1-L expression to be largely restricted to neural tissues in mice including the dorsal root ganglion (DRG) and hippocampus, whereas Calm1-S was more broadly expressed. smFISH revealed that both Calm1-S and Calm1-L were subcellularly localized to neural processes of primary hippocampal neurons. In contrast, cultured DRG showed restriction of Calm1-L to soma. To investigate the in vivo functions of Calm1-L, we implemented a CRISPR-Cas9 gene editing strategy to delete a small region encompassing the Calm1 distal poly(A) site. This eliminated Calm1-L expression while maintaining expression of Calm1-S Mice lacking Calm1-L (Calm1ΔL/ΔL ) exhibited disorganized DRG migration in embryos, and reduced experience-induced neuronal activation in the adult hippocampus. These data indicate that Calm1-L plays functional roles in the central and peripheral nervous systems.
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Affiliation(s)
- Bongmin Bae
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Hannah N Gruner
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Maebh Lynch
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Ting Feng
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Kevin So
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Daniel Oliver
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Grant S Mastick
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Wei Yan
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Simon Pieraut
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Pedro Miura
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
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22
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MicroRNA-31 Regulates Expression of Wntless in Both Drosophila melanogaster and Human Oral Cancer Cells. Int J Mol Sci 2020; 21:ijms21197232. [PMID: 33007980 PMCID: PMC7582764 DOI: 10.3390/ijms21197232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/27/2022] Open
Abstract
Recent comparative studies have indicated distinct expression profiles of short, non-coding microRNAs (miRNAs) in various types of cancer, including oral squamous cell carcinoma (OSCC). In this study, we employed a hybrid approach using Drosophila melanogaster as well as OSCC cell lines to validate putative targets of oral cancer-related miRNAs both in vivo and in vitro. Following overexpression of Drosophila miR-31, we found a significant decrease in the size of the imaginal wing discs and downregulation of a subset of putative targets, including wntless (wls), an important regulator of the Wnt signaling pathway. Parallel experiments performed in OSCC cells have also confirmed a similar miR-31-dependent regulation of human WLS that was not initially predicted as targets of human miR-31. Furthermore, we found subsequent downregulation of cyclin D1 and c-MYC, two of the main transcriptional targets of Wnt signaling, suggesting a potential role of miR-31 in regulating the cell cycle and proliferation of OSCC cells. Taken together, our Drosophila-based in vivo system in conjunction with the human in vitro platform will thus provide a novel insight into a mammal-to-Drosophila-to-mammal approach to validate putative targets of human miRNA and to better understand the miRNA-target relationships that play an important role in the pathophysiology of oral cancer.
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23
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Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
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24
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TLR4 promotes microglial pyroptosis via lncRNA-F630028O10Rik by activating PI3K/AKT pathway after spinal cord injury. Cell Death Dis 2020; 11:693. [PMID: 32826878 PMCID: PMC7443136 DOI: 10.1038/s41419-020-02824-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/17/2022]
Abstract
Neuroinflammation plays a crucial role in the secondary phase of spinal cord injury (SCI), and is initiated following the activation of toll-like receptor 4 (TLR4). However, the downstream mechanism remains unknown. Pyroptosis is a form of inflammatory programmed cell death, which is closely involved in neuroinflammation, and it can be regulated by TLR4 according to a recent research. In addition, several studies have shown that long non-coding RNAs (lncRNAs) based mechanisms were related to signal transduction downstream of TLR4 in the regulation of inflammation. Thus, in this study, we want to determine whether TLR4 can regulate pyroptosis after SCI via lncRNAs. Our results showed that TLR4 was activated following SCI and promoted the expression of lncRNA-F630028O10Rik. This lncRNA functioned as a ceRNA for miR-1231-5p/Col1a1 axis and enhanced microglial pyroptosis after SCI by activating the PI3K/AKT pathway. Furthermore, we determined STAT1 was the upstream transcriptional factor of IncRNA-F630028O10Rik and was induced by the damage-responsive TLR4/MyD88 signal. Our findings provide new insights and a novel therapeutic strategy for treating SCI.
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25
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Hoyos M, Huber M, Förstner KU, Papenfort K. Gene autoregulation by 3' UTR-derived bacterial small RNAs. eLife 2020; 9:58836. [PMID: 32744240 PMCID: PMC7398697 DOI: 10.7554/elife.58836] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/23/2020] [Indexed: 01/01/2023] Open
Abstract
Negative feedback regulation, that is the ability of a gene to repress its own synthesis, is the most abundant regulatory motif known to biology. Frequently reported for transcriptional regulators, negative feedback control relies on binding of a transcription factor to its own promoter. Here, we report a novel mechanism for gene autoregulation in bacteria relying on small regulatory RNA (sRNA) and the major endoribonuclease, RNase E. TIER-seq analysis (transiently-inactivating-an-endoribonuclease-followed-by-RNA-seq) revealed ~25,000 RNase E-dependent cleavage sites in Vibrio cholerae, several of which resulted in the accumulation of stable sRNAs. Focusing on two examples, OppZ and CarZ, we discovered that these sRNAs are processed from the 3' untranslated region (3' UTR) of the oppABCDF and carAB operons, respectively, and base-pair with their own transcripts to inhibit translation. For OppZ, this process also triggers Rho-dependent transcription termination. Our data show that sRNAs from 3' UTRs serve as autoregulatory elements allowing negative feedback control at the post-transcriptional level.
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Affiliation(s)
- Mona Hoyos
- Friedrich Schiller University Jena, Institute of Microbiology, Jena, Germany.,Faculty of Biology I, Ludwig-Maximilians-University of Munich, Martinsried, Germany
| | - Michaela Huber
- Friedrich Schiller University Jena, Institute of Microbiology, Jena, Germany.,Faculty of Biology I, Ludwig-Maximilians-University of Munich, Martinsried, Germany
| | - Konrad U Förstner
- TH Köln - University of Applied Sciences, Institute of Information Science, Cologne, Germany.,ZB MED - Information Centre for Life Sciences, Cologne, Germany
| | - Kai Papenfort
- Friedrich Schiller University Jena, Institute of Microbiology, Jena, Germany.,Faculty of Biology I, Ludwig-Maximilians-University of Munich, Martinsried, Germany.,Microverse Cluster, Friedrich Schiller University Jena, Jena, Germany
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26
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Zhang Z, So K, Peterson R, Bauer M, Ng H, Zhang Y, Kim JH, Kidd T, Miura P. Elav-Mediated Exon Skipping and Alternative Polyadenylation of the Dscam1 Gene Are Required for Axon Outgrowth. Cell Rep 2020; 27:3808-3817.e7. [PMID: 31242415 PMCID: PMC7092717 DOI: 10.1016/j.celrep.2019.05.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 04/18/2019] [Accepted: 05/22/2019] [Indexed: 12/19/2022] Open
Abstract
Many metazoan genes express alternative long 3′ UTR isoforms in the nervous system, but their functions remain largely unclear. In Drosophila melanogaster, the Dscam1 gene generates short and long (Dscam1-L) 3′ UTR isoforms because of alternative polyadenylation (APA). Here, we found that the RNA-binding protein Embryonic Lethal Abnormal Visual System (Elav) impacts Dscam1 biogenesis at two levels, including regulation of long 3′ UTR biogenesis and skipping of an upstream exon (exon 19). MinION long-read sequencing confirmed the connectivity of this alternative splicing event to the long 3′ UTR. Knockdown or CRISPR deletion of Dscam1-L impaired axon outgrowth in Drosophila. The Dscam1 long 3′ UTR was found to be required for correct Elav-mediated skipping of exon 19. Elav thus co-regulates APA and alternative splicing to generate specific Dscam1 transcripts that are essential for neural development. This coupling of APA to alternative splicing might represent a new class of regulated RNA processing. Like most metazoan genes, Dscam1 expresses alternative short and long 3′ UTR mRNAs. Zhang et al. find that loss of Dscam1 long 3′ UTR transcripts impairs axon outgrowth in Drosophila. Long-read sequencing reveals that these long 3′ UTR mRNAs preferentially skip an upstream exon, altering Dscam1 amino acid sequence.
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Affiliation(s)
- Zhiping Zhang
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Kevin So
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Ryan Peterson
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Matthew Bauer
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Henry Ng
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Yong Zhang
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Jung Hwan Kim
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Thomas Kidd
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Pedro Miura
- Department of Biology, University of Nevada, Reno, Reno, NV, USA.
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27
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Elhasnaoui J, Miano V, Ferrero G, Doria E, Leon AE, Fabricio ASC, Annaratone L, Castellano I, Sapino A, De Bortoli M. DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3'-End Usage. Cancers (Basel) 2020; 12:cancers12061453. [PMID: 32503257 PMCID: PMC7352480 DOI: 10.3390/cancers12061453] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022] Open
Abstract
DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1 expression is analyzed in 30 public datasets and, additionally, by qRT-PCR in tumors from 93 BC patients, to uncover correlations with clinical data. Moreover, the effect of DSCAM-AS1 knockdown on gene expression and alternative splicing is studied by RNA-Seq in MCF-7 cells. We confirm DSCAM-AS1 overexpression in high grade Luminal A, B, and HER2+ BCs and find a significant correlation with disease relapse. In total, 908 genes are regulated by DSCAM-AS1-silencing, primarily involved in the cell cycle and inflammatory response. Noteworthily, the analysis of alternative splicing and isoform regulation reveals 2085 splicing events regulated by DSCAM-AS1, enriched in alternative polyadenylation sites, 3′UTR (untranslated region) shortening and exon skipping events. Finally, the DSCAM-AS1-interacting splicing factor heterogeneous nuclear ribonucleoprotein L (hnRNPL) is predicted as the most enriched RBP for exon skipping and 3′UTR events. The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.
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Affiliation(s)
- Jamal Elhasnaoui
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
| | - Valentina Miano
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Giulio Ferrero
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Department of Computer Science, University of Turin, 10149 Turin, Italy
| | - Elena Doria
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
| | - Antonette E. Leon
- Regional Center for Biomarkers, Department of Clinical Pathology, Azienda ULSS 3 Serenissima, Campo SS Giovanni e Paolo 6777, 30122 Venice, Italy; (A.E.L.); (A.S.C.F.)
| | - Aline S. C. Fabricio
- Regional Center for Biomarkers, Department of Clinical Pathology, Azienda ULSS 3 Serenissima, Campo SS Giovanni e Paolo 6777, 30122 Venice, Italy; (A.E.L.); (A.S.C.F.)
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
| | - Isabella Castellano
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Turin, Italy
| | - Michele De Bortoli
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Correspondence: ; Tel.: +39-0116-7050-58
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Emerging Roles for 3' UTRs in Neurons. Int J Mol Sci 2020; 21:ijms21103413. [PMID: 32408514 PMCID: PMC7279237 DOI: 10.3390/ijms21103413] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/14/2022] Open
Abstract
The 3′ untranslated regions (3′ UTRs) of mRNAs serve as hubs for post-transcriptional control as the targets of microRNAs (miRNAs) and RNA-binding proteins (RBPs). Sequences in 3′ UTRs confer alterations in mRNA stability, direct mRNA localization to subcellular regions, and impart translational control. Thousands of mRNAs are localized to subcellular compartments in neurons—including axons, dendrites, and synapses—where they are thought to undergo local translation. Despite an established role for 3′ UTR sequences in imparting mRNA localization in neurons, the specific RNA sequences and structural features at play remain poorly understood. The nervous system selectively expresses longer 3′ UTR isoforms via alternative polyadenylation (APA). The regulation of APA in neurons and the neuronal functions of longer 3′ UTR mRNA isoforms are starting to be uncovered. Surprising roles for 3′ UTRs are emerging beyond the regulation of protein synthesis and include roles as RBP delivery scaffolds and regulators of alternative splicing. Evidence is also emerging that 3′ UTRs can be cleaved, leading to stable, isolated 3′ UTR fragments which are of unknown function. Mutations in 3′ UTRs are implicated in several neurological disorders—more studies are needed to uncover how these mutations impact gene regulation and what is their relationship to disease severity.
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Abstract
Hfq (host factor for phage Q beta) is key for posttranscriptional gene regulation in many bacteria. Hfq's function is to stabilize sRNAs and to facilitate base-pairing with trans-encoded target mRNAs. Loss of Hfq typically results in pleiotropic phenotypes, and, in the major human pathogen Vibrio cholerae, Hfq inactivation has been linked to reduced virulence, failure to produce biofilms, and impaired intercellular communication. However, the RNA ligands of Hfq in V. cholerae are currently unknown. Here, we used RIP-seq (RNA immunoprecipitation followed by high-throughput sequencing) analysis to identify Hfq-bound RNAs in V. cholerae Our work revealed 603 coding and 85 noncoding transcripts associated with Hfq, including 44 sRNAs originating from the 3' end of mRNAs. Detailed investigation of one of these latter transcripts, named FarS (fatty acid regulated sRNA), showed that this sRNA is produced by RNase E-mediated maturation of the fabB 3'UTR, and, together with Hfq, inhibits the expression of two paralogous fadE mRNAs. The fabB and fadE genes are antagonistically regulated by the major fatty acid transcription factor, FadR, and we show that, together, FadR, FarS, and FadE constitute a mixed feed-forward loop regulating the transition between fatty acid biosynthesis and degradation in V. cholerae Our results provide the molecular basis for studies on Hfq in V. cholerae and highlight the importance of a previously unrecognized sRNA for fatty acid metabolism in this major human pathogen.
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Pharmacogenomics of poor drug metabolism in Greyhounds: Cytochrome P450 (CYP) 2B11 genetic variation, breed distribution, and functional characterization. Sci Rep 2020; 10:69. [PMID: 31919457 PMCID: PMC6952448 DOI: 10.1038/s41598-019-56660-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/13/2019] [Indexed: 01/11/2023] Open
Abstract
Greyhounds recover more slowly from certain injectable anesthetics than other dog breeds. Previous studies implicate cytochrome P450 (CYP) 2B11 as an important clearance mechanism for these drugs and suggest Greyhounds are deficient in CYP2B11. However, no CYP2B11 gene mutations have been identified that explain this deficiency in Greyhounds. The objectives of this study were to provide additional evidence for CYP2B11 deficiency in Greyhounds, determine the mechanisms underlying this deficiency, and identify CYP2B11 mutations that contribute to this phenotype in Greyhounds. Greyhound livers metabolized CYP2B11 substrates slower, possessed lower CYP2B11 protein abundance, but had similar or higher mRNA expression than other breeds. Gene resequencing identified three CYP2B11 haplotypes, H1 (reference), H2, and H3 that were differentiated by mutations in the gene 3'-untranslated region (3'-UTR). Compared with 63 other dog breeds, Greyhounds had the highest CYP2B11-H3 allele frequency, while CYP2B11-H2 was widely distributed across most breeds. Using 3'-UTR luciferase reporter constructs, CYP2B11-H3 showed markedly lower gene expression (over 70%) compared to CYP2B11-H1 while CYP2B11-H2 expression was intermediate. Truncated mRNA transcripts were observed in CYP2B11-H2 and CYP2B11-H3 but not CYP2B11-H1 transfected cells. Our results implicate CYP2B11 3'-UTR mutations as a cause of decreased CYP2B11 enzyme expression in Greyhounds through reduced translational efficiency.
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31
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Sudmant PH, Lee H, Dominguez D, Heiman M, Burge CB. Widespread Accumulation of Ribosome-Associated Isolated 3' UTRs in Neuronal Cell Populations of the Aging Brain. Cell Rep 2019; 25:2447-2456.e4. [PMID: 30485811 DOI: 10.1016/j.celrep.2018.10.094] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/24/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022] Open
Abstract
Particular brain regions and cell populations exhibit increased susceptibility to aging-related stresses. Here, we describe the age-specific and brain-region-specific accumulation of ribosome-associated 3' UTR RNAs that lack the 5' UTR and open reading frame. Our study reveals that this phenomenon impacts hundreds of genes in aged D1 spiny projection neurons of the mouse striatum and also occurs in the aging human brain. Isolated 3' UTR accumulation is tightly correlated with mitochondrial gene expression and oxidative stress, with full-length mRNA expression that is reduced but not eliminated, and with production of short 3' UTR-encoded peptides. Depletion of the oxidation-sensitive Fe-S cluster ribosome recycling factor ABCE1 induces the accumulation of 3' UTRs, consistent with a model in which ribosome stalling and mRNA cleavage by No-Go decay yields isolated 3' UTR RNAs protected by ribosomes. Isolated 3' UTR accumulation is a hallmark of brain aging, likely reflecting regional differences in metabolism and oxidative stress.
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Affiliation(s)
- Peter H Sudmant
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Hyeseung Lee
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Daniel Dominguez
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Myriam Heiman
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.
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Ciolli Mattioli C, Rom A, Franke V, Imami K, Arrey G, Terne M, Woehler A, Akalin A, Ulitsky I, Chekulaeva M. Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments. Nucleic Acids Res 2019; 47:2560-2573. [PMID: 30590745 PMCID: PMC6411841 DOI: 10.1093/nar/gky1270] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/27/2018] [Accepted: 12/13/2018] [Indexed: 01/01/2023] Open
Abstract
The proper subcellular localization of RNAs and local translational regulation is crucial in highly compartmentalized cells, such as neurons. RNA localization is mediated by specific cis-regulatory elements usually found in mRNA 3′UTRs. Therefore, processes that generate alternative 3′UTRs—alternative splicing and polyadenylation—have the potential to diversify mRNA localization patterns in neurons. Here, we performed mapping of alternative 3′UTRs in neurites and soma isolated from mESC-derived neurons. Our analysis identified 593 genes with differentially localized 3′UTR isoforms. In particular, we have shown that two isoforms of Cdc42 gene with distinct functions in neuronal polarity are differentially localized between neurites and soma of mESC-derived and mouse primary cortical neurons, at both mRNA and protein level. Using reporter assays and 3′UTR swapping experiments, we have identified the role of alternative 3′UTRs and mRNA transport in differential localization of alternative CDC42 protein isoforms. Moreover, we used SILAC to identify isoform-specific Cdc42 3′UTR-bound proteome with potential role in Cdc42 localization and translation. Our analysis points to usage of alternative 3′UTR isoforms as a novel mechanism to provide for differential localization of functionally diverse alternative protein isoforms.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Aviv Rom
- Weizmann Institute of Science, Rehovot, Israel
| | - Vedran Franke
- BIMSB Bioinformatics platform, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Koshi Imami
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Gerard Arrey
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mandy Terne
- Developmental Biology / Signal Transduction, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Andrew Woehler
- BIMSB Light Microscopy platform, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Altuna Akalin
- BIMSB Bioinformatics platform, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | | | - Marina Chekulaeva
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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Transregulation of microRNA miR-21 promoter by AP-1 transcription factor in cervical cancer cells. Cancer Cell Int 2019; 19:214. [PMID: 31427899 PMCID: PMC6694678 DOI: 10.1186/s12935-019-0931-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/05/2019] [Indexed: 11/28/2022] Open
Abstract
Background Gene expression profiles have demonstrated that miR-21 expression is altered in almost all types of cancers and it has been classified as an oncogenic microRNA. Persistent HPV infection is the main etiologic agent in cervical cancer and induces genetic instability, including disruption of microRNA gene expression. In the present study, we analyzed the underlying mechanism of how AP-1 transcription factor can active miR-21 gene expression in cervical cancer cells. Methods To identify that c-Fos and c-Jun regulate the expression of miR-21 we performed RT-qPCR and western blot assays. We analyzed the interaction of AP-1 with miR-21 promoter by EMSA and ChIP assays and determined the mechanism of its regulation by reporter construct plasmids. We identified the nuclear translocation of c-Fos and c-Jun by immunofluorescence microscopy assays. Results We demonstrated that c-Fos and c-Jun proteins are expressed and regulate the expression of miR-21 in cervical cancer cells. DNA sequence analysis revealed the presence of AP-1 DNA-binding sites in the human miR-21 promoter region. EMSA analyses confirmed the interactions of the miR-21 upstream transcription factor AP-1. ChIP assays further showed the binding of c-Fos to AP-1 sequences from the miR-21 core promoter in vivo. Functional analysis of AP-1 sequences of miR-21 in reporter plasmids demonstrated that these sequences increase the miR-21 promoter activation. Conclusions Our findings suggest a physical interaction and functional cooperation between AP-1 transcription factor in the miR-21 promoter and may explain the effect of AP-1 on miR-21 gene expression in cervical cancer cells.
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Wang R, Li G, Zhuang G, Sun S, Song Z. Overexpression of microRNA-423-3p indicates poor prognosis and promotes cell proliferation, migration, and invasion of lung cancer. Diagn Pathol 2019; 14:53. [PMID: 31164163 PMCID: PMC6549275 DOI: 10.1186/s13000-019-0831-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/23/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Lung cancer is one of the common malignant tumors worldwide with high incidence and mortality. MicroRNA-423-3p (miR-423-3p) acts as an oncogene in several types of cancers. The aim of this study is to reveal the clinical significance and biological function of miR-423-3p in lung cancer. METHODS The expression of miR-423-3p was detected in lung cancer specimens by reverse transcription-quantitative polymerase chain reaction (qRT-PCR) assay. Kaplan-Meier survival and Cox regression analyses were used to investigate the prognostic significance of miR-423-3p in lung cancer. CCK-8 and Transwell assays were used to determine the functional role of miR-423-3p in lung cancer. RESULTS We observed that miR-423-3p was significantly upregulated in lung cancer tissues and cell lines. Overexpression of miR-423-3p was significantly associated with lymph node metastasis, TNM stage, and poor prognosis. Multivariate Cox regression analysis results showed that miR-423-3p was an independent prognostic indicator for lung cancer patients. Results of functional analyses revealed that overexpression of miR-423-3p promoted cell proliferation, migration, and invasion in lung cancer cells. CONCLUSIONS These results indicated that miR-423-3p acts as an oncogene and promotes cell proliferation migration, and invasion of lung cancer. And miR-423-3p may serve as a potential prognostic biomarker and therapeutic target for the treatment of lung cancer.
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Affiliation(s)
- Rukun Wang
- Department of Thoracic Surgery, Affiliated Hospital of Weifang Medical University, Weifang, 261061, Shandong, China
| | - Gaofeng Li
- Department of Thyroid and Breast Surgery, Weifang Cancer Hospital, Weifang, 261041, Shandong, China
| | - Guoyan Zhuang
- Department of Outpatient, Weifang Cancer Hospital, Weifang, 261041, Shandong, China
| | - Shuying Sun
- Department of Nursing, Weifang Cancer Hospital, Weifang, 261041, Shandong, China
| | - Zhihui Song
- Department of Thoracic Surgery, Weifang Cancer Hospital, Weifang, 261041, Shandong, China.
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Networks of mRNA Processing and Alternative Splicing Regulation in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:1-27. [PMID: 31342435 DOI: 10.1007/978-3-030-19966-1_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNA processing events introduce an intricate layer of complexity into gene expression processes, supporting a tremendous level of diversification of the genome's coding and regulatory potential, particularly in vertebrate species. The recent development of massive parallel sequencing methods and their adaptation to the identification and quantification of different RNA species and the dynamics of mRNA metabolism and processing has generated an unprecedented view over the regulatory networks that are established at this level, which contribute to sustain developmental, tissue specific or disease specific gene expression programs. In this chapter, we provide an overview of the recent evolution of transcriptome profiling methods and the surprising insights that have emerged in recent years regarding distinct mRNA processing events - from the 5' end to the 3' end of the molecule.
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Andreassi C, Crerar H, Riccio A. Post-transcriptional Processing of mRNA in Neurons: The Vestiges of the RNA World Drive Transcriptome Diversity. Front Mol Neurosci 2018; 11:304. [PMID: 30210293 PMCID: PMC6121099 DOI: 10.3389/fnmol.2018.00304] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022] Open
Abstract
Neurons are morphologically complex cells that rely on the compartmentalization of protein expression to develop and maintain their extraordinary cytoarchitecture. This formidable task is achieved, at least in part, by targeting mRNA to subcellular compartments where they are rapidly translated. mRNA transcripts are the conveyor of genetic information from DNA to the translational machinery, however, they are also endowed with additional functions linked to both the coding sequence (open reading frame, or ORF) and the flanking 5′ and 3′ untranslated regions (UTRs), that may harbor coding-independent functions. In this review, we will highlight recent evidences supporting new coding-dependent and -independent functions of mRNA and discuss how nuclear and cytoplasmic post-transcriptional modifications of mRNA contribute to localization and translation in mammalian cells with specific emphasis on neurons. We also describe recently developed techniques that can be employed to study RNA dynamics at subcellular level in eukaryotic cells in developing and regenerating neurons.
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Affiliation(s)
- Catia Andreassi
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Hamish Crerar
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Antonella Riccio
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
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