1
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Wang Q, Liu L, Gou X, Zhang T, Zhao Y, Xie Y, Zhou J, Liu Y, Song K. The 3'‑untranslated region of XB130 regulates its mRNA stability and translational efficiency in non‑small cell lung cancer cells. Oncol Lett 2023; 26:427. [PMID: 37720672 PMCID: PMC10502931 DOI: 10.3892/ol.2023.14013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023] Open
Abstract
Silencing XB130 inhibits cell proliferation and epithelial-mesenchymal transition in non-small cell lung cancer (NSCLC), suggesting that downregulating XB130 expression may impede NSCLC progression. However, the molecular mechanism underlying the regulation of XB130 expression remains unclear. In the present study, the role of the 3'-untranslated region (3'-UTR) in the regulation of XB130 expression was investigated. Recombinant psiCHECK-2 vectors with wild-type, truncated, or mutant XB130 3'-UTR were constructed, and the effects of these insertions on reporter gene expression were examined using a dual-luciferase reporter assay and reverse transcription-quantitative PCR. Additionally, candidate proteins that regulated XB130 expression by binding to critical regions of the XB130 3'-UTR were screened for using an RNA pull-down assay, followed by mass spectrometry and western blotting. The results revealed that insertion of the entire XB130 3'-UTR (1,218 bp) enhanced reporter gene expression. Positive regulatory elements were primarily found in nucleotides 113-989 of the 3'-UTR, while negative regulatory elements were found in the 1-112 and 990-1,218 regions of the 3'-UTR. Deletion analyses identified nucleotides 113-230 and 503-660 of the 3'-UTR as two major fragments that likely promote XB130 expression by increasing mRNA stability and translation rate. Additionally, a U-rich element in the 970-1,053 region of the 3'-UTR was identified as a negative regulatory element that inhibited XB130 expression by suppressing translation. Furthermore, seven candidate proteins that potentially regulated XB130 expression by binding to the 113-230, 503-660, and 970-1,053 regions of the 3'-UTR were identified, shedding light on the regulatory mechanism of XB130 expression. Collectively, these results suggested that complex sequence integrations in the mRNA 3'-UTR variably affected XB130 expression in NSCLC cells.
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Affiliation(s)
- Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Lingling Liu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Xuanjing Gou
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Ting Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yan Zhao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yuan Xie
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Jianjiang Zhou
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Ying Liu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Kewei Song
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
- Department of Sport and Health, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
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2
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Choi D, Kang W, Park S, Son B, Park T. Identification of Glucocorticoid Receptor Target Genes That Potentially Inhibit Collagen Synthesis in Human Dermal Fibroblasts. Biomolecules 2023; 13:978. [PMID: 37371558 DOI: 10.3390/biom13060978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Over several decades, excess glucocorticoids (GCs) of endogenous or exogenous origin have been recognized to significantly inhibit collagen synthesis and accelerate skin aging. However, little is known regarding their molecular mechanisms. We hypothesized that the action of GCs on collagen production is at least partially through the glucocorticoid receptor (GR) and its target genes, and therefore aimed to identify GR target genes that potentially inhibit collagen synthesis in Hs68 human dermal fibroblasts. We first confirmed that dexamethasone, a synthetic GC, induced canonical GR signaling in dermal fibroblasts. We then collected 108 candidates for GR target genes reported in previous studies on GR target genes and verified that 17 genes were transcriptionally upregulated in dexamethasone-treated dermal fibroblasts. Subsequently, by individual knockdown of the 17 genes, we identified that six genes, AT-rich interaction domain 5B, FK506 binding protein 5, lysyl oxidase, methylenetetrahydrofolate dehydrogenase (NADP + dependent) 2, zinc finger protein 36, and zinc fingers and homeoboxes 3, are potentially involved in GC-mediated inhibition of collagen synthesis. The present study sheds light on the molecular mechanisms of GC-mediated skin aging and provides a basis for further research on the biological characteristics of individual GR target genes.
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Affiliation(s)
- Dabin Choi
- Department of Food and Nutrition, BK21 FOUR, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Wesuk Kang
- Department of Food and Nutrition, BK21 FOUR, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Soyoon Park
- Department of Food and Nutrition, BK21 FOUR, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Bomin Son
- Department of Food and Nutrition, BK21 FOUR, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
| | - Taesun Park
- Department of Food and Nutrition, BK21 FOUR, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
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3
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Pashler AL, Towler BP, Jones CI, Haime HJ, Burgess T, Newbury SF. Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs. RNA (NEW YORK, N.Y.) 2021; 27:1265-1280. [PMID: 34266995 PMCID: PMC8457002 DOI: 10.1261/rna.078872.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
XRN1 is a highly conserved exoribonuclease which degrades uncapped RNAs in a 5'-3' direction. Degradation of RNAs by XRN1 is important in many cellular and developmental processes and is relevant to human disease. Studies in D. melanogaster demonstrate that XRN1 can target specific RNAs, which have important consequences for developmental pathways. Osteosarcoma is a malignancy of the bone and accounts for 2% of all pediatric cancers worldwide. Five-year survival of patients has remained static since the 1970s and therefore furthering our molecular understanding of this disease is crucial. Previous work has shown a down-regulation of XRN1 in osteosarcoma cells; however, the transcripts regulated by XRN1 which might promote osteosarcoma remain elusive. Here, we confirm reduced levels of XRN1 in osteosarcoma cell lines and patient samples and identify XRN1-sensitive transcripts in human osteosarcoma cells. Using RNA-seq in XRN1-knockdown SAOS-2 cells, we show that 1178 genes are differentially regulated. Using a novel bioinformatic approach, we demonstrate that 134 transcripts show characteristics of direct post-transcriptional regulation by XRN1. Long noncoding RNAs (lncRNAs) are enriched in this group, suggesting that XRN1 normally plays an important role in controlling lncRNA expression in these cells. Among potential lncRNAs targeted by XRN1 is HOTAIR, which is known to be up-regulated in osteosarcoma and contributes to disease progression. We have also identified G-rich and GU motifs in post-transcriptionally regulated transcripts which appear to sensitize them to XRN1 degradation. Our results therefore provide significant insights into the specificity of XRN1 in human cells which are relevant to disease.
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Affiliation(s)
- Amy L Pashler
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Benjamin P Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Christopher I Jones
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Hope J Haime
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Tom Burgess
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Sarah F Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
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4
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [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: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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5
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Carmi G, Gorohovski A, Mukherjee S, Frenkel-Morgenstern M. Non-optimal codon usage preferences of coronaviruses determine their promiscuity for infecting multiple hosts. FEBS J 2021; 288:5201-5223. [PMID: 33756061 DOI: 10.1111/febs.15835] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/09/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022]
Abstract
Circulating animal coronaviruses occasionally infect humans. The SARS-CoV-2 is responsible for the current worldwide outbreak of COVID-19 that has resulted in 2 112 844 deaths as of late January 2021. We compared genetic code preferences in 496 viruses, including 34 coronaviruses and 242 corresponding hosts, to uncover patterns that distinguish single- and 'promiscuous' multiple-host-infecting viruses. Based on a codon usage preference score, promiscuous viruses were shown to significantly employ nonoptimal codons, namely codons that involve 'wobble' binding to anticodons, as compared to single-host viruses. The codon adaptation index (CAI) and the effective number of codons (ENC) were calculated for all viruses and hosts. Promiscuous viruses were less adapted hosts vs single-host viruses (P-value = 4.392e-11). All coronaviruses exploit nonoptimal codons to infect multiple hosts. We found that nonoptimal codon preferences at the beginning of viral coding sequences enhance the translational efficiency of viral proteins within the host. Finally, coronaviruses lack endogenous RNA degradation motifs to a significant degree, thereby increasing viral mRNA burden and infection load. To conclude, we found that promiscuously infecting coronaviruses prefer nonoptimal codon usage to remove degradation motifs from their RNAs and to dramatically increase their viral RNA production rates.
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Affiliation(s)
- Gon Carmi
- Cancer Genomics and BioComputing of Complex Diseases Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Alessandro Gorohovski
- Cancer Genomics and BioComputing of Complex Diseases Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,The Data Science Institute, Bar-Ilan University, Ramat Gan, Israel.,The Dangoor Center for Personalized Medicine, Bar-Ilan University, Ramat Gan, Israel
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6
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Menendez-Gil P, Toledo-Arana A. Bacterial 3'UTRs: A Useful Resource in Post-transcriptional Regulation. Front Mol Biosci 2021; 7:617633. [PMID: 33490108 PMCID: PMC7821165 DOI: 10.3389/fmolb.2020.617633] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Bacterial messenger RNAs (mRNAs) are composed of 5′ and 3′ untranslated regions (UTRs) that flank the coding sequences (CDSs). In eukaryotes, 3′UTRs play key roles in post-transcriptional regulatory mechanisms. Shortening or deregulation of these regions is associated with diseases such as cancer and metabolic disorders. Comparatively, little is known about the functions of 3′UTRs in bacteria. Over the past few years, 3′UTRs have emerged as important players in the regulation of relevant bacterial processes such as virulence, iron metabolism, and biofilm formation. This MiniReview is an update for the different 3′UTR-mediated mechanisms that regulate gene expression in bacteria. Some of these include 3′UTRs that interact with the 5′UTR of the same transcript to modulate translation, 3′UTRs that are targeted by specific ribonucleases, RNA-binding proteins and small RNAs (sRNAs), and 3′UTRs that act as reservoirs of trans-acting sRNAs, among others. In addition, recent findings regarding a differential evolution of bacterial 3′UTRs and its impact in the species-specific expression of orthologous genes are also discussed.
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Affiliation(s)
- Pilar Menendez-Gil
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC) - Gobierno de Navarra, Navarra, Spain
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología (IdAB), Consejo Superior de Investigaciones Científicas (CSIC) - Gobierno de Navarra, Navarra, Spain
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7
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Wang L, Zhang S, Zhang W, Cheng G, Khan R, Junjvlieke Z, Li S, Zan L. miR-424 Promotes Bovine Adipogenesis Through an Unconventional Post-Transcriptional Regulation of STK11. Front Genet 2020; 11:145. [PMID: 32194625 PMCID: PMC7064614 DOI: 10.3389/fgene.2020.00145] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/07/2020] [Indexed: 11/26/2022] Open
Abstract
Adipose tissue is the largest energy reservoir and secretory organ in the animal body, and is essential for maintaining normal physiological functions and metabolic balance. MicroRNAs regulate the process of adipogenic differentiation through post-transcriptional regulatory mechanisms. In the present study, miR-424 was upregulated during bovine adipocyte differentiation both in vivo and in vitro. The overexpression and interference of miR-424 exhibited the positive regulatory role in the differentiation of bovine adipocytes. Furthermore, miR-424 directly binds to the three prime untranslated region (3' UTR) of serine/threonine kinase 11 (STK11, also called LKB1), a master upstream gene in the AMP-activated protein kinase (AMPK) cascade, and up-regulates its expression. Functional studies showed that the knockdown of STK11 attenuated the pro-adipogenic effect of miR-424. Post-transcriptional regulation of STK11 by miR-424 was mediated potentially in an RNA binding protein (RBP) binding site-dependent manner. In conclusion, our study shows that miR-424 promotes bovine adipogenesis through an unconventional post-transcriptional regulation of STK11, which may serve as a potential target for the regulation of bovine adipogenesis and the improvement of livestock breeding efficiency.
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Affiliation(s)
- Li Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Song Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenzhen Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zainaguli Junjvlieke
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shijun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, China
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8
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Abstract
Noncoding RNAs (ncRNAs) have received much attention due to their central role in gene expression and translational regulation as well as due to their involvement in several biological processes and disease development. Small noncoding RNAs (sncRNAs), such as microRNAs and piwiRNAs, have been thoroughly investigated and functionally characterized. Long noncoding RNAs (lncRNAs), known to play an important role in chromatin-interacting transcription regulation, posttranscriptional regulation, cell-to-cell signaling, and protein regulation, are also being investigated to further elucidate their functional roles.Next-generation sequencing (NGS) technologies have greatly aided in characterizing the ncRNAome. Moreover, the coupling of NGS technology together with bioinformatics tools has been essential to the genome-wide detection of RNA modifications in ncRNAs. RNA editing, a common human co-transcriptional and posttranscriptional modification, is a dynamic biological phenomenon able to alter the sequence and the structure of primary transcripts (both coding and noncoding RNAs) during the maturation process, consequently influencing the biogenesis, as well as the function, of ncRNAs. In particular, the dysregulation of the RNA editing machineries have been associated with the onset of human diseases.In this chapter we discuss the potential functions of ncRNA editing and describe the knowledge base and bioinformatics resources available to investigate such phenomenon.
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Ma F, Lin P, Chen Q, Lu X, Zhang YE, Wu CI. Direct measurement of pervasive weak repression by microRNAs and their role at the network level. BMC Genomics 2018; 19:362. [PMID: 29764374 PMCID: PMC5952853 DOI: 10.1186/s12864-018-4757-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/02/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A gene regulatory network (GRN) comprises many weak links that are often regulated by microRNAs. Since miRNAs rarely repress their target genes by more than 30%, doubts have been expressed about the biological relevance of such weak effects. These doubts raise the possibility of under-estimation as miRNA repression is usually estimated indirectly from equilibrium expression levels. RESULTS To measure miRNA repression directly, we inhibited transcript synthesis in Drosophila larvae and collected time-course data on mRNA abundance, the decline of which reflects transcript degradation. The rate of target degradation in the absence of miR310s, a moderately expressed miRNA family, was found to decrease by 5 to 15%. A conventional analysis that does not remove transcript synthesis yields an estimate of 6.5%, within the range of the new estimates. These data permit further examinations of the repression mechanisms by miRNAs including seed matching types, APA (alternative polyadenylation) sites, effects of other highly-expressed miRNAs and the length of 3'UTR. Our direct measurements suggest the latter two factors have a measurable effect on decay rate. CONCLUSION The direct measurement confirms pervasive weak repression by miRNAs, supporting the conclusions based on indirect assays. The confirmation suggests that this weak repression may indeed be miRNAs' main function. In this context, we discuss the recent proposal that weak repression is "cumulatively powerful" in stabilizing GRNs.
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Affiliation(s)
- Fuqiang Ma
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pei Lin
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Qingjian Chen
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chung-I Wu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA.
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10
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Abstract
Viruses alter host-cell gene expression at many biochemical levels, such as transcription, translation, mRNA splicing and mRNA decay in order to create a cellular environment suitable for viral replication. In this review, we discuss mechanisms by which viruses manipulate host-gene expression at the level of mRNA decay in order to enable the virus to evade host antiviral responses to allow viral survival and replication. We discuss different cellular RNA decay pathways, including the deadenylation-dependent mRNA decay pathway, and various strategies that viruses exploit to manipulate these pathways in order to create a virus-friendly cellular environment.
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Affiliation(s)
- Liang Guo
- Department of Medicine, Division of Infectious Diseases & International Medicine, Program in Infection & Immunity, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA.,Graduate Program in Comparative & Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Irina Vlasova-St Louis
- Department of Medicine, Division of Infectious Diseases & International Medicine, Program in Infection & Immunity, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul R Bohjanen
- Department of Medicine, Division of Infectious Diseases & International Medicine, Program in Infection & Immunity, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology Training Program, University of Minnesota, Minneapolis, MN 55455, USA.,Graduate Program in Comparative & Molecular Bioscience, University of Minnesota, Minneapolis, MN 55455, USA
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11
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The AU-rich element landscape across human transcriptome reveals a large proportion in introns and regulation by ELAVL1/HuR. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:167-177. [PMID: 29413897 DOI: 10.1016/j.bbagrm.2017.12.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/13/2017] [Accepted: 12/13/2017] [Indexed: 01/19/2023]
Abstract
Adenylate-uridylate (AU)-rich elements (AREs) are sequence instability elements that are known to be located in the 3' untranslated regions (UTR) in thousands of human transcripts. AREs regulate the expression of many genes at the post-transcriptional level, and they are essential for many normal cellular functions. We conducted a transcriptome-wide screen for AREs and found that they are most abundant in introns, with up to 25% of introns containing AREs corresponding to 58% of human genes. Clustering studies of ARE size, complexity, and distribution revealed that, in introns, longer AREs with two or more overlapping repeats are more abundant than in the 3'UTR, and only introns can contain very long AREs with 6-14 overlapping AUUUA pentamers. We found that intronic sites of the ARE binding proteins HuR/ELAVL1, ZFP36/TTP, AUF1, and BRF1/ZFP36L1 overlap with the intronic AREs with HuR being most abundant. Accordingly, RNA-IP experiments demonstrated a specific association of HuR with reporter and endogenous pre-mRNAs that contain intronic AREs. Moreover, HuR knockdown led to a significant general reduction in the mRNA levels of genes that contain intronic AREs and to a specific reduction in the expression of ARE-intronic reporters. The data represent bioinformatics analysis for key RNA-binding proteins interactions with intronic AREs and provide experimental evidence for HuR binding to AREs. The widespread distribution of intronic AREs and their particular association with HuR and HuR binding sites indicates that more than half of human genes can be regulated post-transcriptionally by AREs.
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12
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Vlasova-St Louis I, Bohjanen PR. Post-transcriptional regulation of cytokine and growth factor signaling in cancer. Cytokine Growth Factor Rev 2016; 33:83-93. [PMID: 27956133 DOI: 10.1016/j.cytogfr.2016.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 11/28/2016] [Indexed: 12/11/2022]
Abstract
Cytokines and growth factors regulate cell proliferation, differentiation, migration and apoptosis, and play important roles in coordinating growth signal responses during development. The expression of cytokine genes and the signals transmitted through cytokine receptors are tightly regulated at several levels, including transcriptional and post-transcriptional levels. A majority of cytokine mRNAs, including growth factor transcripts, contain AU-rich elements (AREs) in their 3' untranslated regions that control gene expression by regulating mRNA degradation and changing translational rates. In addition, numerous proteins involved in transmitting signals downstream of cytokine receptors are regulated at the level of mRNA degradation by GU-rich elements (GREs) found in their 3' untranslated regions. Abnormal stabilization and overexpression of ARE or GRE-containing transcripts had been observed in many malignancies, which is a consequence of the malfunction of RNA-binding proteins. In this review, we briefly summarize the role of AREs and GREs in regulating mRNA turnover to coordinate cytokine and growth factor expression, and we describe how dysregulation of mRNA degradation mechanisms contributes to the development and progression of cancer.
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Affiliation(s)
| | - Paul R Bohjanen
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
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13
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House RP, Talwar S, Hazard ES, Hill EG, Palanisamy V. RNA-binding protein CELF1 promotes tumor growth and alters gene expression in oral squamous cell carcinoma. Oncotarget 2016; 6:43620-34. [PMID: 26498364 PMCID: PMC4791255 DOI: 10.18632/oncotarget.6204] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/09/2015] [Indexed: 12/15/2022] Open
Abstract
The RNA binding protein CELF1 (also known as CUGBP1) is emerging as a critical regulator of cancer cell proliferation and apoptosis. Here, to provide a global prospective of CELF1 regulation of oral squamous cell carcinoma, we performed RNA-sequencing in oral cancer cells and CELF1 overexpression analysis in non-malignant human oral keratinocytes. Our approaches identified 1283 mRNAs differentially regulated as a function of CELF1 expression and more importantly CELF1 promoted alternative splicing of several target pre-mRNAs, which are known to be involved in various cancer biological processes. Overexpression of CELF1 in non-malignant human oral keratinocytes protected cells against oxidative damage and altered gene expression patterns. Finally, we provide evidence that reduction of CELF1 protein using a xenograft tumorigenesis mouse model decreased tumor growth. Altogether, these data provided a comprehensive view of the CELF1 mRNA regulatory network in oral cancer and suggests that CELF1 and/or its target mRNAs are viable candidates for therapeutic intervention.
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Affiliation(s)
- Reniqua P House
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Sudha Talwar
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - E Starr Hazard
- Division of Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Elizabeth G Hill
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Viswanathan Palanisamy
- Department of Oral Health Sciences and Center for Oral Health Research, College of Dental Medicine, Medical University of South Carolina, Charleston, SC, USA
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14
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Chen CYA, Shyu AB. Emerging Themes in Regulation of Global mRNA Turnover in cis. Trends Biochem Sci 2016; 42:16-27. [PMID: 27647213 DOI: 10.1016/j.tibs.2016.08.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 11/25/2022]
Abstract
mRNA is the molecule that conveys genetic information from DNA to the translation apparatus. mRNAs in all organisms display a wide range of stability, and mechanisms have evolved to selectively and differentially regulate individual mRNA stability in response to intracellular and extracellular cues. In recent years, three seemingly distinct aspects of RNA biology-mRNA N6-methyladenosine (m6A) modification, alternative 3' end processing and polyadenylation (APA), and mRNA codon usage-have been linked to mRNA turnover, and all three aspects function to regulate global mRNA stability in cis. Here, we discuss the discovery and molecular dissection of these mechanisms in relation to how they impact the intrinsic decay rate of mRNA in eukaryotes, leading to transcriptome reprogramming.
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Affiliation(s)
- Chyi-Ying A Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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15
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Khabar KSA. Hallmarks of cancer and AU-rich elements. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27251431 PMCID: PMC5215528 DOI: 10.1002/wrna.1368] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/05/2016] [Accepted: 05/09/2016] [Indexed: 12/14/2022]
Abstract
Post‐transcriptional control of gene expression is aberrant in cancer cells. Sustained stabilization and enhanced translation of specific mRNAs are features of tumor cells. AU‐rich elements (AREs), cis‐acting mRNA decay determinants, play a major role in the posttranscriptional regulation of many genes involved in cancer processes. This review discusses the role of aberrant ARE‐mediated posttranscriptional processes in each of the hallmarks of cancer, including sustained cellular growth, resistance to apoptosis, angiogenesis, invasion, and metastasis. WIREs RNA 2017, 8:e1368. doi: 10.1002/wrna.1368 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Khalid S A Khabar
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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16
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Rolle K, Piwecka M, Belter A, Wawrzyniak D, Jeleniewicz J, Barciszewska MZ, Barciszewski J. The Sequence and Structure Determine the Function of Mature Human miRNAs. PLoS One 2016; 11:e0151246. [PMID: 27031951 PMCID: PMC4816427 DOI: 10.1371/journal.pone.0151246] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/15/2016] [Indexed: 12/31/2022] Open
Abstract
Micro RNAs (miRNAs) (19–25 nucleotides in length) belong to the group of non-coding RNAs are the most abundant group of posttranscriptional regulators in multicellular organisms. They affect a gene expression by binding of fully or partially complementary sequences to the 3’-UTR of target mRNA. Furthermore, miRNAs present a mechanism by which genes with diverse functions on multiple pathways can be simultaneously regulated at the post-transcriptional level. However, little is known about the specific pathways through which miRNAs with specific sequence or structural motifs regulate the cellular processes. In this paper we showed the broad and deep characteristics of mature miRNAs according to their sequence and structural motifs. We investigated a distinct group of miRNAs characterized by the presence of specific sequence motifs, such as UGUGU, GU-repeats and purine/pyrimidine contents. Using computational function and pathway analysis of their targeted genes, we were able to observe the relevance of sequence and the type of targeted mRNAs. As the consequence of the sequence analysis we finally provide the comprehensive description of pathways, biological processes and proteins associated with the distinct group of characterized miRNAs. Here, we found that the specific group of miRNAs with UGUGU can activate the targets associated to the interferon induction pathway or pathways prominently observed during carcinogenesis. GU-rich miRNAs are prone to regulate mostly processes in neurogenesis, whereas purine/pyrimidine rich miRNAs could be involved rather in transport and/or degradation of RNAs. Additionally, we have also analyzed the simple sequence repeats (SSRs). Their variation within mature miRNAs might be critical for normal miRNA regular activity. Expansion or contraction of SSRs in mature miRNA might directly affect its mRNA interaction or even change the function of that distinct miRNA. Our results prove that due to the specific sequence features, these molecules can also be involved in well-defined cellular processes depending on their sequence contents. The pathway mapping and theoretical gene target identification allowed us to create a biological framework to show the relevance of the specific miRNAs in regulation the distinct type of targets.
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Affiliation(s)
- Katarzyna Rolle
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
- * E-mail: (JB); (KR)
| | - Monika Piwecka
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Agnieszka Belter
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Dariusz Wawrzyniak
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Jaroslaw Jeleniewicz
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Miroslawa Z. Barciszewska
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
- * E-mail: (JB); (KR)
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17
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Vlasova-St Louis I, Bohjanen PR. Feedback Regulation of Kinase Signaling Pathways by AREs and GREs. Cells 2016; 5:cells5010004. [PMID: 26821046 PMCID: PMC4810089 DOI: 10.3390/cells5010004] [Citation(s) in RCA: 12] [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: 12/11/2015] [Revised: 01/20/2016] [Accepted: 01/20/2016] [Indexed: 12/18/2022] Open
Abstract
In response to environmental signals, kinases phosphorylate numerous proteins, including RNA-binding proteins such as the AU-rich element (ARE) binding proteins, and the GU-rich element (GRE) binding proteins. Posttranslational modifications of these proteins lead to a significant changes in the abundance of target mRNAs, and affect gene expression during cellular activation, proliferation, and stress responses. In this review, we summarize the effect of phosphorylation on the function of ARE-binding proteins ZFP36 and ELAVL1 and the GRE-binding protein CELF1. The networks of target mRNAs that these proteins bind and regulate include transcripts encoding kinases and kinase signaling pathways (KSP) components. Thus, kinase signaling pathways are involved in feedback regulation, whereby kinases regulate RNA-binding proteins that subsequently regulate mRNA stability of ARE- or GRE-containing transcripts that encode components of KSP.
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Affiliation(s)
- Irina Vlasova-St Louis
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Microbiology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Paul R Bohjanen
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Microbiology, University of Minnesota, Minneapolis, MN 55455, USA.
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18
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Fallmann J, Sedlyarov V, Tanzer A, Kovarik P, Hofacker IL. AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements. Nucleic Acids Res 2015; 44:D90-5. [PMID: 26602692 PMCID: PMC4702876 DOI: 10.1093/nar/gkv1238] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/02/2015] [Indexed: 12/31/2022] Open
Abstract
AREsite2 represents an update for AREsite, an on-line resource for the investigation of AU-rich elements (ARE) in human and mouse mRNA 3′UTR sequences. The new updated and enhanced version allows detailed investigation of AU, GU and U-rich elements (ARE, GRE, URE) in the transcriptome of Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans and Drosophila melanogaster. It contains information on genomic location, genic context, RNA secondary structure context and conservation of annotated motifs. Improvements include annotation of motifs not only in 3′UTRs but in the whole gene body including introns, additional genomes, and locally stable secondary structures from genome wide scans. Furthermore, we include data from CLIP-Seq experiments in order to highlight motifs with validated protein interaction. Additionally, we provide a REST interface for experienced users to interact with the database in a semi-automated manner. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite
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Affiliation(s)
- Jörg Fallmann
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria
| | - Vitaly Sedlyarov
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Andrea Tanzer
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria
| | - Pavel Kovarik
- Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstraße 29, A-1090 Vienna, Austria Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
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19
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Bohjanen PR, Moua ML, Guo L, Taye A, Vlasova-St Louis IA. Altered CELF1 binding to target transcripts in malignant T cells. RNA (NEW YORK, N.Y.) 2015; 21:1757-1769. [PMID: 26249002 PMCID: PMC4574752 DOI: 10.1261/rna.049940.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/29/2015] [Indexed: 06/04/2023]
Abstract
The RNA-binding protein, CELF1, binds to a regulatory sequence known as the GU-rich element (GRE) and controls a network of mRNA transcripts that regulate cellular activation, proliferation, and apoptosis. We performed immunoprecipitation using an anti-CELF1 antibody, followed by identification of copurified transcripts using microarrays. We found that CELF1 is bound to a distinct set of target transcripts in the H9 and Jurkat malignant T-cell lines, compared with primary human T cells. CELF1 was not phosphorylated in resting normal T cells, but in malignant T cells, phosphorylation of CELF1 correlated with its inability to bind to GRE-containing mRNAs that served as CELF1 targets in normal T cells. Lack of binding by CELF1 to these mRNAs in malignant T cells correlated with stabilization and increased expression of these transcripts. Several of these GRE-containing transcripts that encode regulators of cell growth were also stabilized and up-regulated in primary tumor cells from patients with T-cell acute lymphoblastic leukemia. Interestingly, transcripts encoding numerous suppressors of cell proliferation that served as targets of CELF1 in malignant T cells, but not normal T cells, exhibited accelerated degradation and reduced expression in malignant compared with normal T cells, consistent with the known function of CELF1 to mediate degradation of bound transcripts. Overall, CELF1 dysfunction in malignant T cells led to the up-regulation of a subset of GRE-containing transcripts that promote cell growth and down-regulation of another subset that suppress cell growth, producing a net effect that would drive a malignant phenotype.
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Affiliation(s)
- Paul R Bohjanen
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Department of Microbiology, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Mai Lee Moua
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Liang Guo
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ammanuel Taye
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Irina A Vlasova-St Louis
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
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20
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Patrushev LI, Kovalenko TF. Functions of noncoding sequences in mammalian genomes. BIOCHEMISTRY (MOSCOW) 2015; 79:1442-69. [PMID: 25749159 DOI: 10.1134/s0006297914130021] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Most of the mammalian genome consists of nucleotide sequences not coding for proteins. Exons of genes make up only 3% of the human genome, while the significance of most other sequences remains unknown. Recent genome studies with high-throughput methods demonstrate that the so-called noncoding part of the genome may perform important functions. This hypothesis is supported by three groups of experimental data: 1) approximately 10% of the sequences, most of which are located in noncoding parts of the genome, is evolutionarily conserved and thus can be of functional importance; 2) up to 99% of the mammalian genome is being transcribed forming short and long noncoding RNAs in addition to common mRNA; and 3) mutations in noncoding parts of the genome can be accompanied by progression of pathological states of the organism. In the light of these data, in the review we consider the functional role of numerous known sequences of noncoding parts of the genome including introns, DNA methylation regions, enhancers and locus control regions, insulators, S/MAR sequences, pseudogenes, and genes of noncoding RNAs, as well as transposons and simple repeats of centromeric and telomeric regions of chromosomes. The assumption is made that the intergenic noncoding sequences without definite/clear functions can be involved in spatial organization of genetic loci in interphase nuclei.
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Affiliation(s)
- L I Patrushev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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21
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Robinson SR, Oliver AW, Chevassut TJ, Newbury SF. The 3' to 5' Exoribonuclease DIS3: From Structure and Mechanisms to Biological Functions and Role in Human Disease. Biomolecules 2015; 5:1515-39. [PMID: 26193331 PMCID: PMC4598762 DOI: 10.3390/biom5031515] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 12/03/2022] Open
Abstract
DIS3 is a conserved exoribonuclease and catalytic subunit of the exosome, a protein complex involved in the 3' to 5' degradation and processing of both nuclear and cytoplasmic RNA species. Recently, aberrant expression of DIS3 has been found to be implicated in a range of different cancers. Perhaps most striking is the finding that DIS3 is recurrently mutated in 11% of multiple myeloma patients. Much work has been done to elucidate the structural and biochemical characteristics of DIS3, including the mechanistic details of its role as an effector of RNA decay pathways. Nevertheless, we do not understand how DIS3 mutations can lead to cancer. There are a number of studies that pertain to the function of DIS3 at the organismal level. Mutant phenotypes in S. pombe, S. cerevisiae and Drosophila suggest DIS3 homologues have a common role in cell-cycle progression and microtubule assembly. DIS3 has also recently been implicated in antibody diversification of mouse B-cells. This article aims to review current knowledge of the structure, mechanisms and functions of DIS3 as well as highlighting the genetic patterns observed within myeloma patients, in order to yield insight into the putative role of DIS3 mutations in oncogenesis.
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Affiliation(s)
- Sophie R Robinson
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK.
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Timothy J Chevassut
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK.
| | - Sarah F Newbury
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK.
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22
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Vlasova-St Louis I, Bohjanen PR. Post-transcriptional regulation of cytokine signaling by AU-rich and GU-rich elements. J Interferon Cytokine Res 2015; 34:233-41. [PMID: 24697201 DOI: 10.1089/jir.2013.0108] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cytokines are necessary for cell communication to enable responses to external stimuli that are imperative for the survival and maintenance of homeostasis. Dysfunction of the cytokine network has detrimental effects on intra- and extracellular environments. Thus, it is critical that the expression of cytokines and the signals transmitted by cytokines to target cells are tightly regulated at numerous levels, including transcriptional and post-transcriptional levels. Here, we briefly summarize the role of AU-rich elements (AREs) in the regulation of cytokine gene expression at the post-transcriptional level and describe a role for GU-rich elements (GREs) in coordinating the regulation of cytokine signaling. GREs function as post-transcriptional regulators of proteins that control cellular activation, growth, and apoptosis. GREs and AREs work in concert to coordinate cytokine signal transduction pathways. The precise regulation of cytokine signaling is particularly important, because its dysregulation can lead to human diseases.
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23
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Gao J, Wang Z, Shao K, Fan L, Yang L, Song H, Liu M, Wang Z, Wang X, Zhang Q. Identification and characterization of a Sox2 homolog in the Japanese flounder Paralichthys olivaceus. Gene 2014; 544:165-76. [DOI: 10.1016/j.gene.2014.04.062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 04/15/2014] [Accepted: 04/20/2014] [Indexed: 12/23/2022]
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24
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Khabar KSA. Post-transcriptional control of cytokine gene expression in health and disease. J Interferon Cytokine Res 2014; 34:215-9. [PMID: 24552151 DOI: 10.1089/jir.2013.0151] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Post-transcriptional control of cytokine gene expression is essential for rapid and transient response to stimuli and external stress. In health, post-transcriptional control is exerted by a number of trans-acting RNA-binding proteins and cis-acting sequence elements. These elements exist largely in the 3' untranslated region and comprise microRNA targets and notably AU-rich elements, and exert regulated mRNA decay and translation repression. Defects in this control can lead to increased and sustained production of pro-inflammatory mediators contributing to several chronic inflammatory disease and cancer states. This introduction to the Journal's special issue on the topic summarizes, in a non-comprehensive list, the types of RNA-binding protein and their target cytokines, and potential contributions to disease, and presents the highlights of the individual reviews.
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Affiliation(s)
- Khalid S A Khabar
- Department of BioMolecular Research, King Faisal Specialist Hospital and Research Centre , Riyadh, Saudi Arabia
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25
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Mahmoud L, Al-Enezi F, Al-Saif M, Warsy A, Khabar KSA, Hitti EG. Sustained stabilization of Interleukin-8 mRNA in human macrophages. RNA Biol 2014; 11:124-33. [PMID: 24525793 DOI: 10.4161/rna.27863] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The mRNAs of most inflammatory mediators are short-lived due to AU-rich elements (AREs) in their 3'-untranslated regions. AREs ensure a low basal level of expression during homeostasis and a transient nature of expression during the inflammatory response. Here, we report that the mRNA of the pro-inflammatory chemokine IL-8, which contains an archetypal ARE, is unexpectedly constitutively abundant and highly stable in primary human monocytes and macrophages. Using the pre-monocyte-like THP-1 cell line that can differentiate into macrophage-like cells, we show that a low level of unstable IL-8 mRNA in undifferentiated cells (half-life<30 min) becomes constitutively elevated and the mRNA is dramatically stabilized in differentiated THP-1 cells with a half-life of more than 15 h similar to primary monocytes and macrophages. In contrast, the level and stability of TNF-α mRNA also containing an ARE is only slightly affected by differentiation; it remains low and unstable in primary macrophages and differentiated THP-1 cells with an estimated half-life of less than 20 min. This differentiation-dependent stabilization of IL-8 mRNA is p38 MAPK-independent and is probably coupled with reduced protein translation. Reporter assays in THP-1 cells suggest that the ARE alone is not sufficient for the constitutive stabilization in macrophage-like cells and imply an effect of the natural biogenesis of the transcript on the stabilization of the mature form. We present a novel, cell type-dependent sustained stabilization of an ARE-containing mRNA with similarities to situations found in disease.
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Affiliation(s)
- Linah Mahmoud
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia
| | - Fatma Al-Enezi
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia; Department of Biochemistry; King Saud University; Riyadh, Saudi Arabia
| | - Maher Al-Saif
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia
| | - Arjumand Warsy
- Department of Biochemistry; King Saud University; Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia
| | - Edward G Hitti
- Molecular Biomedicine Program; King Faisal Specialist Hospital and Research Center; Riyadh, Saudi Arabia
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26
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Abstract
SIGNIFICANCE Production of proteins requires the synthesis, maturation, and export of mRNAs before their translation in the cytoplasm. Endogenous and exogenous sources of DNA damage pose a challenge to the co-ordinated regulation of gene expression, because the integrity of the DNA template can be compromised by DNA lesions. Cells recognize and respond to this DNA damage through a variety of DNA damage responses (DDRs). Failure to deal with DNA damage appropriately can lead to genomic instability and cancer. RECENT ADVANCES The p53 tumor suppressor plays a dominant role in DDR-dependent changes in gene expression, but this transcription factor is not solely responsible for all changes. Recent evidence indicates that RNA metabolism is integral to DDRs as well. In particular, post-transcriptional processes are emerging as important contributors to these complex responses. CRITICAL ISSUES Transcriptional, post-transcriptional, and translational regulation of gene expression is subject to changes in response to DNA damage. How these processes are intertwined in the unfolding of DDR is not fully understood. FUTURE DIRECTIONS Many complex regulatory responses combine to determine cell fate after DNA damage. Understanding how transcriptional, post-transcriptional, and translational processes interdigitate to create a web of regulatory interactions will be one of the key challenges to fully understand DDRs.
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Affiliation(s)
- Bruce C McKay
- Department of Biology, Institute of Biochemistry, Carleton University , Ottawa, Canada
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27
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Vlasova-St Louis I, Dickson AM, Bohjanen PR, Wilusz CJ. CELFish ways to modulate mRNA decay. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:695-707. [PMID: 23328451 DOI: 10.1016/j.bbagrm.2013.01.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/03/2013] [Accepted: 01/05/2013] [Indexed: 12/14/2022]
Abstract
The CELF family of RNA-binding proteins regulates many steps of mRNA metabolism. Although their best characterized function is in pre-mRNA splice site choice, CELF family members are also powerful modulators of mRNA decay. In this review we focus on the different modes of regulation that CELF proteins employ to mediate mRNA decay by binding to GU-rich elements. After starting with an overview of the importance of CELF proteins during development and disease pathogenesis, we then review the mRNA networks and cellular pathways these proteins regulate and the mechanisms by which they influence mRNA decay. Finally, we discuss how CELF protein activity is modulated during development and in response to cellular signals. We conclude by highlighting the priorities for new experiments in this field. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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28
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Singh N, Sharma R, George A, Singla SK, Palta P, Manik R, Chauhan MS, Singh D. Cloning and characterization of buffalo NANOG gene: alternative transcription start sites, splicing, and polyadenylation in embryonic stem cell-like cells. DNA Cell Biol 2012; 31:721-31. [PMID: 22011250 PMCID: PMC3358104 DOI: 10.1089/dna.2011.1410] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/02/2011] [Accepted: 09/02/2011] [Indexed: 01/06/2023] Open
Abstract
NANOG is a critical homeodomain transcription factor responsible for maintaining embryonic stem cell (ESC) self-renewal and pluripotency. In the present study, we isolated, sequenced, and characterized the NANOG gene in buffalo ESC-like cells. Here, we demonstrated that NANOG mRNA is expressed as multiple isoforms and uses four alternative transcriptional start sites (TSSs) and five different polyadenylation sites. The TSSs identified by 5'-RNA ligase-mediated rapid amplification of cDNA ends (RLM-5'-RACE) were positioned at 182, 95, 35, and 17 nucleotides upstream relative to the translation initiation codon. 3'-RACE experiment revealed the presence of tandem polyadenylation signals, which leads to the expression of at least five different 3'-untranslated regions (269, 314, 560, 566, and 829 nucleotides). Expression analysis showed that these alternatively polyadenylated transcripts expressed differentially. Sequence analysis showed that the open reading frame of buffalo NANOG codes for a 300-amino-acid-long protein. Further, results showed that alternative splicing leads to the expression of two types of transcript variants encoded by four and five exons. In silico analysis of cloned 5'-flanking region (3366 nucleotides upstream of translation start codon) identified several putative transcription factors binding sites in addition to a TATA box and CAAT box at -30 and -139 bp (upstream to the distal most TSS), respectively, in the buffalo NANOG promoter.
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Affiliation(s)
- Natwar Singh
- Molecular Endocrinology Laboratory, Animal Biochemistry Division, National Dairy Research Institute (NDRI), Karnal, Haryana, India
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Ruchi Sharma
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Aman George
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Suresh K. Singla
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Prabhat Palta
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Radhaysham Manik
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Manmohan S. Chauhan
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Dheer Singh
- Molecular Endocrinology Laboratory, Animal Biochemistry Division, National Dairy Research Institute (NDRI), Karnal, Haryana, India
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29
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Matoulkova E, Michalova E, Vojtesek B, Hrstka R. The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells. RNA Biol 2012; 9:563-76. [PMID: 22614827 DOI: 10.4161/rna.20231] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The untranslated regions (UTRs) at the 3'end of mRNA transcripts contain important sequences that influence the fate of mRNA and thus proteosynthesis. In this review, we summarize the information known to date about 3'end processing, sequence characteristics including related binding proteins and the role of 3'UTRs in several selected signaling pathways to delineate their importance in the regulatory processes in mammalian cells. In addition to reviewing recent advances in the more well known aspects, such as cleavage and polyadenylation processes that influence mRNA stability and location, we concentrate on some newly emerging concepts of the role of the 3'UTR, including alternative polyadenylation sites in relation to proliferation and differentiation and the recognition of the multi-functional properties of non-coding RNAs, including miRNAs that commonly target the 3'UTR. The emerging picture is of a highly complex set of regulatory systems that include autoregulation, cooperativity and competition to fine tune proteosynthesis in context-dependent manners.
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30
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Neff AT, Lee JY, Wilusz J, Tian B, Wilusz CJ. Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells. Genome Res 2012; 22:1457-67. [PMID: 22534399 PMCID: PMC3409259 DOI: 10.1101/gr.134312.111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pluripotency is a unique state in which cells can self-renew indefinitely but also retain the ability to differentiate into other cell types upon receipt of extracellular cues. Although it is clear that stem cells have a distinct transcriptional program, little is known about how alterations in post-transcriptional mechanisms, such as mRNA turnover, contribute to the achievement and maintenance of pluripotency. Here we have assessed the rates of decay for the majority of mRNAs expressed in induced pluripotent stem (iPS) cells and the fully differentiated human foreskin fibroblasts (HFFs) they were derived from. Comparison of decay rates in the two cell types led to the discovery of three independent regulatory mechanisms that allow coordinated turnover of specific groups of mRNAs. One mechanism results in increased stability of many histone mRNAs in iPS cells. A second pathway stabilizes a large set of zinc finger protein mRNAs, potentially through reduced levels of miRNAs that target them. Finally, a group of transcripts bearing 3' UTR C-rich sequence elements, many of which encode transcription factors, are significantly less stable in iPS cells. Intriguingly, two poly(C)-binding proteins that recognize this type of element are reciprocally expressed in iPS and HFF cells. Overall, our results highlight the importance of post-transcriptional control in pluripotent cells and identify miRNAs and RNA-binding proteins whose activity may coordinately control expression of a wide range of genes in iPS cells.
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Affiliation(s)
- Ashley T Neff
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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31
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Turner M, Hodson DJ. An emerging role of RNA-binding proteins as multifunctional regulators of lymphocyte development and function. Adv Immunol 2012; 115:161-85. [PMID: 22608259 DOI: 10.1016/b978-0-12-394299-9.00006-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Sequence-specific RNA-binding proteins (RBP) and the regulation of RNA decay have long been recognized as important regulators of the inflammatory response. RBP influence gene expression throughout the lifespan of the mRNA by regulating splicing, polyadenylation, cellular localization, translation, and decay. Increasing evidence now indicates that these proteins, together with the RNA decay machinery that they recruit, also regulate the development and activation of lymphocytes. The activity of RBP is regulated by the same signal transduction pathways that govern lymphocyte development and differentiation in response to antigen and cytokine receptor engagement. Roles for these proteins in regulating the diverse functions of lymphocytes are becoming increasingly apparent.
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Affiliation(s)
- Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
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