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Al-Obaide M, Ishmakej A, Brown C, Mazzella M, Agosta P, Perez-Cruet M, Chaudhry GR. The potential role of integrin alpha 6 in human mesenchymal stem cells. Front Genet 2022; 13:968228. [PMID: 36212156 PMCID: PMC9535380 DOI: 10.3389/fgene.2022.968228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Human mesenchymal stem cells (MSCs) are isolated from various adult and perinatal tissues. Although mesenchymal stem cells from multiple sources exhibit similar morphology and cell surface markers, they differ in their properties. In this study, we determined that the expression of integrin alpha 6 (ITGA6) and ITGA6 antisense RNA (ITGA6-AS1) correlates with the proliferation, cell size, and differentiation potential. The expression of ITGA6 was inversely correlated with ITGA6-AS1 in MSCs. The expression of ITGA6 was higher, but ITGA6-AS1 was lower in MSCs from cord placenta junction, cord tissue, and Wharton's jelly. In contrast, ITGA6 expression was lower, while ITGA6-AS1 was higher in MSCs from the placenta. The bioinformatic analysis showed that ITGA6 genomic DNA transcribes ITGA6-AS1 from the reverse strand, overlapping ITGA6 exon-2. Additionally, we identify several putative promoters (P1-P10) of ITGA6. ITGA6-P10 is CG rich and contains CGI. EMBOSS Cpgplot software revealed a CGI length of 180 bp that extends from nucleotide 125 to 304 of the P10 sequence. We suggest that the post-transcriptional regulation of the ITGA6 in mesenchymal stem cells is controlled by the ITGA6-AS1, which could be a critical factor responsible for the heterogeneity in function and cell fate of human MSCs. These results may provide further impetus for investigations to unravel the mechanisms of ITGA6 regulation that could help maintain or improve the properties of mesenchymal stem cells.
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Affiliation(s)
- Mohammed Al-Obaide
- Department of Biological Sciences, Oakland University, Rochester, MI, United States.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI, United States
| | - Albi Ishmakej
- Department of Biological Sciences, Oakland University, Rochester, MI, United States.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI, United States
| | - Christina Brown
- Department of Biological Sciences, Oakland University, Rochester, MI, United States.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI, United States
| | - Matteo Mazzella
- Department of Biological Sciences, Oakland University, Rochester, MI, United States.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI, United States
| | - Patrina Agosta
- Ascension Providence Hospital, Southfield, MI, United States
| | - Mick Perez-Cruet
- OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI, United States.,Department of Neurosurgery, Beaumont Health, Royal Oak, MI, United States
| | - G Rasul Chaudhry
- Department of Biological Sciences, Oakland University, Rochester, MI, United States.,OU-WB Institute for Stem Cell and Regenerative Medicine, Oakland University, Rochester, MI, United States
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52
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Melhuish Beaupre LM, Brown GM, Braganza NA, Kennedy JL, Gonçalves VF. Mitochondria's role in sleep: Novel insights from sleep deprivation and restriction studies. World J Biol Psychiatry 2022; 23:1-13. [PMID: 33821750 DOI: 10.1080/15622975.2021.1907723] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVES/METHODS The biology underlying sleep is not yet fully elucidated, but it is known to be complex and largely influenced by circadian rhythms. Compelling evidence supports of a link among circadian rhythms, sleep and metabolism, which suggests a role for mitochondria. These organelles play a significant role in energy metabolism via oxidative phosphorylation (OXPHOS) and several mitochondrial enzymes display circadian oscillations. However, the interplay between mitochondria and sleep is not as well-known. This review summarises human and animal studies that have examined the role of mitochondria in sleep. Literature searches were conducted using PubMed and Google Scholar. RESULTS Using various models of sleep deprivation, animal studies support the involvement of mitochondria in sleep via differential gene and protein expression patterns, OXPHOS enzyme activity, and morphology changes. Human studies are more limited but also show differences in OXPHOS enzyme activity and protein levels among individuals who have undergone sleep deprivation or suffer from different forms of insomnia. CONCLUSIONS Taken altogether, both types of study provide evidence for mitochondria's involvement in the sleep-wake cycle. We briefly discuss the potential clinical implications of these studies.
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Affiliation(s)
- Lindsay M Melhuish Beaupre
- Department of Molecular Brain Science Research, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Gregory M Brown
- Department of Molecular Brain Science Research, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Nicole A Braganza
- Department of Molecular Brain Science Research, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - James L Kennedy
- Department of Molecular Brain Science Research, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Vanessa F Gonçalves
- Department of Molecular Brain Science Research, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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53
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Lohani S, Funato Y, Akieda Y, Mizutani K, Takai Y, Ishitani T, Miki H. A novel role of PRL in regulating epithelial cell density by inducing apoptosis at confluence. J Cell Sci 2021; 135:273809. [PMID: 34931244 DOI: 10.1242/jcs.258550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
Maintaining proper epithelial cell density is essential for the survival of multicellular organisms. While regulation of cell density through apoptosis is well known, its mechanistic details remain elusive. Here, we report the involvement of membrane-anchored phosphatase of regenerating liver (PRL), originally known for its role in cancer malignancy, in this process. In epithelial MDCK cells, upon confluence, doxycycline-induced expression of PRL upregulated apoptosis, reducing the cell density. This could be circumvented by artificially reducing the cell density via stretching the cell-seeded silicon chamber. Moreover, siRNA-mediated knockdown of endogenous PRL blocked apoptosis, leading to greater cell density. Mechanistically, PRL promoted apoptosis by upregulating the translation of E-cadherin and activating TGF-β pathway. Morpholino-mediated inhibition of PRL expression in zebrafish embryos caused developmental defect with reduced apoptosis and increased epithelial cell density during convergent extension. This study revealed a novel role of PRL in regulating density-dependent apoptosis in vertebrate epithelium.
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Affiliation(s)
- Sweksha Lohani
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuki Akieda
- Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kiyohito Mizutani
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
| | - Yoshimi Takai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0047, Japan
| | - Tohru Ishitani
- Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
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54
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Yin M, Cheng M, Liu C, Wu K, Xiong W, Fang J, Li Y, Zhang B. HNRNPA2B1 as a trigger of RNA switch modulates the miRNA-mediated regulation of CDK6. iScience 2021; 24:103345. [PMID: 34805798 PMCID: PMC8590077 DOI: 10.1016/j.isci.2021.103345] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/17/2021] [Accepted: 10/22/2021] [Indexed: 01/04/2023] Open
Abstract
The functional inactivation of tumor suppressor microRNA (miRNA) is closely related to the tumorigenesis of cancer. There are instances where the miRNA and the corresponding target both exist in a cell, but the target gene silencing do not occur as expected. Herein, we found that both miR-506 and its target CDK6 are highly co-expressed in lung cancer cells. Sequence analyses suggested that a miR-506 binding site (1648–1654) and a cis-element (1785–1795) for binding by heterogeneous nuclear ribonucleoprotein A2/B1 (HNRNPA2B1) are evolutionarily conserved and forms a stem structure in the 3′ untranslated region (3′UTR) of CDK6. Furthermore, HNRNPA2B1 can bind to the stem structure to denature it and recruit the RNA helicase DExH-box helicase 9 (DHX9) to the 3′UTR, which ultimately facilitates miRNAs-mediated CDK6 silencing. These results indicate that the cis-element of the 3′UTR of CDK6, where HNRNPA2B1 binds, serves as an RNA switch to regulate miRNAs’ function in cancer cells. Both miR-506 and its target CDK6 are highly co-expressed in lung cancer HNRNPA2B1 facilitates miR-506-mediated CDK6 silence by switching structure in 3′UTR HNRNPA2B1 also recruits the DHX9 to the 3′UTR of its targets HNRNPA2B1 extensively regulates miRNAs-mediated gene silencing through binding to 3′UTR
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Affiliation(s)
- Menghui Yin
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou, Guangdong 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meidie Cheng
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou, Guangdong 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengli Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou, Guangdong 510530, China
| | - Keli Wu
- School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Wei Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou, Guangdong 510530, China
| | - Ji Fang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou, Guangdong 510530, China
| | - Yinxiong Li
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou, Guangdong 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Public Health, Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Biliang Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou, Guangdong 510530, China
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55
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Zhang L, Li M, Yan P, Fu J, Zhang L, Li X, Han W. A novel adenylate isopentenyltransferase 5 regulates shoot branching via the ATTTA motif in Camellia sinensis. BMC PLANT BIOLOGY 2021; 21:521. [PMID: 34753426 PMCID: PMC8577036 DOI: 10.1186/s12870-021-03254-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/23/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Shoot branching is one of the important agronomic traits affecting yields and quality of tea plant (Camellia sinensis). Cytokinins (CTKs) play critical roles in regulating shoot branching. However, whether and how differently alternative splicing (AS) variant of CTKs-related genes can influence shoot branching of tea plant is still not fully elucidated. RESULTS In this study, five AS variants of CTK biosynthetic gene adenylate isopentenyltransferase (CsA-IPT5) with different 3' untranslated region (3' UTR) and 5' UTR from tea plant were cloned and investigated for their regulatory effects. Transient expression assays showed that there were significant negative correlations between CsA-IPT5 protein expression, mRNA expression of CsA-IPT5 AS variants and the number of ATTTA motifs, respectively. Shoot branching processes induced by exogenous 6-BA or pruning were studied, where CsA-IPT5 was demonstrated to regulate protein synthesis of CsA-IPT5, as well as the biosynthesis of trans-zeatin (tZ)- and isopentenyladenine (iP)-CTKs, through transcriptionally changing ratios of its five AS variants in these processes. Furthermore, the 3' UTR AS variant 2 (3AS2) might act as the predominant AS transcript. CONCLUSIONS Together, our results indicate that 3AS2 of the CsA-IPT5 gene is potential in regulating shoot branching of tea plant and provides a gene resource for improving the plant-type of woody plants.
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Affiliation(s)
- Liping Zhang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Menghan Li
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Peng Yan
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Jianyu Fu
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Lan Zhang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Xin Li
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
| | - Wenyan Han
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Sciences, No. 9 Meiling South Road, Xihu District, Hangzhou, 310008 Zhejiang China
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56
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Egorov AA, Alexandrov AI, Urakov VN, Makeeva DS, Edakin RO, Kushchenko AS, Gladyshev VN, Kulakovskiy IV, Dmitriev SE. A standard knockout procedure alters expression of adjacent loci at the translational level. Nucleic Acids Res 2021; 49:11134-11144. [PMID: 34606617 PMCID: PMC8565318 DOI: 10.1093/nar/gkab872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/11/2021] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
The Saccharomyces cerevisiae gene deletion collection is widely used for functional gene annotation and genetic interaction analyses. However, the standard G418-resistance cassette used to produce knockout mutants delivers strong regulatory elements into the target genetic loci. To date, its side effects on the expression of neighboring genes have never been systematically assessed. Here, using ribosome profiling data, RT-qPCR, and reporter expression, we investigated perturbations induced by the KanMX module. Our analysis revealed significant alterations in the transcription efficiency of neighboring genes and, more importantly, severe impairment of their mRNA translation, leading to changes in protein abundance. In the ‘head-to-head’ orientation of the deleted and neighboring genes, knockout often led to a shift of the transcription start site of the latter, introducing new uAUG codon(s) into the expanded 5′ untranslated region (5′ UTR). In the ‘tail-to-tail’ arrangement, knockout led to activation of alternative polyadenylation signals in the neighboring gene, thus altering its 3′ UTR. These events may explain the so-called neighboring gene effect (NGE), i.e. false genetic interactions of the deleted genes. We estimate that in as much as ∼1/5 of knockout strains the expression of neighboring genes may be substantially (>2-fold) deregulated at the level of translation.
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Affiliation(s)
- Artyom A Egorov
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny 141700, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia
| | - Alexander I Alexandrov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,FRC of Biotechnology of the Russian Academy of Sciences, Bach Institute of Biochemistry, Moscow 119071, Russia
| | - Valery N Urakov
- FRC of Biotechnology of the Russian Academy of Sciences, Bach Institute of Biochemistry, Moscow 119071, Russia
| | - Desislava S Makeeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia
| | - Roman O Edakin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Artem S Kushchenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ivan V Kulakovskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, 1 Olympic Ave, Sochi 354340, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
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57
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Association Between ATP Citrate Lyase (ACLY) Gene Polymorphism and Fattening, Slaughter and Pork Quality Traits in Polish Pigs. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2021-0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The primary aim of this study was to estimate the relationship between ATP citrate lyase (ACLY) gene polymorphism (c.*523 T>C) and fattening and pork quality traits. Investigations were carried out on 526 pigs represented by three breeds: Polish Landrace (n=269), Polish Large White (n=189) and Puławska (n=68). ACLY genotypes were determined by PCR–RFLP method. It was demonstrated that the analyzed polymorphism had significant influence (P<0.05 and P≤0.01) on several economically important traits in pigs, e.g. average daily gain, average backfat thickness, lean meat percentage. The results obtained allow for application of c.*523 T>C polymorphism in breeding programs to improve the pig population in terms of fattening and slaughter traits. However, this breeding program may have a slight negative effect on meat texture parameters.
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58
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Amin ND, Senturk G, Costaguta G, Driscoll S, O'Leary B, Bonanomi D, Pfaff SL. A hidden threshold in motor neuron gene networks revealed by modulation of miR-218 dose. Neuron 2021; 109:3252-3267.e6. [PMID: 34450025 DOI: 10.1016/j.neuron.2021.07.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/01/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
Disruption of homeostatic microRNA (miRNA) expression levels is known to cause human neuropathology. However, the gene regulatory and phenotypic effects of altering a miRNA's in vivo abundance (rather than its binary gain or loss) are not well understood. By genetic combination, we generated an allelic series of mice expressing varying levels of miR-218, a motor neuron-selective gene regulator associated with motor neuron disease. Titration of miR-218 cellular dose unexpectedly revealed complex, non-ratiometric target mRNA dose responses and distinct gene network outputs. A non-linearly responsive regulon exhibited a steep miR-218 dose-dependent threshold in repression that, when crossed, resulted in severe motor neuron synaptic failure and death. This work demonstrates that a miRNA can govern distinct gene network outputs at different expression levels and that miRNA-dependent phenotypes emerge at particular dose ranges because of hidden regulatory inflection points of their underlying gene networks.
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Affiliation(s)
- Neal D Amin
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Gokhan Senturk
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Giancarlo Costaguta
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shawn Driscoll
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Brendan O'Leary
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dario Bonanomi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Samuel L Pfaff
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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59
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Adetula AA, Fan X, Zhang Y, Yao Y, Yan J, Chen M, Tang Y, Liu Y, Yi G, Li K, Tang Z. Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs ( Sus-scrofa). RNA Biol 2021; 18:439-450. [PMID: 34314293 PMCID: PMC8677025 DOI: 10.1080/15476286.2021.1954380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/08/2022] Open
Abstract
RNA editing generates genetic diversity in mammals by altering amino acid sequences, miRNA targeting site sequences, influencing the stability of targeted RNAs, and causing changes in gene expression. However, the extent to which RNA editing affect gene expression via modifying miRNA binding site remains unexplored. Here, we first profiled the dynamic A-to-I RNA editome across tissues of Duroc and Luchuan pigs. The RNA editing events at the miRNA binding sites were generated. The biological function of the differentially edited gene in skeletal muscle was further characterized in pig muscle-derived satellite cells. RNA editome analysis revealed a total of 171,909 A-to-I RNA editing sites (RESs), and examination of its features showed that these A-to-I editing sites were mainly located in SINE retrotransposons PRE-1/Pre0_SS element. Analysis of differentially edited sites (DESs) revealed a total of 4,552 DESs across tissues between Duroc and Luchuan pigs, and functional category enrichment analysis of differentially edited gene (DEG) sets highlighted a significant association and enrichment of tissue-developmental pathways including TGF-beta, PI3K-Akt, AMPK, and Wnt signaling pathways. Moreover, we found that RNA editing events at the miRNA binding sites in the 3'-UTR of HSPA12B mRNA could prevent the miRNA-mediated mRNA downregulation of HSPA12B in the muscle-derived satellite (MDS) cell, consistent with the results obtained from the Luchuan skeletal muscle. This study represents the most systematic attempt to characterize the significance of RNA editing in regulating gene expression, particularly in skeletal muscle, constituting a new layer of regulation to understand the genetic mechanisms behind phenotype variance in animals.Abbreviations: A-to-I: Adenosine-to-inosine; ADAR: Adenosine deaminase acting on RNA; RES: RNA editing site; DEG: Differentially edited gene; DES: Differentially edited site; FDR: False discovery rate; GO: Gene Ontology; KEGG: Kyoto Encyclopaedia of Genes and Genomes; MDS cell: musclederived satellite cell; RPKM: Reads per kilobase of exon model in a gene per million mapped reads; UTR: Untranslated coding regions.
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Affiliation(s)
- Adeyinka A. Adetula
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinhao Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongsheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yilong Yao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junyu Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Muya Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yijie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
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60
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Frydas A, Cacace R, van der Zee J, Van Broeckhoven C, Wauters E. Genetic variants in progranulin upstream open reading frames increase downstream protein expression. Neurobiol Aging 2021; 110:113-121. [PMID: 34620513 DOI: 10.1016/j.neurobiolaging.2021.09.007] [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: 05/03/2021] [Revised: 08/29/2021] [Accepted: 09/05/2021] [Indexed: 11/25/2022]
Abstract
Premature termination codon (PTC) mutations in the granulin gene (GRN) lead to loss-of-function (LOF) of the progranulin protein (PGRN), causing frontotemporal lobar degeneration (FTLD) by haploinsufficiency. GRN expression is regulated at multiple levels, including the 5' untranslated region (UTR). The main 5' UTR of GRN and an alternative 5' UTR, contain upstream open reading frames (uORFs). These mRNA elements generally act as cis-repressors of translation. Disruption of each uORF of the alternative 5' UTR, increases protein expression with the 2 ATG-initiated uORFs being capable of initiating translation. We performed targeted sequencing of the uORF regions in a Flanders-Belgian cohort of patients with frontotemporal dementia (FTD) and identified 2 genetic variants, one in each 5' UTR. Both variants increase downstream protein levels, with the main 5' UTR variant rs76783532 causing a significant 1.5-fold increase in protein expression. We observed that the presence of functional uORFs in the alternative 5' UTR act as potential regulators of PGRN expression and demonstrate that genetic variation within GRN uORFs can alter their function.
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Affiliation(s)
- Alexandros Frydas
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Rita Cacace
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Julie van der Zee
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Eline Wauters
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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61
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Jeeva S, Kim KH, Shin CH, Wang BZ, Kang SM. An Update on mRNA-Based Viral Vaccines. Vaccines (Basel) 2021; 9:965. [PMID: 34579202 PMCID: PMC8473183 DOI: 10.3390/vaccines9090965] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/23/2022] Open
Abstract
With the success of COVID-19 vaccines, newly created mRNA vaccines against other infectious diseases are beginning to emerge. Here, we review the structural elements required for designing mRNA vaccine constructs for effective in vitro synthetic transcription reactions. The unprecedently speedy development of mRNA vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was enabled with previous innovations in nucleoside modifications during in vitro transcription and lipid nanoparticle delivery materials of mRNA. Recent updates are briefly described in the status of mRNA vaccines against SARS-CoV-2, influenza virus, and other viral pathogens. Unique features of mRNA vaccine platforms and future perspectives are discussed.
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Affiliation(s)
| | | | | | | | - Sang-Moo Kang
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA; (S.J.); (K.-H.K.); (C.H.S.); (B.-Z.W.)
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62
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Gao P, Zhao X, Yu K, Zhu Z. Circ_0084582 Facilitates Cell Growth, Migration, Invasion, and Angiopoiesis in Osteosarcoma via Mediating the miR-485-3p/JAG1 Axis. Front Genet 2021; 12:690956. [PMID: 34421997 PMCID: PMC8375504 DOI: 10.3389/fgene.2021.690956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
Osteosarcoma (OS) is the most representative bone cancer, and circular RNAs serve as pivotal regulators in the progression of OS. This research was designed to explore the role and functional mechanism of circ_0084582 in OS. Circ_0084582, microRNA-485-3p (miR-485-3p), and Jagged1 (JAG1) levels were measured by quantitative real-time polymerase chain reaction. Cell proliferation was examined via 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT) assay. Cell cycle progression was analyzed by flow cytometry. Wound healing and transwell assays were performed for evaluating cell migration and invasion. Angiopoiesis was assessed using the tube formation assay. Protein detection was conducted using Western blot. The target relation was identified by the dual-luciferase reporter assay, RNA immunoprecipitation (RIP) assay, and RNA pull-down assay. A xenograft experiment was applied for analyzing the effect of circ_0084582 on OS in vivo. Circ_0084582 was highly expressed in OS tissues and cells. Circ_0084582 knockdown reduced cell proliferation, cell cycle progression, migration, invasion, and angiopoiesis of OS cells. JAG1 was upregulated in OS, and its overexpression reversed the effects of circ_0084582 knockdown on OS cells. Circ_0084582 targeted miR-485-3p, and miR-485-3p targeted JAG1, and circ_0084582 could affect the JAG1 level by sponging miR-485-3p. The function of circ_0084582 in OS progression was also achieved by sponging miR-485-3p. Circ_0084582 knockdown decreased OS growth in vivo partly by the miR-485-3p–mediated JAG1 downregulation. These results indicate that circ_0084582 functions as a tumorigenic factor in OS via the regulation of miR-485-3p/JAG1 axis.
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Affiliation(s)
- Peng Gao
- Department of Orthopedics Surgery, The Second Hospital of Xuzhou Coal Mining Group, Xuzhou, China
| | - Xincheng Zhao
- Department of Orthopedics Surgery, The Second Hospital of Xuzhou Coal Mining Group, Xuzhou, China
| | - Keying Yu
- Department of Orthopedics Surgery, The Second Hospital of Xuzhou Coal Mining Group, Xuzhou, China
| | - Ziqiang Zhu
- Department of Orthopedics Surgery, The General Hospital of Xuzhou Coal Mining Group, Xuzhou, China
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63
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Challa S, Khulpateea BR, Nandu T, Camacho CV, Ryu KW, Chen H, Peng Y, Lea JS, Kraus WL. Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers. Cell 2021; 184:4531-4546.e26. [PMID: 34314702 PMCID: PMC8380725 DOI: 10.1016/j.cell.2021.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/11/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Defects in translation lead to changes in the expression of proteins that can serve as drivers of cancer formation. Here, we show that cytosolic NAD+ synthesis plays an essential role in ovarian cancer by regulating translation and maintaining protein homeostasis. Expression of NMNAT-2, a cytosolic NAD+ synthase, is highly upregulated in ovarian cancers. NMNAT-2 supports the catalytic activity of the mono(ADP-ribosyl) transferase (MART) PARP-16, which mono(ADP-ribosyl)ates (MARylates) ribosomal proteins. Depletion of NMNAT-2 or PARP-16 leads to inhibition of MARylation, increased polysome association and enhanced translation of specific mRNAs, aggregation of their translated protein products, and reduced growth of ovarian cancer cells. Furthermore, MARylation of the ribosomal proteins, such as RPL24 and RPS6, inhibits polysome assembly by stabilizing eIF6 binding to ribosomes. Collectively, our results demonstrate that ribosome MARylation promotes protein homeostasis in cancers by fine-tuning the levels of protein synthesis and preventing toxic protein aggregation.
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Affiliation(s)
- Sridevi Challa
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Beman R Khulpateea
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cristel V Camacho
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Keun W Ryu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yan Peng
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jayanthi S Lea
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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64
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Li Y, Zhang M, Feng H, Mahati S. The Tumorigenic Properties of EZH2 are Mediated by MiR-26a in Uveal Melanoma. Front Mol Biosci 2021; 8:713542. [PMID: 34381816 PMCID: PMC8350384 DOI: 10.3389/fmolb.2021.713542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/28/2021] [Indexed: 12/04/2022] Open
Abstract
Background: The polycomb group protein enhancer of zeste homolog 2 (EZH2) has been found to be highly expressed in various tumors, and microRNA-26a (miR-26a) is often unmodulated in cancers. However, the functions of these two molecules in uveal melanoma (UM) and their relationships have not been reported. Methods: We explored the effects of the miR-26a–EZH2 axis in UM by examining the levels of miR-26a and EZH2. The EZH2 levels in various tumor types and the correlations between EZH2 levels and overall survival and disease-free survival were reanalyzed. The binding of miR-26a to the 3′-untranslated region of EZH2 mRNA was measured using the luciferase reporter assay. The regulation of EZH2 gene expression by miR-26a was also identified, and the effect of elevated EZH2 expression on UM cell function was further examined. Results: miR-26a was downregulated and EZH2 was upregulated in UM cells. Overexpression of miR-26a inhibited cell proliferation, and knockdown of EZH2 suppressed cell growth. EZH2 was a direct target of miR-26a in UM cells. The knockout of EZH2 mimicked the tumor inhibition of miR-26a in UM cells, whereas the reintroduction of EZH2 abolished this effect. In addition, a network of EZH2 and its interacting proteins (UBC, CDK1, HDAC1, SUZ12, EED) was found to participate in miR-26a-mediated tumor progression. Conclusion: The newly identified miR-26a–EZH2 axis may be a potential target for the development of treatment strategies for UM.
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Affiliation(s)
- Yao Li
- Department of Ophthalmology, Xinjiang Medical University Affiliated First Hospital, Urumqi, China
| | - Mingmei Zhang
- Department of Ophthalmology, Xinjiang Medical University Affiliated First Hospital, Urumqi, China
| | - Huayin Feng
- Department of Ophthalmology, Xinjiang Medical University Affiliated First Hospital, Urumqi, China
| | - Shaya Mahati
- Department of Oncology, Xinjiang Medical University Affiliated First Hospital, Urumqi, China
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65
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Zhu W, Xu J, Chen S, Chen J, Liang Y, Zhang C, Li Q, Lai J, Li L. Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 3' untranslated regions in translatomic variation in plants. PLANT COMMUNICATIONS 2021; 2:100181. [PMID: 34327320 PMCID: PMC8299070 DOI: 10.1016/j.xplc.2021.100181] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 05/12/2023]
Abstract
The translatome, a profile of the translational status of genetic information within cells, provides a new perspective on gene expression. Although many plant genomes have been sequenced, comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques. Here, we developed a new technique termed 3' ribosome-profiling sequencing (3'Ribo-seq) for reliable, robust translatomic profiling. 3'Ribo-seq combines polysome profiling and 3' selection with a barcoding and pooling strategy. Systematic translatome profiling of different tissues of Arabidopsis, rice, and maize using conventional ribosome profiling (Ribo-seq) and 3'Ribo-seq revealed many novel translational genomic loci, thereby complementing functional genome annotation in plants. Using the low-cost, efficient 3'Ribo-seq technique and genome-wide association mapping of translatome expression (eGWAS), we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci (eQTLs). Notably, local eQTLs are significantly enriched in the 3' untranslated regions of genes. Detailed eQTL analysis suggested that sequence variation around the polyadenylation (polyA) signal motif plays a key role in translatomic variation. Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 3'Ribo-seq, which paves the way for deep translatomic analysis at the population level.
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Affiliation(s)
- Wanchao Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Sijia Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yan Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
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66
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Translation Initiation Regulated by RNA-Binding Protein in Mammals: The Modulation of Translation Initiation Complex by Trans-Acting Factors. Cells 2021; 10:cells10071711. [PMID: 34359885 PMCID: PMC8306974 DOI: 10.3390/cells10071711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/03/2021] [Accepted: 07/04/2021] [Indexed: 12/15/2022] Open
Abstract
Protein synthesis is tightly regulated at each step of translation. In particular, the formation of the basic cap-binding complex, eukaryotic initiation factor 4F (eIF4F) complex, on the 5' cap structure of mRNA is positioned as the rate-limiting step, and various cis-elements on mRNA contribute to fine-tune spatiotemporal protein expression. The cis-element on mRNAs is recognized and bound to the trans-acting factors, which enable the regulation of the translation rate or mRNA stability. In this review, we focus on the molecular mechanism of how the assembly of the eIF4F complex is regulated on the cap structure of mRNAs. We also summarize the fine-tuned regulation of translation initiation by various trans-acting factors through cis-elements on mRNAs.
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67
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Li L, Huang KL, Gao Y, Cui Y, Wang G, Elrod ND, Li Y, Chen YE, Ji P, Peng F, Russell WK, Wagner EJ, Li W. An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability. Nat Genet 2021; 53:994-1005. [PMID: 33986536 DOI: 10.1038/s41588-021-00864-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/05/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies have identified thousands of noncoding variants associated with human traits and diseases. However, the functional interpretation of these variants is a major challenge. Here, we constructed a multi-tissue atlas of human 3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs), containing approximately 0.4 million common genetic variants associated with the APA of target genes, identified in 46 tissues isolated from 467 individuals (Genotype-Tissue Expression Project). Mechanistically, 3'aQTLs can alter poly(A) motifs, RNA secondary structure and RNA-binding protein-binding sites, leading to thousands of APA changes. Our CRISPR-based experiments indicate that such 3'aQTLs can alter APA regulation. Furthermore, we demonstrate that mapping 3'aQTLs can identify APA regulators, such as La-related protein 4. Finally, 3'aQTLs are colocalized with approximately 16.1% of trait-associated variants and are largely distinct from other QTLs, such as expression QTLs. Together, our findings show that 3'aQTLs contribute substantially to the molecular mechanisms underlying human complex traits and diseases.
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Affiliation(s)
- Lei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yipeng Gao
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Gao Wang
- The Gertrude H. Sergievsky Center and Department of Neurology, Columbia University, New York, NY, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yumei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yiling Elaine Chen
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Fanglue Peng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA.
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68
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Parbin S, Damodharan S, Rajyaguru PI. Arginine methylation and cytoplasmic mRNA fate: An exciting new partnership. Yeast 2021; 38:441-452. [PMID: 34048611 DOI: 10.1002/yea.3653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022] Open
Abstract
Posttranslational modifications play a crucial role in regulating gene expression. Among these modifications, arginine methylation has recently attracted tremendous attention due to its role in multiple cellular functions. This review discusses the recent advances that have established arginine methylation as a major player in determining cytoplasmic messenger RNA (mRNA) fate. We specifically focus on research that implicates arginine methylation in regulating mRNA translation, decay, and RNA granule dynamics. Based on this research, we highlight a few emerging future avenues that will lead to exciting discoveries in this field.
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Affiliation(s)
- Sabnam Parbin
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Integrative Genomics Core Unit, University Medical Centre, Göttingen, Göttingen, Germany
| | - Subha Damodharan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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69
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Hsieh HH, Chen YA, Chang YJ, Wang HH, Yu YH, Lin SW, Huang YJ, Lin S, Chang CJ. The functional characterization of phosphorylation of tristetraprolin at C-terminal NOT1-binding domain. JOURNAL OF INFLAMMATION-LONDON 2021; 18:22. [PMID: 34090459 PMCID: PMC8180021 DOI: 10.1186/s12950-021-00288-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/20/2021] [Indexed: 12/26/2022]
Abstract
Background Tristetraprolin (TTP) family proteins contain conserved tandem CCCH zinc-finger binding to AU-rich elements and C-terminal NOT1-binding domain. TTP is phosphorylated extensively in cells, and its mRNA destabilization activity is regulated by protein phosphorylation. Methods We generated an antibody against phospho-Serine316 located at the C-terminal NOT1-binding site and examined TTP phosphorylation in LPS-stimulated RAW264.7 cells. Knockout of TTP was created in RAW264.7 cells using CRISPR/Cas9 gene editing to explore TTP functions. Results We demonstrated that Ser316 was phosphorylated by p90 ribosomal S6 kinase 1 (RSK1) and p38-activated protein kinase (MK2) and dephosphorylated by Protein Phosphatase 2A (PP2A). A phosphorylation-mimic mutant of S316D resulted in dissociation with the CCR4-NOT deadenylase complex through weakening interaction with CNOT1. Furthermore, Ser316 and serines 52 and 178 were independently contributed to the CCR4-NOT complex recruitment in the immunoprecipitation assay using phosphor-mimic mutants. In RAW264.7 macrophages, TTP was induced, and Ser316 was phosphorylated through RSK1 and MK2 by LPS stimulation. Knockout of TTP resulted in TNFα mRNA increased due to mRNA stabilization. Overexpression of non-phosphorylated S316A TTP mutant can restore TTP activity and lead to TNFα mRNA decreased. GST pull-down and RNA pull-down analyses demonstrated that endogenous TTP with Ser316 phosphorylation decreased the interaction with CNOT1. Conclusions Our results suggest that the TTP-mediated mRNA stability is modulated by Ser316 phosphorylation via regulating the TTP interaction with the CCR4-NOT deadenylase complex. Supplementary Information The online version contains supplementary material available at 10.1186/s12950-021-00288-2.
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Affiliation(s)
- Hsin-Hui Hsieh
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan
| | - Yen-An Chen
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan
| | - Yao-Jen Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hsin-Hui Wang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Pediatrics, Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ya-Han Yu
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yin-Jung Huang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Steven Lin
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ching-Jin Chang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan. .,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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Mitschka S, Fansler MM, Mayr C. Generation of 3'UTR knockout cell lines by CRISPR/Cas9-mediated genome editing. Methods Enzymol 2021; 655:427-457. [PMID: 34183132 DOI: 10.1016/bs.mie.2021.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In addition to the protein code, messenger RNAs (mRNAs) also contain untranslated regions (UTRs). 3'UTRs span the region between the translational stop codon and the poly(A) tail. Sequence elements located in 3'UTRs are essential for pre-mRNA processing. 3'UTRs also contain elements that can regulate protein abundance, localization, and function. At least half of all human genes use alternative cleavage and polyadenylation (APA) to further diversify the regulatory potential of protein functions. Traditional gene editing approaches are designed to disrupt the production of functional proteins. Here, we describe a method that allows investigators to manipulate 3'UTR sequences of endogenous genes for both single- 3'UTR and multi-3'UTR genes. As 3'UTRs can regulate individual functions of proteins, techniques to manipulate 3'UTRs at endogenous gene loci will help to disentangle multi-functionality of proteins. Furthermore, the ability to directly examine the impact of gene regulatory elements in 3'UTRs will provide further insights into their functional significance.
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Affiliation(s)
- Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Mervin M Fansler
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY, United States
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY, United States.
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71
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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Li Y, Shen QS, Peng Q, Ding W, Zhang J, Zhong X, An NA, Ji M, Zhou WZ, Li CY. Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. Brief Bioinform 2021; 22:6273384. [PMID: 33973996 PMCID: PMC8574621 DOI: 10.1093/bib/bbab157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/22/2021] [Accepted: 04/04/2021] [Indexed: 11/26/2022] Open
Abstract
Rhesus macaque is a unique nonhuman primate model for human evolutionary and translational study, but the error-prone gene models critically limit its applications. Here, we de novo defined full-length macaque gene models based on single molecule, long-read transcriptome sequencing in four macaque tissues (frontal cortex, cerebellum, heart and testis). Overall, 8 588 227 poly(A)-bearing complementary DNA reads with a mean length of 14 106 nt were generated to compile the backbone of macaque transcripts, with the fine-scale structures further refined by RNA sequencing and cap analysis gene expression sequencing data. In total, 51 605 macaque gene models were accurately defined, covering 89.7% of macaque or 75.7% of human orthologous genes. Based on the full-length gene models, we performed a human–macaque comparative analysis on polyadenylation (PA) regulation. Using macaque and mouse as outgroup species, we identified 79 distal PA events newly originated in humans and found that the strengthening of the distal PA sites, rather than the weakening of the proximal sites, predominantly contributes to the origination of these human-specific isoforms. Notably, these isoforms are selectively constrained in general and contribute to the temporospatially specific reduction of gene expression, through the tinkering of previously existed mechanisms of nuclear retention and microRNA (miRNA) regulation. Overall, the protocol and resource highlight the application of bioinformatics in integrating multilayer genomics data to provide an intact reference for model animal studies, and the isoform switching detected may constitute a hitherto underestimated regulatory layer in shaping the human-specific transcriptome and phenotypic changes.
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Affiliation(s)
- Yumei Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qi Peng
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Wanqiu Ding
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Xiaoming Zhong
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ni A An
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Mingjun Ji
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Beijing, China
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
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73
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Mitschka S, Mayr C. Endogenous p53 expression in human and mouse is not regulated by its 3'UTR. eLife 2021; 10:65700. [PMID: 33955355 PMCID: PMC8137139 DOI: 10.7554/elife.65700] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 05/05/2021] [Indexed: 12/14/2022] Open
Abstract
The TP53 gene encodes the tumor suppressor p53 which is functionally inactivated in many human cancers. Numerous studies suggested that 3′UTR-mediated p53 expression regulation plays a role in tumorigenesis and could be exploited for therapeutic purposes. However, these studies did not investigate post-transcriptional regulation of the native TP53 gene. Here, we used CRISPR/Cas9 to delete the human and mouse TP53/Trp53 3′UTRs while preserving endogenous mRNA processing. This revealed that the endogenous 3′UTR is not involved in regulating p53 mRNA or protein expression neither in steady state nor after genotoxic stress. Using reporter assays, we confirmed the previously observed repressive effects of the isolated 3′UTR. However, addition of the TP53 coding region to the reporter had a dominant negative impact on expression as its repressive effect was stronger and abrogated the contribution of the 3′UTR. Our data highlight the importance of genetic models in the validation of post-transcriptional gene regulatory effects.
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Affiliation(s)
- Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
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Wu L, Xia L, Chen X, Ruan M, Li L, Xia R. Long non-coding RNA LINC01003 suppresses the development of multiple myeloma by targeting miR-33a-5p/PIM1 axis. Leuk Res 2021; 106:106565. [PMID: 33865032 DOI: 10.1016/j.leukres.2021.106565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Numerous long non-coding RNAs (lncRNAs) are reported to affect the progression of multiple myeloma (MM). This study is aimed to explore the role and downstream mechanism of lncRNA LINC01003 in MM. MATERIALS AND METHODS Xenograft tumor assay was used to assess the function of LINC01003 in MM in vivo. The mRNA expression levels of LINC01003, miR-33a-5p, and PIM1 were determined by quantitative real-time polymerase chain reaction. Cell viability was examined by MTT assay. Relative protein levels of apoptosis-related factors (Bcl-2 and Bax) and proviral integration site of the Moloney leukemia virus kinase 1 (PIM1) were detected via western blot. Adhesion-related proteins were measured by Enzyme-linked immunosorbent assay was used to determine the levels of adhesion-related proteins. Besides, the target relation among LINC01003, miR-33a-5p and PIM1 was tested via dual-luciferase reporter assay. RESULTS Low expression of LINC01003 was observed in MM cell lines and peripheral blood samples of MM patients. Both LINC01003 up-regulation and miR-33a-5p down-regulation repressed cell viability and adhesion, and promoted apoptosis of MM cells. Moreover, LINC01003 suppressed the growth of xenograft tumor in mice. We then identified miR-33a-5p as a downstream target of LINC01003, and confirmed that PIM1 was a direct target gene of miR-33a-5p. Both high expression of miR-33a-5p and low expression of PIM1 reversed the suppressive effects of LINC01003 overexpression on cell adhesion and viability, and the promoting effect on apoptosis in MM cells. CONCLUSION LINC01003 functioned as a sponge of miR-33a-5p to inhibit the development MM by regulating PIM1 expression.
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Affiliation(s)
- Linlin Wu
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Shushan District, Hefei City, Anhui Province, 230032, China
| | - Liang Xia
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Shushan District, Hefei City, Anhui Province, 230032, China
| | - Xiaowen Chen
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Shushan District, Hefei City, Anhui Province, 230032, China
| | - Min Ruan
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Shushan District, Hefei City, Anhui Province, 230032, China
| | - Lingling Li
- Department of Hematology of Anhui No.2 Provincial People's Hospital, No. 1868, Dangshan Road, Hefei City, Anhui Province, 230041, China
| | - Ruixiang Xia
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Shushan District, Hefei City, Anhui Province, 230032, China.
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75
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Leppek K, Byeon GW, Kladwang W, Wayment-Steele HK, Kerr CH, Xu AF, Kim DS, Topkar VV, Choe C, Rothschild D, Tiu GC, Wellington-Oguri R, Fujii K, Sharma E, Watkins AM, Nicol JJ, Romano J, Tunguz B, Participants E, Barna M, Das R. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.29.437587. [PMID: 33821271 PMCID: PMC8020971 DOI: 10.1101/2021.03.29.437587] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases, including COVID-19. However, their optimization is hindered by mRNA instability and inefficient protein expression. Here, we describe design principles that overcome these barriers. We develop a new RNA sequencing-based platform called PERSIST-seq to systematically delineate in-cell mRNA stability, ribosome load, as well as in-solution stability of a library of diverse mRNAs. We find that, surprisingly, in-cell stability is a greater driver of protein output than high ribosome load. We further introduce a method called In-line-seq, applied to thousands of diverse RNAs, that reveals sequence and structure-based rules for mitigating hydrolytic degradation. Our findings show that "superfolder" mRNAs can be designed to improve both stability and expression that are further enhanced through pseudouridine nucleoside modification. Together, our study demonstrates simultaneous improvement of mRNA stability and protein expression and provides a computational-experimental platform for the enhancement of mRNA medicines.
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Affiliation(s)
- Kathrin Leppek
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Adele F Xu
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Do Soon Kim
- Department of Biochemistry, Stanford University, California 94305, USA
| | - Ved V Topkar
- Program in Biophysics, Stanford University, Stanford, California 94305, USA
| | - Christian Choe
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Daphna Rothschild
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Gerald C Tiu
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | | | - Kotaro Fujii
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Eesha Sharma
- Department of Biochemistry, Stanford University, California 94305, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Jonathan Romano
- Eterna Massive Open Laboratory
- Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, New York, 14260, USA
| | - Bojan Tunguz
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Maria Barna
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, California 94305, USA
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He P, Zhang C, Chen G, Shen S. Loss of lncRNA SNHG8 promotes epithelial-mesenchymal transition by destabilizing CDH1 mRNA. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1858-1867. [PMID: 33754289 DOI: 10.1007/s11427-020-1895-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/22/2021] [Indexed: 10/21/2022]
Abstract
Long non-coding RNAs (lncRNAs) are widely involved in a variety of biological processes, including epithelial-mesenchymal transition (EMT). In the current study, we found that lncRNA small nucleolar RNA host gene 8 (SNHG8) was tightly correlated with EMT-associated gene signatures, and was down-regulated by Zinc finger E-box-binding homeobox 1 (ZEB1) during EMT progress. Functionally, knockdown of SNHG8 induced EMT in epithelial cells, through destabilizing the CDH1 mRNA dependent on a 17-nucleotide sequence shared by SNHG8 and CDH1. In addition, analysis with public database showed that SNHG8 tended to be down-regulated in different cancer types and the lower expression of SNHG8 predicted poorer prognosis. Taken together, our study reports a ZEB1-repressed lncRNA SNHG8 which is important for stabilizing CDH1 mRNA, thereby maintaining the epithelial status of epithelial cells.
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Affiliation(s)
- Ping He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Cheng Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guoqiang Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shaoming Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Verma S, Mishra R, Malik A, Chaudhary P, Malhotra SS, Panda AK, Gupta SK. miR-27b-5p inhibits BeWo cells fusion by regulating WNT2B and enzyme involved in progesterone synthesis. Am J Reprod Immunol 2021; 86:e13409. [PMID: 33639023 DOI: 10.1111/aji.13409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
PROBLEM The miRNAs show placenta-specific expression patterns, which alter during pregnancy-related complications. In present study, the role of miR-27b-5p during forskolin-mediated BeWo cells fusion has been investigated. METHOD OF STUDY The fusion of BeWo cells in response to forskolin treatment (25 µM) was studied by desmoplakin I+II staining. Expression profile of miR-27b-5p by qRT-PCR and its targets HSD3β1 and WNT2B by qRT-PCR and in Western blot were studied. The effect of overexpression of miR-27b-5p and silencing of HSD3β1 & WNT2B by siRNA on forskolin-mediated BeWo cells fusion and secretion of hCG and progesterone by ELISA was investigated. RESULTS Time-dependent down-regulation in the expression of miR-27b-5p in forskolin-treated BeWo cells has been confirmed by qRT-PCR. Overexpression of miR-27b-5p significantly inhibits forskolin-mediated BeWo cells fusion as well as hCG & progesterone secretion. HSD3β1 and WNT2B were identified as targets of miR-27b-5p and are up-regulated in forskolin-treated BeWo cells. Overexpression of miR-27b-5p in BeWo cells downregulates their expression. Further, luciferase reporter assay revealed that miR-27b-5p directly target expression of both HSD3β1 and WNT2B. Silencing of both HSD3β1 and WNT2B leads to a significant reduction in forskolin-mediated BeWo cells fusion with concomitant decrease in the secretion of progesterone or/and hCG. Decrease in forskolin-mediated cells fusion observed in miR-27b-5p mimic transfected BeWo cells could be rescued by the overexpression of both HSD3β1 and WNT2B. CONCLUSION These observations suggest that reduced miR-27b-5p in forskolin-treated BeWo cells leads to increased secretion of progesterone and hCG due to loss of repressional control on HSD3β1 and WNT2B.
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Affiliation(s)
- Sonam Verma
- Reproductive Cell Biology Lab, National Institute of Immunology, New Delhi, India
| | - Richa Mishra
- Reproductive Cell Biology Lab, National Institute of Immunology, New Delhi, India
| | - Ankita Malik
- Reproductive Cell Biology Lab, National Institute of Immunology, New Delhi, India
| | - Piyush Chaudhary
- Reproductive Cell Biology Lab, National Institute of Immunology, New Delhi, India
| | - Sudha Saryu Malhotra
- Reproductive Cell Biology Lab, National Institute of Immunology, New Delhi, India
| | - Amulya K Panda
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Satish Kumar Gupta
- Reproductive Cell Biology Lab, National Institute of Immunology, New Delhi, India
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Mehta N, Li R, Zhang D, Soomro A, He J, Zhang I, MacDonald M, Gao B, Krepinsky JC. miR299a-5p promotes renal fibrosis by suppressing the antifibrotic actions of follistatin. Sci Rep 2021; 11:88. [PMID: 33420269 PMCID: PMC7794215 DOI: 10.1038/s41598-020-80199-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/15/2020] [Indexed: 01/29/2023] Open
Abstract
Caveolin-1 (cav-1), an integral protein of the membrane microdomains caveolae, is required for synthesis of matrix proteins by glomerular mesangial cells (MC). Previously, we demonstrated that the antifibrotic protein follistatin (FST) is transcriptionally upregulated in cav-1 knockout MC and that its administration is protective against renal fibrosis. Here, we screened cav-1 wild-type and knockout MC for FST-targeting microRNAs in order to identity novel antifibrotic therapeutic targets. We identified that miR299a-5p was significantly suppressed in cav-1 knockout MC, and this was associated with stabilization of the FST 3'UTR. Overexpression and inhibition studies confirmed the role of miR299a-5p in regulating FST expression. Furthermore, the profibrotic cytokine TGFβ1 was found to stimulate the expression of miR299a-5p and, in turn, downregulate FST. Through inhibition of FST, miR299a-5p overexpression augmented, while miR299a-5p inhibition diminished TGFβ1 profibrotic responses, whereas miR299a-5p overexpression re-enabled cav-1 knockout MC to respond to TGFβ1. In vivo, miR299a-5p was upregulated in the kidneys of mice with chronic kidney disease (CKD). miR299a-5p inhibition protected these mice against renal fibrosis and CKD severity. Our data demonstrate that miR299a-5p is an important post-transcriptional regulator of FST, with its upregulation an important pathogenic contributor to renal fibrosis. Thus, miR299a-5p inhibition offers a potential novel therapeutic approach for CKD.
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Affiliation(s)
- Neel Mehta
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Renzhong Li
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Dan Zhang
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Asfia Soomro
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Juehua He
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Ivan Zhang
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Melissa MacDonald
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Bo Gao
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Joan C Krepinsky
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Canada.
- St. Joseph's Hospital, 50 Charlton Ave East, Rm T3311, Hamilton, ON, L8N 4A6, Canada.
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Pasquali D, Torella A, Accardo G, Esposito D, Del Vecchio Blanco F, Salvatore D, Sabatino P, Pacini F, Barbato F, Castagna MG, Cantara S, Nigro V. BROX haploinsufficiency in familial nonmedullary thyroid cancer. J Endocrinol Invest 2021; 44:165-171. [PMID: 32385852 DOI: 10.1007/s40618-020-01286-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND The familial nonmedullary thyroid cancer (FNMTC) is suspected to be a Mendelian condition in up to 3-8% of thyroid cancers. The susceptibility chromosomal loci and genes of 95% of FNMTC cases remain to be characterized. The inheritance of FNMTC appears to be autosomal dominant with incomplete penetrance and variable expressivity. The finding of the causative gene of FNMTC and the identification of patients at risk that need genetic testing were our aim. METHODS We analyzed by whole-exome sequencing patients and non-affected relatives of five families with at least two family members affected by papillary thyroid cancer, selecting for new or extremely rare variants with predicted pathogenic value. RESULTS A family showed, in all three affected members, a new loss-of-function variant (frameshift deletion) in BROX gene at 1q41 that was absent from all internal and external databases. In a second family with three affected relatives, we found an additional new BROX variant. The smaller families presented no variants in BROX or in the other causative genes studied. CONCLUSIONS BROX could be a new causative gene for FNMTC. Variants in BROX may result in the haploinsufficiency of a key gene involved in the morphogenesis of MVBs, in the endosomal sorting of cargo proteins, and in EGFR. Functional studies are needed to support this result. The thorough genomic analysis by NGS in all families with three or more affected members should become a routine approach to obtain a comprehensive genetic view and find confirmative second cases.
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Affiliation(s)
- D Pasquali
- Department of Medical and Surgical Advanced Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy.
| | - A Torella
- Genetica Medica, Dipartimento di Medicina di Precisione, University of Campania"Luigi Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - G Accardo
- Department of Medical and Surgical Advanced Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - D Esposito
- Department of Endocrinology, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - F Del Vecchio Blanco
- Genetica Medica, Dipartimento di Medicina di Precisione, University of Campania"Luigi Vanvitelli", Naples, Italy
| | - D Salvatore
- Department of Public Health, University of Naples "Federico II", Naples, Italy
| | - P Sabatino
- Azienda Sanitaria Locale Salerno, Naples, Italy
| | - F Pacini
- Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - F Barbato
- Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - M G Castagna
- Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - S Cantara
- Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - V Nigro
- Genetica Medica, Dipartimento di Medicina di Precisione, University of Campania"Luigi Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
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80
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Moslehi R, Tsao HS, Zeinomar N, Stagnar C, Fitzpatrick S, Dzutsev A. Integrative genomic analysis implicates ERCC6 and its interaction with ERCC8 in susceptibility to breast cancer. Sci Rep 2020; 10:21276. [PMID: 33277540 PMCID: PMC7718875 DOI: 10.1038/s41598-020-77037-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
Up to 30% of all breast cancer cases may be inherited and up to 85% of those may be due to segregation of susceptibility genes with low and moderate risk [odds ratios (OR) ≤ 3] for (mostly peri- and post-menopausal) breast cancer. The majority of low/moderate-risk genes, particularly those with minor allele frequencies (MAF) of < 30%, have not been identified and/or validated due to limitations of conventional association testing approaches, which include the agnostic nature of Genome Wide Association Studies (GWAS). To overcome these limitations, we used a hypothesis-driven integrative genomics approach to test the association of breast cancer with candidate genes by analyzing multi-omics data. Our candidate-gene association analyses of GWAS datasets suggested an increased risk of breast cancer with ERCC6 (main effect: 1.29 ≤ OR ≤ 2.91, 0.005 ≤ p ≤ 0.04, 11.8 ≤ MAF ≤ 40.9%), and implicated its interaction with ERCC8 (joint effect: 3.03 ≤ OR ≤ 5.31, 0.01 ≤ pinteraction ≤ 0.03). We found significant upregulation of ERCC6 (p = 7.95 × 10-6) and ERCC8 (p = 4.67 × 10-6) in breast cancer and similar frequencies of ERCC6 (1.8%) and ERCC8 (0.3%) mutations in breast tumors to known breast cancer susceptibility genes such as BLM (1.9%) and LSP1 (0.3%). Our integrative genomics approach suggests that ERCC6 may be a previously unreported low- to moderate-risk breast cancer susceptibility gene, which may also interact with ERCC8.
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Affiliation(s)
- Roxana Moslehi
- School of Public Health, Cancer Research Center, University at Albany, State University of New York (SUNY), Albany, NY, 12144, USA.
| | - Hui-Shien Tsao
- School of Public Health, Cancer Research Center, University at Albany, State University of New York (SUNY), Albany, NY, 12144, USA
- New York State Office of Children and Family Services, New York, USA
| | - Nur Zeinomar
- School of Public Health, Cancer Research Center, University at Albany, State University of New York (SUNY), Albany, NY, 12144, USA
- Mailman School of Public Health, Columbia University, New York, USA
| | - Cristy Stagnar
- School of Public Health, Cancer Research Center, University at Albany, State University of New York (SUNY), Albany, NY, 12144, USA
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, USA
| | - Sean Fitzpatrick
- School of Public Health, Cancer Research Center, University at Albany, State University of New York (SUNY), Albany, NY, 12144, USA
| | - Amiran Dzutsev
- Cancer Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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81
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Variants in the RARRES2 gene are associated with serum chemerin and increase the risk of diabetic kidney disease in type 2 diabetes. Int J Biol Macromol 2020; 165:1574-1580. [DOI: 10.1016/j.ijbiomac.2020.10.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/26/2020] [Accepted: 10/04/2020] [Indexed: 12/19/2022]
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82
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Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing. Sci Rep 2020; 10:20496. [PMID: 33235226 PMCID: PMC7686369 DOI: 10.1038/s41598-020-77520-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
Long-read sequencing (LRS) has become a standard approach for transcriptome analysis in recent years. Bovine alphaherpesvirus 1 (BoHV-1) is an important pathogen of cattle worldwide. This study reports the profiling of the dynamic lytic transcriptome of BoHV-1 using two long-read sequencing (LRS) techniques, the Oxford Nanopore Technologies MinION, and the LoopSeq synthetic LRS methods, using multiple library preparation protocols. In this work, we annotated viral mRNAs and non-coding transcripts, and a large number of transcript isoforms, including transcription start and end sites, as well as splice variants of BoHV-1. Our analysis demonstrated an extremely complex pattern of transcriptional overlaps.
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83
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Oe S, Koike T, Hirahara Y, Tanaka S, Hayashi S, Nakano Y, Kase M, Noda Y, Yamada H, Kitada M. AUF1, an mRNA decay factor, has a discordant role in Cpeb1 expression. Biochem Biophys Res Commun 2020; 534:491-497. [PMID: 33220927 DOI: 10.1016/j.bbrc.2020.11.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/12/2020] [Indexed: 12/19/2022]
Abstract
Cytoplasmic polyadenylation element binding protein 1 (CPEB1) regulates polyadenylation and subsequent translation of CPE-containing mRNAs involved in various physiological and pathological phenomena. Although the significance of CPEB1-mediated translational regulation has recently been reported, the detailed regulatory mechanism of Cpeb1 expression remains unclear. To elucidate the post-transcriptional regulatory mechanisms of Cpeb1 expression, we constructed reporter plasmids containing various deletions or mutations in the Cpeb1 mRNA 3' untranslated region (3'UTR). We investigated their expression levels in Neuro2a neuroblastoma cells. We found that Cpeb1 expression is regulated through an AU-rich element in its 3'UTR. Furthermore, the mRNA decay factor AU-rich binding factor 1 (AUF1) regulates Cpeb1 expression, and knockdown of AUF1 upregulates Cpeb1 mRNA expression but results in a decrease in CPEB1 protein levels. These findings indicate that AUF1 has a discordant role in the expression of Cpeb1.
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Affiliation(s)
- Souichi Oe
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan.
| | - Taro Koike
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Yukie Hirahara
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Susumu Tanaka
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Shinichi Hayashi
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Yosuke Nakano
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Masahiko Kase
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Yasuko Noda
- Department of Anatomy, Bio-imaging and Neuro-cell Science, Jichi Medical University, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hisao Yamada
- Biwako Professional University of Rehabilitation, Higashi-Ohmi, Shiga, 527-0145, Japan
| | - Masaaki Kitada
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
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84
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Sia KC, Fu ZY, Calne RY, Nathwani AC, Lee KO, Gan SU. Modification of a Constitutive to Glucose-Responsive Liver-Specific Promoter Resulted in Increased Efficacy of Adeno-Associated Virus Serotype 8-Insulin Gene Therapy of Diabetic Mice. Cells 2020; 9:cells9112474. [PMID: 33202992 PMCID: PMC7696068 DOI: 10.3390/cells9112474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/02/2023] Open
Abstract
We have previously used a hepatotropic adeno-associated viral (AAV) vector with a modified human insulin gene to treat diabetic mice. The HLP (hybrid liver-specific promoter) used was constitutively active and non-responsive to glucose. In this study, we examined the effects of addition of glucose responsive elements (R3G) and incorporation of a 3' albumin enhancer (3'iALB) on insulin expression. In comparison with the original promoter, glucose responsiveness was only observed in the modified promoters in vitro with a 36 h lag time before the peak expression. A 50% decrease in the number of viral particles at 5 × 109 vector genome (vg)/mouse was required by AAV8-R3GHLP-hINSco to reduce the blood sugar level to near normoglycemia when compared to the original AAV8-HLP-hINSco that needed 1 × 1010 vg/mouse. The further inclusion of an 860 base-pairs 3'iALB enhancer component in the 3' untranslated region increased the in vitro gene expression significantly but this increase was not observed when the packaged virus was systemically injected in vivo. The addition of R3G to the HLP promoter in the AAV8-human insulin vector increased the insulin expression and secretion, thereby lowering the required dosage for basal insulin treatment. This in turn reduces the risk of liver toxicity and cost of vector production.
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Affiliation(s)
- Kian Chuan Sia
- Department of Surgery, National University of Singapore, Singapore 117597, Singapore; (K.C.S.); (Z.Y.F.); (R.Y.C.)
| | - Zhen Ying Fu
- Department of Surgery, National University of Singapore, Singapore 117597, Singapore; (K.C.S.); (Z.Y.F.); (R.Y.C.)
| | - Roy Y. Calne
- Department of Surgery, National University of Singapore, Singapore 117597, Singapore; (K.C.S.); (Z.Y.F.); (R.Y.C.)
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Amit C. Nathwani
- Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK;
| | - Kok Onn Lee
- Department of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Shu Uin Gan
- Department of Surgery, National University of Singapore, Singapore 117597, Singapore; (K.C.S.); (Z.Y.F.); (R.Y.C.)
- Correspondence: ; Tel.: +65-6601-2465
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85
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Mušo M, Dumbell R, Pulit S, Sinnott-Armstrong N, Laber S, Zolkiewski L, Bentley L, Claussnitzer M, Cox RD. A lead candidate functional single nucleotide polymorphism within the WARS2 gene associated with waist-hip-ratio does not alter RNA stability. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194640. [PMID: 33007465 PMCID: PMC7695619 DOI: 10.1016/j.bbagrm.2020.194640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 11/06/2022]
Abstract
We have prioritised a single nucleotide polymorphism (SNP) rs2645294 as one candidate functional SNP in the TBX15-WARS2 waist-hip-ratio locus using posterior probability analysis. This SNP is located in the 3' untranslated region of the WARS2 (tryptophanyl tRNA synthetase 2, mitochondrial) gene with which it has an expression quantitative trait in subcutaneous white adipose tissue. We show that transcripts of the WARS2 gene in a human white adipose cell line, heterozygous for the rs2645294 SNP, showed allelic imbalance. We tested whether the rs2645294 SNP altered WARS2 RNA stability using three different methods: actinomycin-D inhibition and RNA decay, mature and nascent RNA analysis and luciferase reporter assays. We found no evidence of a difference in RNA stability between the rs2645294 alleles indicating that the allelic expression imbalance was likely due to transcriptional regulation.
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Affiliation(s)
- Milan Mušo
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Rebecca Dumbell
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Sara Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Big Data Institute, Li Ka Shing Center for Health Information and Discovery, Oxford University, Oxford, UK; Program in Medical Population Genetics, Broad Institute, Cambridge, MA, USA
| | | | - Samantha Laber
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Louisa Zolkiewski
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Liz Bentley
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Melina Claussnitzer
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Gerontology Division, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Institute of Nutritional Science, University of Hohenheim, Stuttgart, Germany
| | - Roger D Cox
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK.
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86
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Gupta R, Schrooders Y, Hauser D, van Herwijnen M, Albrecht W, Ter Braak B, Brecklinghaus T, Castell JV, Elenschneider L, Escher S, Guye P, Hengstler JG, Ghallab A, Hansen T, Leist M, Maclennan R, Moritz W, Tolosa L, Tricot T, Verfaillie C, Walker P, van de Water B, Kleinjans J, Caiment F. Comparing in vitro human liver models to in vivo human liver using RNA-Seq. Arch Toxicol 2020; 95:573-589. [PMID: 33106934 PMCID: PMC7870774 DOI: 10.1007/s00204-020-02937-6] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2020] [Indexed: 01/29/2023]
Abstract
The liver plays an important role in xenobiotic metabolism and represents a primary target for toxic substances. Many different in vitro cell models have been developed in the past decades. In this study, we used RNA-sequencing (RNA-Seq) to analyze the following human in vitro liver cell models in comparison to human liver tissue: cancer-derived cell lines (HepG2, HepaRG 3D), induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-HLCs), cancerous human liver-derived assays (hPCLiS, human precision cut liver slices), non-cancerous human liver-derived assays (PHH, primary human hepatocytes) and 3D liver microtissues. First, using CellNet, we analyzed whether these liver in vitro cell models were indeed classified as liver, based on their baseline expression profile and gene regulatory networks (GRN). More comprehensive analyses using non-differentially expressed genes (non-DEGs) and differential transcript usage (DTU) were applied to assess the coverage for important liver pathways. Through different analyses, we noticed that 3D liver microtissues exhibited a high similarity with in vivo liver, in terms of CellNet (C/T score: 0.98), non-DEGs (10,363) and pathway coverage (highest for 19 out of 20 liver specific pathways shown) at the beginning of the incubation period (0 h) followed by a decrease during long-term incubation for 168 and 336 h. PHH also showed a high degree of similarity with human liver tissue and allowed stable conditions for a short-term cultivation period of 24 h. Using the same metrics, HepG2 cells illustrated the lowest similarity (C/T: 0.51, non-DEGs: 5623, and pathways coverage: least for 7 out of 20) with human liver tissue. The HepG2 are widely used in hepatotoxicity studies, however, due to their lower similarity, they should be used with caution. HepaRG models, iPSC-HLCs, and hPCLiS ranged clearly behind microtissues and PHH but showed higher similarity to human liver tissue than HepG2 cells. In conclusion, this study offers a resource of RNA-Seq data of several biological replicates of human liver cell models in vitro compared to human liver tissue.
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Affiliation(s)
- Rajinder Gupta
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Yannick Schrooders
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Duncan Hauser
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Marcel van Herwijnen
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Wiebke Albrecht
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Bas Ter Braak
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9503, 2300 RA, Leiden, The Netherlands
| | - Tim Brecklinghaus
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Jose V Castell
- Instituto de Investigación Sanitaria La Fe, Experimental Hepatology Unit, Valencia, Spain
| | - Leroy Elenschneider
- Fraunhofer Institute for Toxicology and Experimental Medicine Preclinical Pharmacology and In-Vitro Toxicology, Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Sylvia Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine Preclinical Pharmacology and In-Vitro Toxicology, Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Patrick Guye
- InSphero AG, Wagistrasse 27, 8952, Schlieren, Switzerland
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Tanja Hansen
- Fraunhofer Institute for Toxicology and Experimental Medicine Preclinical Pharmacology and In-Vitro Toxicology, Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated, Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Richard Maclennan
- Cyprotex Discovery, No 24 Mereside, Alderley Park, Cheshire, SK10 4TG, UK
| | | | - Laia Tolosa
- Instituto de Investigación Sanitaria La Fe, Unidad Hepatología Experimental, Valencia, Spain
| | - Tine Tricot
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Paul Walker
- Cyprotex Discovery, No 24 Mereside, Alderley Park, Cheshire, SK10 4TG, UK
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9503, 2300 RA, Leiden, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.
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87
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Li J, Durose WW, Ito J, Kakita A, Iguchi Y, Katsuno M, Kunisawa K, Shimizu T, Ikenaka K. Exploring the factors underlying remyelination arrest by studying the post-transcriptional regulatory mechanisms of cystatin F gene. J Neurochem 2020; 157:2070-2090. [PMID: 32947653 DOI: 10.1111/jnc.15190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/11/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022]
Abstract
Remyelination plays an important role in determining the fate of demyelinating disorders. However, it is arrested during chronic disease states. Cystatin F, a papain-like lysosomal cysteine proteinase inhibitor, is a crucial regulator of demyelination and remyelination. Using hemizygous proteolipid protein transgenic 4e (PLP4e/- ) mice, an animal model of chronic demyelination, we found that cystatin F mRNA expression was induced at 2.5 months of age and up-regulated in the early phase of demyelination, but significantly decreased in the chronic phase. We next investigated cystatin F regulatory factors as potential mechanisms of remyelination arrest in chronic demyelinating disorders. We used the CysF-STOP-tetO::Iba-mtTA mouse model, in which cystatin F gene expression is driven by the tetracycline operator. Interestingly, we found that forced cystatin F mRNA over-expression was eventually decreased. Our findings show that cystatin F expression is modulated post-transcriptionally. We next identified embryonic lethal, abnormal vision, drosophila like RNA-binding protein 1 (ELAVL-1), and miR29a as cystatin F mRNA stabilizing and destabilizing factors, respectively. These roles were confirmed in vitro in NIH3T3 cells. Using postmortem plaque samples from human multiple sclerosis patients, we also confirmed that ELAVL-1 expression was highly correlated with the previously reported expression pattern of cystatin F. These data indicate the important roles of ELAVL-1 and miR29a in regulating cystatin F expression. Furthermore, they provide new insights into potential therapeutic targets for demyelinating disorders.
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Affiliation(s)
- Jiayi Li
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Wilaiwan Wisessmith Durose
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom, Thailand.,Department of Pediatrics, Hematology University of Minnesota, Minneapolis, MN, USA
| | - Junko Ito
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yohei Iguchi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuo Kunisawa
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Research Division of Advanced Diagnostic System, Graduate School of Health Sciences, Fujita Health University, Toyoake, Japan
| | - Takeshi Shimizu
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Department of Neurophysiology and Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Kazuhiro Ikenaka
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
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88
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Nail AN, Spear BT, Peterson ML. Highly homologous mouse Cyp2a4 and Cyp2a5 genes are differentially expressed in the liver and both express long non-coding antisense RNAs. Gene 2020; 767:145162. [PMID: 32987105 DOI: 10.1016/j.gene.2020.145162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/04/2020] [Accepted: 09/17/2020] [Indexed: 11/16/2022]
Abstract
The mammalian Cytochrome P450 (Cyp) gene superfamily encodes enzymes involved in numerous metabolic pathways and are frequently expressed in the liver. Despite the remarkably high sequence similarity of Cyp2a4 and Cyp2a5 genes and their surrounding genomic regions, they exhibit differences in expression in the adult mouse liver. For example, Cyp2a4 is highly female-biased whereas Cyp2a5 is only moderately female-biased and Cyp2a4, but not Cyp2a5, is activated in liver cancer. We hypothesized that the limited sequence differences may help us identify the basis for this differential expression. An antisense expressed sequence tag had been uniquely annotated to the Cyp2a4 gene which led us to investigate this transcript as a possible regulator of this gene. We characterized the full-length antisense transcript and also discovered a similar transcript in the Cyp2a5 gene. These transcripts are nuclear long noncoding RNAs that are expressed similarly to their sense mRNA counterparts. This includes the sex-biased and liver tumor differences seen between the Cyp2a4 and Cyp2a5 genes, but we also find that these two genes and their antisense transcripts are expressed within different zones of the liver structure. Interestingly, while the differences in sex-biased expression of the mRNAs are established 1-2 months after birth, the antisense transcripts exhibit these expression differences earlier, at 3-4 weeks after birth. By analyzing published genomic data, we have identified candidate transcription factor binding sites that could account for differences in Cyp2a4/Cyp2a5 expression. Taken together, these studies characterize the first antisense RNAs within the Cyp supergene family and identify potential transcriptional and post-transcriptional mechanisms governing different Cyp2a4 and Cyp2a5 expression patterns in mouse liver.
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Affiliation(s)
- Alexandra N Nail
- Department of Microbiology, Immunology and Molecular Genetics, USA
| | - Brett T Spear
- Department of Microbiology, Immunology and Molecular Genetics, USA; Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Martha L Peterson
- Department of Microbiology, Immunology and Molecular Genetics, USA; Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA.
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89
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Lu Z, Liu J, Yuan C, Jin M, Quan K, Chu M, Wei C. m 6A mRNA methylation analysis provides novel insights into heat stress responses in the liver tissue of sheep. Genomics 2020; 113:484-492. [PMID: 32976974 DOI: 10.1016/j.ygeno.2020.09.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/31/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
N6-methyladenosine (m6A) mRNA methylation varies in response to stress. However, no map of m6A mRNA methylation has been obtained for sheep, nor is it known what effect this has on regulating heat stress in sheep. Here, we obtained m6A methylation maps of sheep liver tissues with and without heat stress by MeRIP-seq. In total, 8306 m6A peaks associated with 2697 genes were detected in the heat stress group, and 12,958 m6A peaks associated with 5494 genes were detected in the control group. Peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. Methylation levels of heat stress and control sheep were higher near stop codons, although methylation was significantly lower in heat stress sheep. GO and KEGG revealed that differential m6A-containing genes were significantly enriched in the stress response and fat metabolism. Our results showed that m6A mRNA methylation modifications regulate heat stress in sheep.
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Affiliation(s)
- Zengkui Lu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Meilin Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China..
| | - Caihong Wei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China..
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90
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Kim W, Shin JC, Lee KH, Kim KT. PTBP1 Positively Regulates the Translation of Circadian Clock Gene, Period1. Int J Mol Sci 2020; 21:ijms21186921. [PMID: 32967200 PMCID: PMC7555454 DOI: 10.3390/ijms21186921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/19/2020] [Accepted: 09/19/2020] [Indexed: 11/16/2022] Open
Abstract
Circadian oscillations of mRNAs and proteins are the main features of circadian clock genes. Among them, Period1 (Per1) is a key component in negative-feedback regulation, which shows a robust diurnal oscillation and the importance of circadian rhythm and translational regulation of circadian clock genes has been recognized. In the present study, we investigated the 5'-untranslated region (5'-UTR) of the mouse core clock gene, Per1, at the posttranscriptional level, particularly its translational regulation. The 5'-UTR of Per1 was found to promote its translation via an internal ribosomal entry site (IRES). We found that polypyrimidine tract-binding protein 1 (PTBP1) binds to the 5'-UTR of Per1 and positively regulates the IRES-mediated translation of Per1 without affecting the levels of Per1 mRNA. The reduction of PTBP1 level also decreased the endogenous levels of the PER1 protein but not of its mRNA. As for the oscillation of PER1 expression, the disruption of PTBP1 levels lowered the PER1 expression but not the phase of the oscillation. PTBP1 also changed the amplitudes of the mRNAs of other circadian clock genes, such as Cryptochrome 1 (Cry1) and Per3. Our results suggest that the PTBP1 is important for rhythmic translation of Per1 and it fine-tunes the overall circadian system.
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Affiliation(s)
- Wanil Kim
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
| | | | - Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
- Correspondence: (K.-H.L.); (K.-T.K.); Tel.: +82-53-819-7743 (K.-H.L.); +82-54-279-2297 (K.-T.K.)
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology, Cheongam-Ro 77, Pohang, Gyeongbuk 37673, Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Cheongam-Ro 77, Pohang, Gyeongbuk 37673, Korea
- Correspondence: (K.-H.L.); (K.-T.K.); Tel.: +82-53-819-7743 (K.-H.L.); +82-54-279-2297 (K.-T.K.)
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91
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Sayed KS, El-Komy MHM, Shehata H, ElShazly SH, El Desouky ED, Amr KS, ElAraby NM, AlOrbani AM. JAK1 rs310241 and JAK3 rs3008 Genotypes May Increase Susceptibility to Psoriasis: A Case Control Study. Skin Pharmacol Physiol 2020; 33:207-212. [PMID: 32877908 DOI: 10.1159/000509880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/17/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Janus kinases (JAKs) are a family of non-receptor protein tyrosine kinases that are expressed in a variety of tissues. Several JAK-controlled cytokine receptor pathways are incriminated in the initiation and progression of psoriasis. Genetic polymorphisms influencing JAK expression would be anticipated to have a great impact on disease activity. OBJECTIVE The aim of the study was to evaluate the association between JAK1 rs310241 and JAK3 rs3008 polymorphisms and the risk of developing psoriasis. METHODS Blood samples of 150 patients and 120 controls were screened for nucleotide polymorphisms in JAK1 rs310241 and JAK3 rs3008 genes by using polymerase chain reaction (PCR)-restriction fragment length polymorphism technique. RESULTS The GG genotype of the JAK1 rs310241 and JAK3 rs3008 genes was significantly associated with an increase in psoriasis risk (p = 0.000, OR = 7.7, 95% CI = 2.8-21.5; p = 0.003, OR = 3.3, 95% CI = 1.5-6.9, respectively). The G allele of both genes was also associated with psoriasis susceptibility (p = 0.000, OR = 2.0, 95% CI = 1.4-2.8; p = 0.002, OR = 1.7, 95% CI = 1.2-2.4, respectively). CONCLUSION The results indicate a possible association between JAK1 rs310241 and JAK3 rs3008 gene polymorphisms and susceptibility to psoriasis. These findings validate the importance of these molecules in psoriasis and may enable the identification of the individuals most susceptible to the disease.
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Affiliation(s)
- Khadiga S Sayed
- Dermatology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.,Kasr AL-Ainy's Psoriasis Unit (KAPU), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed H M El-Komy
- Dermatology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.,Kasr AL-Ainy's Psoriasis Unit (KAPU), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Hany Shehata
- Department of Dermatology and Venereology, National Research Centre, Giza, Egypt
| | - Sarah H ElShazly
- Dermatology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Eman D El Desouky
- Department of Epidemiology and Biostatistics, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Khalda Sayed Amr
- Medical Molecular Genetics Department, National Research Centre, Giza, Egypt
| | - Nesma M ElAraby
- Medical Molecular Genetics Department, National Research Centre, Giza, Egypt
| | - Aya M AlOrbani
- Dermatology Department, Faculty of Medicine, Cairo University, Cairo, Egypt, .,Kasr AL-Ainy's Psoriasis Unit (KAPU), Faculty of Medicine, Cairo University, Cairo, Egypt,
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92
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Pizarro M, Landi V, Navas F, León J, Martínez A, Fernández J, Delgado J. Nonparametric analysis of casein complex genes' epistasis and their effects on phenotypic expression of milk yield and composition in Murciano-Granadina goats. J Dairy Sci 2020; 103:8274-8291. [DOI: 10.3168/jds.2019-17833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/07/2020] [Indexed: 01/17/2023]
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93
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Seleit I, Bakry OA, Badr E, Mabrouk M. Vitamin D Receptor Gene Polymorphisms Taq-1 and Cdx-1 in Female Pattern Hair Loss. Indian J Dermatol 2020; 65:259-264. [PMID: 32831364 PMCID: PMC7423221 DOI: 10.4103/ijd.ijd_482_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Female pattern hair loss (FPHL) is an important cause of hair loss in adult women and has a major impact on patient's quality of life. It evolves from the progressive miniaturization of follicles that leads to a subsequent decrease of hair density, leading to non-scarring diffuse alopecia, with characteristic clinical, dermoscopic, and histological patterns. Vitamin D receptor (VDR) is expressed in follicular keratinocytes and dermal papilla cells and is shown to have important role in hair growth and regulation of hair cycle. VDR polymorphism was not extensively investigated in hair disorders including FPHL. Aim To investigate the association between VDR gene polymorphism (Cdx-1 and Taq-1) and FPHL to explore if these polymorphisms affect the disease occurrence or influence its clinical presentation. Methods A case-control study was conducted on 30 female patients with FPHL and 30 age-matched female healthy subjects, as a control group. Degree of hair loss was assessed by Ludwig grading. VDR gene polymorphisms, Taq-1 and Cdx-1 were investigated by real time polymerase chain reaction. Results CC genotype, TC genotype, and T allele of Taq-1 were more prevalent in FPHL patients than in control group. They increased disease risk by 12.6, 2.1, and 2.9 folds, respectively. AA genotype, GA genotype, and G allele of Cdx-1 were significantly more prevalent among FPHL patients than in control group. They increased disease risk by 7.5, 5.2, and 5.5 folds, respectively. Conclusion Taq-1 and Cdx-1 can be considered as risk factors for FPHL. They may play role in disease persistence rather than disease initiation. This association may be explained by failure of new anagen growth and decreased proliferation of hair follicle stem cells. Further studies are recommended to confirm current findings.
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Affiliation(s)
- Iman Seleit
- Department of Dermatology, Andrology and STDs, Menoufiya University, Shibeen El Koom, Menoufiya Governorate, Egypt
| | - Ola Ahmed Bakry
- Department of Dermatology, Andrology and STDs, Menoufiya University, Shibeen El Koom, Menoufiya Governorate, Egypt
| | - Eman Badr
- Department of Medical Biochemistry, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Menoufiya Governorate, Egypt
| | - Mai Mabrouk
- Department of Dermatology, Andrology and STDs, Menoufiya University, Shibeen El Koom, Menoufiya Governorate, Egypt
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94
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Yao W, Guo P, Mu Q, Wang Y. Exosome-Derived Circ-PVT1 Contributes to Cisplatin Resistance by Regulating Autophagy, Invasion, and Apoptosis Via miR-30a-5p/YAP1 Axis in Gastric Cancer Cells. Cancer Biother Radiopharm 2020; 36:347-359. [PMID: 32799541 DOI: 10.1089/cbr.2020.3578] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background: Emerging studies manifested that exosomal RNAs had pivotal roles in human cancer therapies. This article aimed to research the regulatory mechanism of exosomal circRNA-plasmacytoma variant translocation 1 (circ-PVT1) in cisplatin (DDP) resistance of gastric cancer (GC). Methods: Exosomes were isolated by ExoQuick® method and ultracentrifugation and then identified through transmission electron microscope and the examination of exosome markers. Related proteins were detected using Western blot. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied for measuring circ-PVT1, microRNA-30a-5p (miR-30a-5p), and Yes-associated protein 1 (YAP1) expression. The half inhibitory concentration (IC50) of DDP was assessed by 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT). Cell apoptosis and invasion were, respectively, determined using flow cytometry and transwell assay. Target relationship was confirmed by dual-luciferase reporter assay. The impact of circ-PVT1 on DDP resistance was explored via xenograft tumor assay. Results: Exosomal circ-PVT1 was upregulated while miR-30a-5p was downregulated in DDP-resistant GC serums and cells. Circ-PVT1 knockdown repressed DDP resistance in DDP-resistant GC cells via promoting apoptosis and decreasing invasion or autophagy by negatively targeting miR-30a-5p. YAP1 was a direct target of miR-30a-5p. MiR-30a-5p overexpression inhibited DDP resistance via reducing YAP1. Circ-PVT1 modulated YAP1 expression by targeting miR-30a-5p. Circ-PVT1 depression expedited DDP sensitivity of GC via miR-30a-5p/YAP1 axis in vivo. Conclusion: Exosomal circ-PVT1 facilitated DDP resistance via modulating autophagy, invasion and apoptosis by miR-30a-5p/YAP1 axis in GC cells. Exosomal circ-PVT1 might be a prospective indicator in DDP therapy of GC.
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Affiliation(s)
- Wenjuan Yao
- Department of Clinical Laboratory, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Peng Guo
- Department of Hepatology and Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Qiming Mu
- Department of Clinical Laboratory, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Yuecheng Wang
- Department of Gastroenterology, Renmin Hospital, Hubei University of Medicine, Shiyan, China
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95
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Laso‐Jadart R, Sugier K, Petit E, Labadie K, Peterlongo P, Ambroise C, Wincker P, Jamet J, Madoui M. Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866). Ecol Evol 2020; 10:8894-8905. [PMID: 32884665 PMCID: PMC7452778 DOI: 10.1002/ece3.6588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/04/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population-scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009-2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR < 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87, p = 5.6 × 10-30), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6%) were under both selection and psADE (p < .05), supporting the hypothesis that natural selection and psADE tends to impact common loci. Population-scale allelic differential expression offers new insights into the gene regulation control in populations and its link with natural selection.
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Affiliation(s)
- Romuald Laso‐Jadart
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
| | - Kevin Sugier
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
| | - Emmanuelle Petit
- CEA, GenoscopeInstitut de Biologie François JacobUniversité Paris‐SaclayEvryFrance
| | - Karine Labadie
- CEA, GenoscopeInstitut de Biologie François JacobUniversité Paris‐SaclayEvryFrance
| | | | | | - Patrick Wincker
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
| | - Jean‐Louis Jamet
- Mediterranean Institute of Oceanology (MIO)AMU‐UTLN UM110CNRS UMR7294, IRDUMR235Equipe Ecologie Marine et Biodiversité (EMBIO)Université de ToulonToulon Cedex 9France
| | - Mohammed‐Amin Madoui
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
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96
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Seenappa V, Joshi MB, Satyamoorthy K. Intricate Regulation of Phosphoenolpyruvate Carboxykinase (PEPCK) Isoforms in Normal Physiology and Disease. Curr Mol Med 2020; 19:247-272. [PMID: 30947672 DOI: 10.2174/1566524019666190404155801] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The phosphoenolpyruvate carboxykinase (PEPCK) isoforms are considered as rate-limiting enzymes for gluconeogenesis and glyceroneogenesis pathways. PEPCK exhibits several interesting features such as a) organelle-specific isoforms (cytosolic and a mitochondrial) in vertebrate clade, b) tissue-specific expression of isoforms and c) organism-specific requirement of ATP or GTP as a cofactor. In higher organisms, PEPCK isoforms are intricately regulated and activated through several physiological and pathological stimuli such as corticoids, hormones, nutrient starvation and hypoxia. Isoform-specific transcriptional/translational regulation and their interplay in maintaining glucose homeostasis remain to be fully understood. Mounting evidence indicates the significant involvement of PEPCK isoforms in physiological processes (development and longevity) and in the progression of a variety of diseases (metabolic disorders, cancer, Smith-Magenis syndrome). OBJECTIVE The present systematic review aimed to assimilate existing knowledge of transcriptional and translational regulation of PEPCK isoforms derived from cell, animal and clinical models. CONCLUSION Based on current knowledge and extensive bioinformatics analysis, in this review we have provided a comparative (epi)genetic understanding of PCK1 and PCK2 genes encompassing regulatory elements, disease-associated polymorphisms, copy number variations, regulatory miRNAs and CpG densities. We have also discussed various exogenous and endogenous modulators of PEPCK isoforms and their signaling mechanisms. A comprehensive review of existing knowledge of PEPCK regulation and function may enable identification of the underlying gaps to design new pharmacological strategies and interventions for the diseases associated with gluconeogenesis.
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Affiliation(s)
- Venu Seenappa
- School of Life Sciences, Manipal Academy of Higher Education, Manipal - 576104, India
| | - Manjunath B Joshi
- School of Life Sciences, Manipal Academy of Higher Education, Manipal - 576104, India
| | - Kapaettu Satyamoorthy
- School of Life Sciences, Manipal Academy of Higher Education, Manipal - 576104, India
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97
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Jia Q, Nie H, Yu P, Xie B, Wang C, Yang F, Wei G, Ni T. HNRNPA1-mediated 3' UTR length changes of HN1 contributes to cancer- and senescence-associated phenotypes. Aging (Albany NY) 2020; 11:4407-4437. [PMID: 31257225 PMCID: PMC6660030 DOI: 10.18632/aging.102060] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/24/2019] [Indexed: 01/10/2023]
Abstract
Cellular senescence has been regarded as a mechanism of tumor suppression. Studying the regulation of gene expression at various levels in cell senescence will shed light on cancer therapy. Alternative polyadenylation (APA) regulates gene expression by altering 3′ untranslated regions (3′ UTR) and plays important roles in diverse biological processes. However, whether APA of a specific gene functions in both cancer and senescence remains unclear. Here, we discovered that 3′ UTR of HN1 (or JPT1) showed shortening in cancers and lengthening in senescence, correlated well with its high expression in cancer cells and low expression in senescent cells, respectively. HN1 transcripts with longer 3′ UTR were less stable and produced less protein. Down-regulation of HN1 induced senescence-associated phenotypes in both normal and cancer cells. Patients with higher HN1 expression had lower survival rates in various carcinomas. Interestingly, down-regulating the splicing factor HNRNPA1 induced 3′ UTR lengthening of HN1 and senescence-associated phenotypes, which could be partially reversed by overexpressing HN1. Together, we revealed for the first time that HNRNPA1-mediated APA of HN1 contributed to cancer- and senescence-related phenotypes. Given senescence is a cancer prevention mechanism, our discovery indicates the HNRNPA1-HN1 axis as a potential target for cancer treatment.
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Affiliation(s)
- Qi Jia
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Hongbo Nie
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P.R. China
| | - Peng Yu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Baiyun Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Fu Yang
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, P.R. China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
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98
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Artificial miRNAs targeting CAG repeat expansion in ORFs cause rapid deadenylation and translation inhibition of mutant transcripts. Cell Mol Life Sci 2020; 78:1577-1596. [PMID: 32696070 PMCID: PMC7904544 DOI: 10.1007/s00018-020-03596-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Polyglutamine (polyQ) diseases are incurable neurological disorders caused by CAG repeat expansion in the open reading frames (ORFs) of specific genes. This type of mutation in the HTT gene is responsible for Huntington’s disease (HD). CAG repeat-targeting artificial miRNAs (art-miRNAs) were shown as attractive therapeutic approach for polyQ disorders as they caused allele-selective decrease in the level of mutant proteins. Here, using polyQ disease models, we aimed to demonstrate how miRNA-based gene expression regulation is dependent on target sequence features. We show that the silencing efficiency and selectivity of art-miRNAs is influenced by the localization of the CAG repeat tract within transcript and the specific sequence context. Furthermore, we aimed to reveal the events leading to downregulation of mutant polyQ proteins and found very rapid activation of translational repression and HTT transcript deadenylation. Slicer-activity of AGO2 was dispensable in this process, as determined in AGO2 knockout cells generated with CRISPR-Cas9 technology. We also showed highly allele-selective downregulation of huntingtin in human HD neural progenitors (NPs). Taken together, art-miRNA activity may serve as a model of the cooperative activity and targeting of ORF regions by endogenous miRNAs.
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99
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Pedrazzoli M, Mazzotti DR, Ribeiro AO, Mendes JV, Bittencourt LRA, Tufik S. A single nucleotide polymorphism in the HOMER1 gene is associated with sleep latency and theta power in sleep electroencephalogram. PLoS One 2020; 15:e0223632. [PMID: 32645048 PMCID: PMC7347117 DOI: 10.1371/journal.pone.0223632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Glutamate is the most excitatory neurotransmitter in the central nervous system and it is involved in the initiation and maintaining of waking and rapid-eye-movement (REM) sleep. Homer proteins act in the trafficking and/or clustering of metabotropic glutamate receptors, and polymorphisms in the HOMER1 gene have been associated with phenotypes related to glutamate signaling dysregulation. In this study, we report the association of a single nucleotide polymorphism (SNP) in the HOMER1 gene (rs3822568) with specific aspects of sleep in a sample of the Brazilian population. To accomplish this, 1,042 individuals were subjected to a full-night polysomnography, and a subset of 983 subjects had rs3822568 genotyping data available. When compared with the A allele carriers, GG genotyped individuals showed higher sleep latency, lower sleep efficiency, reduced number of arousals per hour, lower apnea-hypopnea index (AHI) and lower theta spectral power. In summary, the present findings suggest that the rs3822568 polymorphism in the HOMER1 gene is associated with sleep EEG profiles and might have an impact on sleep quality and sleep structure, with potential to explain inter-individual variation in sleep homeostasis.
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Affiliation(s)
- Mario Pedrazzoli
- School of Arts, Sciences and Humanities, University of São Paulo (USP), São Paulo, Brazil
- * E-mail:
| | - Diego Robles Mazzotti
- Center for Sleep and Circadian Neurobiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Juliana Viana Mendes
- School of Arts, Sciences and Humanities, University of São Paulo (USP), São Paulo, Brazil
| | | | - Sergio Tufik
- Department of Psychobiology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
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100
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CTELS: A Cell-Free System for the Analysis of Translation Termination Rate. Biomolecules 2020; 10:biom10060911. [PMID: 32560154 PMCID: PMC7356799 DOI: 10.3390/biom10060911] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/29/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
Translation termination is the final step in protein biosynthesis when the synthesized polypeptide is released from the ribosome. Understanding this complex process is important for treatment of many human disorders caused by nonsense mutations in important genes. Here, we present a new method for the analysis of translation termination rate in cell-free systems, CTELS (for C-terminally extended luciferase-based system). This approach was based on a continuously measured luciferase activity during in vitro translation reaction of two reporter mRNA, one of which encodes a C-terminally extended luciferase. This extension occupies a ribosomal polypeptide tunnel and lets the completely synthesized enzyme be active before translation termination occurs, i.e., when it is still on the ribosome. In contrast, luciferase molecule without the extension emits light only after its release. Comparing the translation dynamics of these two reporters allows visualization of a delay corresponding to the translation termination event. We demonstrated applicability of this approach for investigating the effects of cis- and trans-acting components, including small molecule inhibitors and read-through inducing sequences, on the translation termination rate. With CTELS, we systematically assessed negative effects of decreased 3′ UTR length, specifically on termination. We also showed that blasticidin S implements its inhibitory effect on eukaryotic translation system, mostly by affecting elongation, and that an excess of eRF1 termination factor (both the wild-type and a non-catalytic AGQ mutant) can interfere with elongation. Analysis of read-through mechanics with CTELS revealed a transient stalling event at a “leaky” stop codon context, which likely defines the basis of nonsense suppression.
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