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Li C, Yoon B, Stefani G, Slack FJ. Lipid kinase PIP5K1A regulates let-7 microRNA biogenesis through interacting with nuclear export protein XPO5. Nucleic Acids Res 2023; 51:9849-9862. [PMID: 37655623 PMCID: PMC10570020 DOI: 10.1093/nar/gkad709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs first discovered in Caenorhabditis elegans. The let-7 miRNA is highly conserved in sequence, biogenesis and function from C. elegans to humans. During miRNA biogenesis, XPO5-mediated nuclear export of pre-miRNAs is a rate-limiting step and, therefore, might be critical for the quantitative control of miRNA levels, yet little is known about how this is regulated. Here we show a novel role for lipid kinase PPK-1/PIP5K1A (phosphatidylinositol-4-phosphate 5-kinase) in regulating miRNA levels. We found that C. elegans PPK-1 functions in the lin-28/let-7 heterochronic pathway, which regulates the strict developmental timing of seam cells. In C. elegans and human cells, PPK-1/PIP5K1A regulates let-7 miRNA levels. We investigated the mechanism further in human cells and show that PIP5K1A interacts with nuclear export protein XPO5 in the nucleus to regulate mature miRNA levels by blocking the binding of XPO5 to pre-let-7 miRNA. Furthermore, we demonstrate that this role for PIP5K1A is kinase-independent. Our study uncovers the novel finding of a direct connection between PIP5K1A and miRNA biogenesis. Given that miRNAs are implicated in multiple diseases, including cancer, this new finding might lead to a novel therapeutic opportunity.
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Affiliation(s)
- Chun Li
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Bohyung Yoon
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Giovanni Stefani
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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2
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C. elegans LIN-28 controls temporal cell fate progression by regulating LIN-46 expression via the 5' UTR of lin-46 mRNA. Cell Rep 2021; 36:109670. [PMID: 34496246 PMCID: PMC8445076 DOI: 10.1016/j.celrep.2021.109670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 07/26/2021] [Accepted: 08/16/2021] [Indexed: 01/02/2023] Open
Abstract
Lin28/LIN-28 is a conserved RNA-binding protein that promotes proliferation and pluripotency and can be oncogenic in mammals. Mammalian Lin28 and C. elegans LIN-28 have been shown to inhibit biogenesis of the conserved cellular differentiation-promoting microRNA let-7 by directly binding to unprocessed let-7 transcripts. Lin28/LIN-28 also bind and regulate many mRNAs in diverse cell types. However, the determinants and consequences of LIN-28-mRNA interactions are not well understood. Here, we report that C. elegans LIN-28 represses the expression of LIN-46, a downstream protein in the heterochronic pathway. We find that lin-28 and sequences within the lin-46 5′ UTR are required to prevent LIN-46 expression at early larval stages. Moreover, we find that precocious LIN-46 expression caused by mutations in the lin-46 5′ UTR is sufficient to cause precocious heterochronic defects similar to those of lin-28(lf) animals. Thus, our findings demonstrate the biological importance of the regulation of individual target mRNAs by LIN-28. Ilbay et al. characterize the role of the 5′ UTR of lin-46, a heterochronic gene in C. elegans and the critical mRNA target of the widely conserved RNA-binding protein LIN-28, demonstrating the importance of the regulation of mRNAs by LIN-28 in vivo along with the conserved microRNA let-7.
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3
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Nelson C, Ambros V. A cohort of Caenorhabditis species lacking the highly conserved let-7 microRNA. G3 (BETHESDA, MD.) 2021; 11:jkab022. [PMID: 33890616 PMCID: PMC8063082 DOI: 10.1093/g3journal/jkab022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/12/2021] [Indexed: 01/13/2023]
Abstract
The let-7 gene encodes a highly conserved microRNA with critical functions integral to cell fate specification and developmental progression in diverse animals. In Caenorhabditis elegans, let-7 is a component of the heterochronic (developmental timing) gene regulatory network, and loss-of-function mutations of let-7 result in lethality during the larval to adult transition due to misregulation of the conserved let-7 target, lin-41. To date, no bilaterian animal lacking let-7 has been characterized. In this study, we identify a cohort of nematode species within the genus Caenorhabditis, closely related to C. elegans, that lack the let-7 microRNA, owing to absence of the let-7 gene. Using Caenorhabditis sulstoni as a representative let-7-lacking species to characterize normal larval development in the absence of let-7, we demonstrate that, except for the lack of let-7, the heterochronic gene network is otherwise functionally conserved. We also report that species lacking let-7 contain a group of divergent let-7 paralogs-also known as the let-7-family of microRNAs-that have apparently assumed the role of targeting the LIN-41 mRNA.
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Affiliation(s)
- Charles Nelson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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4
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Galagali H, Kim JK. The multifaceted roles of microRNAs in differentiation. Curr Opin Cell Biol 2020; 67:118-140. [PMID: 33152557 DOI: 10.1016/j.ceb.2020.08.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are major drivers of cell fate specification and differentiation. The post-transcriptional regulation of key molecular factors by microRNAs contributes to the progression of embryonic and postembryonic development in several organisms. Following the discovery of lin-4 and let-7 in Caenorhabditis elegans and bantam microRNAs in Drosophila melanogaster, microRNAs have emerged as orchestrators of cellular differentiation and developmental timing. Spatiotemporal control of microRNAs and associated protein machinery can modulate microRNA activity. Additionally, adaptive modulation of microRNA expression and function in response to changing environmental conditions ensures that robust cell fate specification during development is maintained. Herein, we review the role of microRNAs in the regulation of differentiation during development.
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Affiliation(s)
- Himani Galagali
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.
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5
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Zhou TE, Zhu T, Rivera JC, Omri S, Tahiri H, Lahaie I, Rouget R, Wirth M, Nattel S, Lodygensky G, Ferbeyre G, Nezhady M, Desjarlais M, Hamel P, Chemtob S. The Inability of the Choroid to Revascularize in Oxygen-Induced Retinopathy Results from Increased p53/miR-Let-7b Activity. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:2340-2356. [PMID: 31430465 DOI: 10.1016/j.ajpath.2019.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/13/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Retinopathy of prematurity (ROP) is characterized by an initial retinal avascularization, followed by pathologic neovascularization. Recently, choroidal thinning has also been detected in children formerly diagnosed with ROP; a similar sustained choroidal thinning is observed in ROP models. But the mechanism underlying the lack of choroidal revascularization remains unclear and was investigated in an oxygen-induced retinopathy (OIR) model. In OIR, evidence of senescence was detected, preceded by oxidative stress in the choroid and the retinal pigment epithelium. This was associated with a global reduction of proangiogenic factors, including insulin-like growth factor 1 receptor (Igf1R). Coincidentally, tumor suppressor p53 was highly expressed in the OIR retinae. Curtailing p53 activity resulted in reversal of senescence, normalization of Igf1r expression, and preservation of choroidal integrity. OIR-induced down-regulation of Igf1r was mediated at least partly by miR-let-7b as i) let-7b expression was augmented throughout and beyond the period of oxygen exposure, ii) let-7b directly targeted Igf1r mRNA, and iii) p53 knock-down blunted let-7b expression, restored Igf1r expression, and elicited choroidal revascularization. Finally, restoration of Igf1r expression rescued choroid thickness. Altogether, this study uncovers a significant mechanism for defective choroidal revascularization in OIR, revealing a new role for p53/let-7b/IGF-1R axis in the retina. Future investigations on this (and connected) pathway could further our understanding of other degenerative choroidopathies, such as geographic atrophy.
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Affiliation(s)
- Tianwei E Zhou
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada; Department of Ophthalmology, Maisonneuve-Rosemont Hospital Research Centre, Université de Montréal, Montréal, Québec, Canada.
| | - Tang Zhu
- Department of Pharmacology, Centre Hospitalier Universitaire Sainte-Justine Hospital, Université de Montréal, Montréal, Québec, Canada
| | - José C Rivera
- Department of Ophthalmology, Maisonneuve-Rosemont Hospital Research Centre, Université de Montréal, Montréal, Québec, Canada; Department of Pharmacology, Centre Hospitalier Universitaire Sainte-Justine Hospital, Université de Montréal, Montréal, Québec, Canada; Department of Ophthalmology, Centre Hospitalier Universitaire Sainte-Justine Hospital, Université de Montréal, Montréal, Québec, Canada
| | - Samy Omri
- Department of Ophthalmology, Maisonneuve-Rosemont Hospital Research Centre, Université de Montréal, Montréal, Québec, Canada
| | - Houda Tahiri
- Department of Ophthalmology, Maisonneuve-Rosemont Hospital Research Centre, Université de Montréal, Montréal, Québec, Canada
| | - Isabelle Lahaie
- Department of Ophthalmology, Maisonneuve-Rosemont Hospital Research Centre, Université de Montréal, Montréal, Québec, Canada
| | - Raphaël Rouget
- Department of Pharmacology, Centre Hospitalier Universitaire Sainte-Justine Hospital, Université de Montréal, Montréal, Québec, Canada
| | - Maëlle Wirth
- Department of Ophthalmology, Maisonneuve-Rosemont Hospital Research Centre, Université de Montréal, Montréal, Québec, Canada
| | - Stanley Nattel
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada; Department of Medicine, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Gregory Lodygensky
- Department of Pediatrics, Sainte-Justine University Hospital Centre, Université de Montréal, Montréal, Québec, Canada
| | - Gerardo Ferbeyre
- Department of Biochemistry, Université de Montréal, Montréal, Québec, Canada
| | - Mohammad Nezhady
- Department of Pathology and Cell Biology, University of Montréal, Montréal, Québec, Canada
| | - Michel Desjarlais
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada; Department of Ophthalmology, Maisonneuve-Rosemont Hospital Research Centre, Université de Montréal, Montréal, Québec, Canada
| | - Patrick Hamel
- Department of Ophthalmology, Centre Hospitalier Universitaire Sainte-Justine Hospital, Université de Montréal, Montréal, Québec, Canada
| | - Sylvain Chemtob
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada; Department of Ophthalmology, Maisonneuve-Rosemont Hospital Research Centre, Université de Montréal, Montréal, Québec, Canada; Department of Pharmacology, Centre Hospitalier Universitaire Sainte-Justine Hospital, Université de Montréal, Montréal, Québec, Canada; Department of Ophthalmology, Centre Hospitalier Universitaire Sainte-Justine Hospital, Université de Montréal, Montréal, Québec, Canada; Department of Pediatrics, Sainte-Justine University Hospital Centre, Université de Montréal, Montréal, Québec, Canada.
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6
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Chen WC, Wei CK, Lee JC. MicroRNA-let-7c suppresses hepatitis C virus replication by targeting Bach1 for induction of haem oxygenase-1 expression. J Viral Hepat 2019; 26:655-665. [PMID: 30706605 DOI: 10.1111/jvh.13072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/17/2018] [Accepted: 01/05/2019] [Indexed: 12/26/2022]
Abstract
MicroRNAs are small noncoding RNAs that are central factors between hepatitis C virus (HCV) and host cellular factors for viral replication and liver disease progression, including liver fibrosis, cirrhosis and hepatocellular carcinoma. In the present study, we found that overexpressing miR-let-7c markedly reduced HCV replication because it induced haem oxygenase-1 (HO-1) expression by targeting HO-1 transcriptional repressor Bach1, ultimately leading to stimulating an antiviral interferon response and blockade of HCV viral protease activity. In contrast, the antiviral actions of miR-let-7c were attenuated by miR-let-7c inhibitor treatment, exogenously expressing Bach1 or suppressing HO-1 activity and expression. A proposed model indicates a key role for miR-let-7c targeting Bach1 to transactivate HO-1-mediated antiviral actions against HCV. miR-let-7c may serve as an attractive target for antiviral development.
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Affiliation(s)
- Wei-Chun Chen
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Ku Wei
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jin-Ching Lee
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.,PhD Program in Life Sciences, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
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7
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The Long Non-Coding RNA lep-5 Promotes the Juvenile-to-Adult Transition by Destabilizing LIN-28. Dev Cell 2019; 49:542-555.e9. [PMID: 30956008 DOI: 10.1016/j.devcel.2019.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 10/02/2018] [Accepted: 03/06/2019] [Indexed: 12/28/2022]
Abstract
Biological roles for most long non-coding RNAs (lncRNAs) remain mysterious. Here, using forward genetics, we identify lep-5, a lncRNA acting in the C. elegans heterochronic (developmental timing) pathway. Loss of lep-5 delays hypodermal maturation and male tail tip morphogenesis (TTM), hallmarks of the juvenile-to-adult transition. We find that lep-5 is a ∼600 nt cytoplasmic RNA that is conserved across Caenorhabditis and possesses three essential secondary structure motifs but no essential open reading frames. lep-5 expression is temporally controlled, peaking prior to TTM onset. Like the Makorin LEP-2, lep-5 facilitates the degradation of LIN-28, a conserved miRNA regulator specifying the juvenile state. Both LIN-28 and LEP-2 associate with lep-5 in vivo, suggesting that lep-5 directly regulates LIN-28 stability and may function as an RNA scaffold. These studies identify a key biological role for a lncRNA: by regulating protein stability, it provides a temporal cue to facilitate the juvenile-to-adult transition.
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8
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Xiang Q, Yang B, Li L, Qiu B, Qiu C, Gao X, Zhou H(J, Min W. Critical role of Lin28-TNFR2 signalling in cardiac stem cell activation and differentiation. J Cell Mol Med 2019; 23:0. [PMID: 30734494 PMCID: PMC6433861 DOI: 10.1111/jcmm.14202] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/04/2019] [Accepted: 01/15/2019] [Indexed: 12/28/2022] Open
Abstract
Tumour necrotic factor receptor-2 (TNFR2) has been to be cardiac-protective and is expressed in cardiac progenitor cells. Our goal is to define the mechanism for TNFR2-mediated cardiac stem cell activation and differentiation. By employing a protocol of in vitro cardiac stem cell (CSC) differentiation from human inducible pluripotent stem cell (hiPSC), we show that expression of TNFR2 precedes expression of CSC markers followed by expression of mature cardiomyocyte proteins. Activation of TNFR2 by a specific agonist promotes whereas inhibition of TNFR2 by neutralizing antibody diminishes hiPSC-based CSC differentiation. Interestingly, pluripotent cell factor RNA-binding protein Lin28 enhances TNFR2 protein expression in early CSC activation by directly binding to a conserved Lin28-motif within the 3'UTR of Tnfr2 mRNA. Furthermore, inhibition of Lin28 blunts TNFR2 expression and TNFR2-dependent CSC activation and differentiation. Our study demonstrates a critical role of Lin28-TNFR2 axis in CSC activation and survival, providing a novel strategy to enhance stem cell-based therapy for the ischaemic heart diseases.
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Affiliation(s)
- Qiuling Xiang
- Yale Stem CenterInterdepartmental Program in Vascular Biology and TherapeuticsDepartment of PathologyYale University School of MedicineNew HavenConnecticut
- Translational Medicine Center, the First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdongChina
- Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Center for Stem Cell Biology and Tissue EngineeringKey Laboratory for Stem Cells and Tissue EngineeringMinistry of Education, Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Bicheng Yang
- Yale Stem CenterInterdepartmental Program in Vascular Biology and TherapeuticsDepartment of PathologyYale University School of MedicineNew HavenConnecticut
| | - Li Li
- Yale Stem CenterInterdepartmental Program in Vascular Biology and TherapeuticsDepartment of PathologyYale University School of MedicineNew HavenConnecticut
- Translational Medicine Center, the First Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdongChina
- Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Bin Qiu
- Yale Stem CenterInterdepartmental Program in Vascular Biology and TherapeuticsDepartment of PathologyYale University School of MedicineNew HavenConnecticut
| | - Caihong Qiu
- Yale Stem CenterInterdepartmental Program in Vascular Biology and TherapeuticsDepartment of PathologyYale University School of MedicineNew HavenConnecticut
| | - Xiao‐Bing Gao
- Department of Comparative Medicine and Obstetrics, Gynecology, and Reproductive SciencesYale University School of MedicineNew HavenConnecticut
| | - Huanjiao (Jenny) Zhou
- Yale Stem CenterInterdepartmental Program in Vascular Biology and TherapeuticsDepartment of PathologyYale University School of MedicineNew HavenConnecticut
| | - Wang Min
- Yale Stem CenterInterdepartmental Program in Vascular Biology and TherapeuticsDepartment of PathologyYale University School of MedicineNew HavenConnecticut
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9
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Kuan II, Lee CC, Chen CH, Lu J, Kuo YS, Wu HC. The extracellular domain of epithelial cell adhesion molecule (EpCAM) enhances multipotency of mesenchymal stem cells through EGFR-LIN28-LET7 signaling. J Biol Chem 2019; 294:7769-7786. [PMID: 30926604 DOI: 10.1074/jbc.ra119.007386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/19/2019] [Indexed: 11/06/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are widely considered to be an attractive cell source for regenerative therapies, but maintaining multipotency and self-renewal in cultured MSCs is especially challenging. Hence, the development and mechanistic description of strategies that help promote multipotency in MSCs will be vital to future clinical use. Here, using an array of techniques and approaches, including cell biology, RT-quantitative PCR, immunoblotting, immunofluorescence, flow cytometry, and ChIP assays, we show that the extracellular domain of epithelial cell adhesion molecule (EpCAM) (EpEX) significantly increases the levels of pluripotency factors through a signaling cascade that includes epidermal growth factor receptor (EGFR), signal transducer and activator of transcription 3 (STAT3), and Lin-28 homolog A (LIN28) and enhances the proliferation of human bone marrow MSCs. Moreover, we found that EpEX-induced LIN28 expression reduces the expression of the microRNA LET7 and up-regulates that of the transcription factor high-mobility group AT-hook 2 (HMGA2), which activates the transcription of pluripotency factors. Surprisingly, we found that EpEX treatment also enhances osteogenesis of MSCs under differentiation conditions, as evidenced by increases in osteogenic markers, including Runt-related transcription factor 2 (RUNX2). Taken together, our results indicate that EpEX stimulates EGFR signaling and thereby context-dependently controls MSC states and activities, promoting cell proliferation and multipotency under maintenance conditions and osteogenesis under differentiation conditions.
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Affiliation(s)
- I-I Kuan
- From the Institute of Cellular and Organismic Biology and
| | - Chi-Chiu Lee
- From the Institute of Cellular and Organismic Biology and
| | - Chien-Hsu Chen
- From the Institute of Cellular and Organismic Biology and
| | - Jean Lu
- Genomic Research Center, Academia Sinica, Taipei 115 and
| | - Yuan-Sung Kuo
- the Department of Surgery, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Han-Chung Wu
- From the Institute of Cellular and Organismic Biology and .,Genomic Research Center, Academia Sinica, Taipei 115 and
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10
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Nelson C, Ambros V. Trans-splicing of the C. elegans let-7 primary transcript developmentally regulates let-7 microRNA biogenesis and let-7 family microRNA activity. Development 2019; 146:dev172031. [PMID: 30770392 PMCID: PMC6432665 DOI: 10.1242/dev.172031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/11/2019] [Indexed: 12/19/2022]
Abstract
The sequence and roles in developmental progression of the microRNA let-7 are conserved. In general, transcription of the let-7 primary transcript (pri-let-7) occurs early in development, whereas processing of the mature let-7 microRNA arises during cellular differentiation. In Caenorhabditiselegans and other animals, the RNA-binding protein LIN-28 post-transcriptionally inhibits let-7 biogenesis at early developmental stages, but the mechanisms by which LIN-28 does this are not fully understood. Nor is it understood how the developmental regulation of let-7 might influence the expression or activities of other microRNAs of the same seed family. Here, we show that pri-let-7 is trans-spliced to the SL1 splice leader downstream of the let-7 precursor stem-loop, which produces a short polyadenylated downstream mRNA, and that this trans-splicing event negatively impacts the biogenesis of mature let-7 microRNA in cis Moreover, this trans-spliced mRNA contains sequences that are complementary to multiple members of the let-7 seed family (let-7fam) and negatively regulates let-7fam function in trans Thus, this study provides evidence for a mechanism by which splicing of a microRNA primary transcript can negatively regulate said microRNA in cis as well as other microRNAs in trans.
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Affiliation(s)
- Charles Nelson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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11
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Lee M, Nguyen TMT, Kim K. In-depth study of lin-28 suggests selectively conserved let-7 independent mechanism in Drosophila. Gene 2019; 687:64-72. [DOI: 10.1016/j.gene.2018.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/03/2018] [Accepted: 11/07/2018] [Indexed: 12/13/2022]
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12
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Mockly S, Seitz H. Inconsistencies and Limitations of Current MicroRNA Target Identification Methods. Methods Mol Biol 2019; 1970:291-314. [PMID: 30963499 DOI: 10.1007/978-1-4939-9207-2_16] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
MicroRNAs and their Argonaute protein partners constitute the RISC complex, which can repress specific target mRNAs. The identification of microRNA targets is of central importance, and various experimental and computational methods have been developed over the last 15 years. Most experimental methods are based on the assumption that mRNAs which interact physically with the RISC complex constitute regulatory targets and, similarly, some computational methods only aim at predicting physical interactors for RISC. Besides specific limitations, which we discuss for each method, the mere concept of assuming a functional role for every detected molecular event is likely to identify many deceptive interactions (i.e., interactions that really exist at the molecular scale, but without controlling any biological function at the macroscopic scale).In order to select biologically important interactions, some computational tools interrogate the phylogenetic conservation of microRNA/mRNA interactions, thus theoretically selecting only biologically relevant targets. Yet even comparative genomics can yield false positives.Conceptual and technical limitations for all these techniques tend to be overlooked by the scientific community. This review sums them up, emphasizing on the implications of these issues on our understanding of microRNA biology.
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Affiliation(s)
- Sophie Mockly
- IGH (CNRS and University of Montpellier), Montpellier, France
| | - Hervé Seitz
- IGH (CNRS and University of Montpellier), Montpellier, France.
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13
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Taranov VV, Zlobin NE, Evlakov KI, Shamustakimova AO, Babakov AV. Contribution of Eutrema salsugineum Cold Shock Domain Structure to the Interaction with RNA. BIOCHEMISTRY (MOSCOW) 2018; 83:1369-1379. [PMID: 30482148 DOI: 10.1134/s000629791811007x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Plant cold shock domain proteins (CSDPs) are DNA/RNA-binding proteins. CSDPs contain the conserved cold shock domain (CSD) in the N-terminal part and a varying number of the CCHC-type zinc finger (ZnF) motifs alternating with glycine-rich regions in the C-terminus. CSDPs exhibit RNA chaperone and RNA-melting activities due to their nonspecific interaction with RNA. At the same time, there are reasons to believe that CSDPs also interact with specific RNA targets. In the present study, we used three recombinant CSDPs from the saltwater cress plant (Eutrema salsugineum) - EsCSDP1, EsCSDP2, EsCSDP3 with 6, 2, and 7 ZnF motifs, respectively, and showed that their nonspecific interaction with RNA is determined by their C-terminal fragments. All three proteins exhibited high affinity to the single-stranded regions over four nucleotides long within RNA oligonucleotides. The presence of guanine in the single- or double-stranded regions was crucial for the interaction with CSDPs. Complementation test using E. coli BX04 cells lacking four cold shock protein genes (ΔcspA, ΔcspB, ΔcspE, ΔcspG) revealed that the specific binding of plant CSDPs with RNA is determined by CSD.
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Affiliation(s)
- V V Taranov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - N E Zlobin
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - K I Evlakov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - A O Shamustakimova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia.
| | - A V Babakov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia.
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14
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Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs. Genetics 2018; 209:651-673. [PMID: 29967059 PMCID: PMC6028246 DOI: 10.1534/genetics.118.300291] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are small, noncoding RNAs that regulate gene expression at the post-transcriptional level in essentially all aspects of Caenorhabditis elegans biology. More than 140 genes that encode microRNAs in C. elegans regulate development, behavior, metabolism, and responses to physiological and environmental changes. Genetic analysis of C. elegans microRNA genes continues to enhance our fundamental understanding of how microRNAs are integrated into broader gene regulatory networks to control diverse biological processes, including growth, cell division, cell fate determination, behavior, longevity, and stress responses. As many of these microRNA sequences and the related processing machinery are conserved over nearly a billion years of animal phylogeny, the assignment of their functions via worm genetics may inform the functions of their orthologs in other animals, including humans. In vivo investigations are especially important for microRNAs because in silico extrapolation of their functions using mRNA target prediction programs can easily assign microRNAs to incorrect genetic pathways. At this mezzanine level of microRNA bioinformatic sophistication, genetic analysis continues to be the gold standard for pathway assignments.
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15
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SRSF2 mutations drive oncogenesis by activating a global program of aberrant alternative splicing in hematopoietic cells. Leukemia 2018; 32:2659-2671. [PMID: 29858584 PMCID: PMC6274620 DOI: 10.1038/s41375-018-0152-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 01/30/2023]
Abstract
Recurrent mutations in the splicing factor SRSF2 are associated with poor clinical outcomes in myelodysplastic syndromes (MDS). Their high frequency suggests these mutations drive oncogenesis, yet the molecular explanation for this process is unclear. SRSF2 mutations could directly affect pre-mRNA splicing of a vital gene product; alternatively, a whole network of gene products could be affected. Here we determine how SRSF2 mutations globally affect RNA binding and splicing in vivo using HITS-CLIP. Remarkably, the majority of differential binding events do not translate into alternative splicing of exons with SRSF2P95H binding sites. Alternative splice alterations appear to be dominated by indirect effects. Importantly, SRSF2P95H targets are enriched in RNA processing and splicing genes, including several members of the hnRNP and SR families of proteins, suggesting a "splicing-cascade" phenotype wherein mutation of a single splicing factor leads to widespread modifications in multiple RNA processing and splicing proteins. We show that splice alteration of HNRNPA2B1, a splicing factor differentially bound and spliced by SRSF2P95H, impairs hematopoietic differentiation in vivo. Our data suggests a model whereby the recurrent mutations in splicing factors set off a cascade of gene regulatory events that together affect hematopoiesis and drive cancer.
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16
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Chatterji P, Rustgi AK. RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer. Trends Mol Med 2018; 24:490-506. [PMID: 29627433 DOI: 10.1016/j.molmed.2018.03.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022]
Abstract
The intestinal epithelium is highly proliferative and consists of crypt invaginations that house stem cells and villus projections with differentiated cells. There exists a dynamic equilibrium between proliferation, migration, differentiation, and senescence that is regulated by several factors. Among these are RNA binding proteins (RBPs) that bind their targets in a both context dependent and independent manner. RBP-RNA complexes act as rheostats by regulating expression of RNAs both co- and post-transcriptionally. This is important, especially in response to intestinal injury, to fuel regeneration. The manner in which these RBPs function in the intestine and their interactions with other pivotal pathways in colorectal cancer may provide a framework for new insights and potential therapeutic applications.
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Affiliation(s)
- Priya Chatterji
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Anil K Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA.
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17
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Köster T, Meyer K. Plant Ribonomics: Proteins in Search of RNA Partners. TRENDS IN PLANT SCIENCE 2018; 23:352-365. [PMID: 29429586 DOI: 10.1016/j.tplants.2018.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/08/2018] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
Research into the regulation of gene expression underwent a shift from focusing on DNA-binding proteins as key transcriptional regulators to RNA-binding proteins (RBPs) that come into play once transcription has been initiated. RBPs orchestrate all RNA-processing steps in the cell. To obtain a global view of in vivo targets, the RNA complement associated with particular RBPs is determined via immunoprecipitation of the RBP and subsequent identification of bound RNAs via RNA-seq. Here, we describe technical advances in identifying RBP in vivo targets and their binding motifs. We provide an up-to-date view of targets of nucleocytoplasmic RBPs collected in arabidopsis. We also discuss current experimental limitations and provide an outlook on how the approaches may advance our understanding of post-transcriptional networks.
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Affiliation(s)
- Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
| | - Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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18
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Ransey E, Björkbom A, Lelyveld VS, Biecek P, Pantano L, Szostak JW, Sliz P. Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution. RNA Biol 2017; 14:1756-1765. [PMID: 28945502 PMCID: PMC5731800 DOI: 10.1080/15476286.2017.1356566] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
It remains a formidable challenge to characterize the diverse complexes of RNA binding proteins and their targets. While crosslink and immunoprecipitation (CLIP) methods are powerful techniques that identify RNA targets on a global scale, the resolution and consistency of these methods is a matter of debate. Here we present a comparative analysis of LIN28-pre-let-7 UV-induced crosslinking using a tandem mass spectrometry (MS/MS) and deep sequencing interrogation of in vitro crosslinked complexes. Interestingly, analyses by the two methods diverge in their identification of crosslinked nucleotide identity – whereas bioinformatics and sequencing analyses suggest guanine in mammalian cells, MS/MS identifies uridine. This work suggests the need for comprehensive analysis and validation of crosslinking methodologies.
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Affiliation(s)
- Elizabeth Ransey
- a Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , MA
| | - Anders Björkbom
- c Department of Molecular Biology and Center for Computational and Integrative Biology , Howard Hughes Medical Institute, Massachusetts General Hospital , Boston , MA , USA.,d Åbo Akademi University , Department of Biosciences , Artillerigatan 6, FI-20520 Åbo , Finland
| | - Victor S Lelyveld
- c Department of Molecular Biology and Center for Computational and Integrative Biology , Howard Hughes Medical Institute, Massachusetts General Hospital , Boston , MA , USA
| | - Przemyslaw Biecek
- e Faculty of Mathematics Informatics and Mechanics, University of Warsaw , Banacha 2, Warsaw , Poland
| | - Lorena Pantano
- f Department of Biostatistics , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| | - Jack W Szostak
- c Department of Molecular Biology and Center for Computational and Integrative Biology , Howard Hughes Medical Institute, Massachusetts General Hospital , Boston , MA , USA
| | - Piotr Sliz
- a Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , MA.,b Division of Molecular Medicine , Boston Children's Hospital , Boston , MA , USA
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19
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Farzaneh M, Attari F, Khoshnam SE. Concise Review: LIN28/let-7 Signaling, a Critical Double-Negative Feedback Loop During Pluripotency, Reprogramming, and Tumorigenicity. Cell Reprogram 2017; 19:289-293. [PMID: 28846452 DOI: 10.1089/cell.2017.0015] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs (miRNAs) with 20-30 nucleotides have recently emerged as the multidimensional regulators of cell fate decisions. Recent improvement in high-throughput sequencing has highlighted the potential role of LIN28/let-7 regulatory network in several developmental events. It was proposed that this pathway might represent a functional signature in cell proliferation, transition between commitment and pluripotency, and regulation of cancer and tumorigenicity. LIN28/let-7 regulatory pathway is one of the excellent examples of the relationship between an miRNA and mRNAs. This review article highlights the potentials of LIN28/let-7 signaling in gene regulatory pathways during pluripotency, reprogramming, and tumorigenicity.
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Affiliation(s)
- Maryam Farzaneh
- 1 Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran, Iran
| | - Farnoosh Attari
- 2 Department of Animal Biology, School of Biology, College of Science, University of Tehran , Tehran, Iran
| | - Seyed Esmaeil Khoshnam
- 3 Department of Physiology, Faculty of Medicine, Physiology Research Center, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran .,4 Student Research Committee, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran
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20
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Brennan E, Wang B, McClelland A, Mohan M, Marai M, Beuscart O, Derouiche S, Gray S, Pickering R, Tikellis C, de Gaetano M, Barry M, Belton O, Ali-Shah ST, Guiry P, Jandeleit-Dahm KAM, Cooper ME, Godson C, Kantharidis P. Protective Effect of let-7 miRNA Family in Regulating Inflammation in Diabetes-Associated Atherosclerosis. Diabetes 2017; 66:2266-2277. [PMID: 28487436 DOI: 10.2337/db16-1405] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/30/2017] [Indexed: 12/15/2022]
Abstract
The let-7 miRNA family plays a key role in modulating inflammatory responses. Vascular smooth muscle cell (SMC) proliferation and endothelial cell (EC) dysfunction are critical in the pathogenesis of atherosclerosis, including in the setting of diabetes. Here we report that let-7 levels are decreased in diabetic human carotid plaques and in a model of diabetes-associated atherosclerosis, the diabetic ApoE-/- mouse. In vitro platelet-derived growth factor (PDGF)- and tumor necrosis factor-α (TNF-α)-induced vascular SMC and EC activation was associated with reduced let-7 miRNA expression via Lin28b, a negative regulator of let-7 biogenesis. Ectopic overexpression of let-7 in SMCs inhibited inflammatory responses including proliferation, migration, monocyte adhesion, and nuclear factor-κB activation. The therapeutic potential of restoring let-7 levels using a let-7 mimic was tested: in vitro in SMCs using an endogenous anti-inflammatory lipid (lipoxin A4), ex vivo in murine aortas, and in vivo via tail vein injection in a 24-h murine model. Furthermore, we delivered let-7 mimic to human carotid plaque ex vivo and observed significant changes to the secretome in response to let-7 therapy. Restoration of let-7 expression could provide a new target for an anti-inflammatory approach in diabetic vascular disease.
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Affiliation(s)
- Eoin Brennan
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Diabetes Complications Research Centre, Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Bo Wang
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Anatomy and Developmental Biology, Central Clinical School, Monash University, Clayton, Victoria, Australia
| | - Aaron McClelland
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Muthukumar Mohan
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia
| | - Mariam Marai
- Diabetes Complications Research Centre, Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Ophelie Beuscart
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Sinda Derouiche
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Stephen Gray
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Raelene Pickering
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia
| | - Chris Tikellis
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia
| | - Monica de Gaetano
- Diabetes Complications Research Centre, Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Mary Barry
- St. Vincent's University Hospital, Dublin, Ireland
| | - Orina Belton
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Syed Tasadaque Ali-Shah
- Centre for Synthesis and Chemical Biology, School of Chemistry and Chemical Biology, University College Dublin, Dublin, Ireland
| | - Patrick Guiry
- Centre for Synthesis and Chemical Biology, School of Chemistry and Chemical Biology, University College Dublin, Dublin, Ireland
| | - Karin A M Jandeleit-Dahm
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia
| | - Mark E Cooper
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia
| | - Catherine Godson
- Diabetes Complications Research Centre, Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Phillip Kantharidis
- JDRF Danielle Alberti Memorial Centre for Diabetes Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Diabetes, Central Clinical School, Monash University, Clayton, Victoria, Australia
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21
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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22
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The heterochronic gene Lin28 regulates amphibian metamorphosis through disturbance of thyroid hormone function. Dev Biol 2017; 425:142-151. [DOI: 10.1016/j.ydbio.2017.03.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 11/21/2022]
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23
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Lee S, Wottrich S, Bonavida B. Crosstalks between Raf-kinase inhibitor protein and cancer stem cell transcription factors (Oct4, KLF4, Sox2, Nanog). Tumour Biol 2017; 39:1010428317692253. [PMID: 28378634 DOI: 10.1177/1010428317692253] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Raf-kinase inhibitor protein has been reported to inhibit both the Raf/mitogen extracellular signal-regulated kinase/extracellular signal-regulated kinase and nuclear factor kappa-light-chain of activated B cells pathways. It has also been reported in cancers that Raf-kinase inhibitor protein behaves as a metastatic suppressor as well as a chemo-immunosensitizing factor to drug/immune-mediated apoptosis. The majority of cancers exhibit low or no levels of Raf-kinase inhibitor protein. Hence, the activities of Raf-kinase inhibitor protein contrast, in part, to those mediated by several cancer stem cell transcription factors for their roles in resistance and metastasis. In this review, the existence of crosstalks in the signaling pathways between Raf-kinase inhibitor protein and several cancer stem cell transcription factors (Oct4, KLF4, Sox2 and Nanog) was assembled. Oct4 is induced by Lin28, and Raf-kinase inhibitor protein inhibits the microRNA binding protein Lin28. The expression of Raf-kinase inhibitor protein inversely correlates with the expression of Oct4. KLF4 does not interact directly with Raf-kinase inhibitor protein, but rather interacts indirectly via Raf-kinase inhibitor protein's regulation of the Oct4/Sox2/KLF4 complex through the mitogen-activated protein kinase pathway. The mechanism by which Raf-kinase inhibitor protein inhibits Sox2 is via the inhibition of the mitogen-activated protein kinase pathway by Raf-kinase inhibitor protein. Thus, Raf-kinase inhibitor protein's relationship with Sox2 is via its regulation of Oct4. Inhibition of extracellular signal-regulated kinase by Raf-kinase inhibitor protein results in the upregulation of Nanog. The inhibition of Oct4 by Raf-kinase inhibitor protein results in the failure of the heterodimer formation of Oct4 and Sox2 that is necessary to bind to the Nanog promoter for the transcription of Nanog. The findings revealed that there exists a direct correlation between the expression of Raf-kinase inhibitor protein and the expression of each of the above transcription factors. Based on these analyses, we suggest that the expression level of Raf-kinase inhibitor protein may be involved in the regulation of the cancer stem cell phenotype.
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Affiliation(s)
- SoHyun Lee
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stephanie Wottrich
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin Bonavida
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
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24
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Borbolis F, Flessa CM, Roumelioti F, Diallinas G, Stravopodis DJ, Syntichaki P. Neuronal function of the mRNA decapping complex determines survival of Caenorhabditis elegans at high temperature through temporal regulation of heterochronic gene expression. Open Biol 2017; 7:160313. [PMID: 28250105 PMCID: PMC5376704 DOI: 10.1098/rsob.160313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/04/2017] [Indexed: 12/18/2022] Open
Abstract
In response to adverse environmental cues, Caenorhabditis elegans larvae can temporarily arrest development at the second moult and form dauers, a diapause stage that allows for long-term survival. This process is largely regulated by certain evolutionarily conserved signal transduction pathways, but it is also affected by miRNA-mediated post-transcriptional control of gene expression. The 5'-3' mRNA decay mechanism contributes to miRNA-mediated silencing of target mRNAs in many organisms but how it affects developmental decisions during normal or stress conditions is largely unknown. Here, we show that loss of the mRNA decapping complex activity acting in the 5'-3' mRNA decay pathway inhibits dauer formation at the stressful high temperature of 27.5°C, and instead promotes early developmental arrest. Our genetic data suggest that this arrest phenotype correlates with dysregulation of heterochronic gene expression and an aberrant stabilization of lin-14 mRNA at early larval stages. Restoration of neuronal dcap-1 activity was sufficient to rescue growth phenotypes of dcap-1 mutants at both high and normal temperatures, implying the involvement of common developmental timing mechanisms. Our work unveils the crucial role of 5'-3' mRNA degradation in proper regulation of heterochronic gene expression programmes, which proved to be essential for survival under stressful conditions.
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Affiliation(s)
- Fivos Borbolis
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens 11527, Greece
- Faculty of Biology, School of Science, University of Athens, Athens, Greece
| | - Christina-Maria Flessa
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens 11527, Greece
- Faculty of Biology, School of Science, University of Athens, Athens, Greece
| | - Fani Roumelioti
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens 11527, Greece
- School of Medicine, University of Athens, Athens, Greece
| | - George Diallinas
- Faculty of Biology, School of Science, University of Athens, Athens, Greece
| | | | - Popi Syntichaki
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens 11527, Greece
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25
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Wang D, Hou L, Nakamura S, Su M, Li F, Chen W, Yan Y, Green CD, Chen D, Zhang H, Antebi A, Han JDJ. LIN-28 balances longevity and germline stem cell number in Caenorhabditis elegans through let-7/AKT/DAF-16 axis. Aging Cell 2017; 16:113-124. [PMID: 27730721 PMCID: PMC5242300 DOI: 10.1111/acel.12539] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 01/23/2023] Open
Abstract
The RNA‐binding protein LIN‐28 was first found to control developmental timing in Caenorhabditis elegans. Later, it was found to play important roles in pluripotency, metabolism, and cancer in mammals. Here we report that a low dosage of lin‐28 enhanced stress tolerance and longevity, and reduced germline stem/progenitor cell number in C. elegans. The germline LIN‐28‐regulated microRNA let‐7 was required for these effects by targeting akt‐1/2 and decreasing their protein levels. AKT‐1/2 and the downstream DAF‐16 transcription factor were both required for the lifespan and germline stem cell effects of lin‐28. The pathway also mediated dietary restriction induced lifespan extension and reduction in germline stem cell number. Thus, the LIN‐28/let‐7/AKT/DAF‐16 axis we delineated here is a program that plays an important role in balancing reproduction and somatic maintenance and their response to the environmental energy level—a central dogma of the ‘evolutionary optimization’ of resource allocation that modulates aging.
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Affiliation(s)
- Dan Wang
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
- University of Chinese Academy of Science; Beijing 100049 China
| | - Lei Hou
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Shuhei Nakamura
- Max Planck Institute for Biology of Ageing; Joseph-Stelzmann-Strasse 9b Cologne 50931 Germany
| | - Ming Su
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Fang Li
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Weiyang Chen
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Yizhen Yan
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
- University of Chinese Academy of Science; Beijing 100049 China
| | - Christopher D. Green
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
| | - Di Chen
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study; Model Animal Research Center; Nanjing University; Nanjing Jiangsu 210061 China
| | - Hong Zhang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing; Joseph-Stelzmann-Strasse 9b Cologne 50931 Germany
| | - Jing-Dong J. Han
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; 320 Yue Yang Road Shanghai 200031 China
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26
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Mullany LE, Herrick JS, Wolff RK, Slattery ML. Single nucleotide polymorphisms within MicroRNAs, MicroRNA targets, and MicroRNA biogenesis genes and their impact on colorectal cancer survival. Genes Chromosomes Cancer 2017; 56:285-295. [PMID: 27859935 DOI: 10.1002/gcc.22434] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/15/2016] [Indexed: 12/21/2022] Open
Abstract
We have shown that single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, miRNA target genes, and miRNA biogenesis genes minimally contribute to colon cancer risk. It is possible that these SNPs alter survival. We analyzed 565 SNPs in or adjacent to microRNAs, target genes, or biogenesis genes, using 1,115 cases and 1,173 controls; 837 cases had survival information. We tested SNPs for associations with colorectal cancer (CRC) survival using a Cox proportional hazard model adjusting for age, study center, gender, AJCC disease stage, and MSI tumor status. Multiple comparison adjustments were made using the step-down Bonferroni correction. SNPs associated with survival (Praw < 0.05) also were assessed with messenger RNA (mRNA). Seven of the 565 SNPs analyzed were associated significantly with CRC survival after adjustment for multiple comparisons. Six of these increased risk of dying, and one, rs12140 (ADAMTS1) decreased risk of dying from CRC (HRR = 0.44, 95% CI (0.24, 0.83; PHolm = 0.011). Six SNPs altered colon cancer risk and five were associated with altered mRNA expression across genotypes. One SNP, rs2059691 (PRKRA), was associated with increased mRNA expression and worse survival, and one SNP, rs6598964 (LIN28A), decreased risk of developing colon cancer [OR = 0.77 95% CI (0.61, 0.98)] and increased risk of dying from CRC (HRR = 2.26 95% CI (1.52, 3.36). PHolm = 0.003). The few SNPs associated with CRC survival, colon cancer risk, or with mRNA expression, resided in genes that influence metastasis and angiogenesis. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Lila E Mullany
- Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, UT
| | - Jennifer S Herrick
- Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, UT
| | - Roger K Wolff
- Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, UT
| | - Martha L Slattery
- Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, UT
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Inverse correlation between the metastasis suppressor RKIP and the metastasis inducer YY1: Contrasting roles in the regulation of chemo/immuno-resistance in cancer. Drug Resist Updat 2017; 30:28-38. [PMID: 28363333 DOI: 10.1016/j.drup.2017.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/28/2016] [Accepted: 01/04/2017] [Indexed: 02/06/2023]
Abstract
Several gene products have been postulated to mediate inherent and/or acquired anticancer drug resistance and tumor metastasis. Among these, the metastasis suppressor and chemo-immuno-sensitizing gene product, Raf Kinase Inhibitor Protein (RKIP), is poorly expressed in many cancers. In contrast, the metastasis inducer and chemo-immuno-resistant factor Yin Yang 1 (YY1) is overexpressed in many cancers. This inverse relationship between RKIP and YY1 expression suggests that these two gene products may be regulated via cross-talks of molecular signaling pathways, culminating in the expression of different phenotypes based on their targets. Analyses of the molecular regulation of the expression patterns of RKIP and YY1 as well as epigenetic, post-transcriptional, and post-translational regulation revealed the existence of several effector mechanisms and crosstalk pathways, of which five pathways of relevance have been identified and analyzed. The five examined cross-talk pathways include the following loops: RKIP/NF-κB/Snail/YY1, p38/MAPK/RKIP/GSK3β/Snail/YY1, RKIP/Smurf2/YY1/Snail, RKIP/MAPK/Myc/Let-7/HMGA2/Snail/YY1, as well as RKIP/GPCR/STAT3/miR-34/YY1. Each loop is comprised of multiple interactions and cascades that provide evidence for YY1's negative regulation of RKIP expression and vice versa. These loops elucidate potential prognostic motifs and targets for therapeutic intervention. Chiefly, these findings suggest that targeted inhibition of YY1 by specific small molecule inhibitors and/or the specific induction of RKIP expression and activity are potential therapeutic strategies to block tumor growth and metastasis in many cancers, as well as to overcome anticancer drug resistance. These strategies present potential alternatives for their synergistic uses in combination with low doses of conventional chemo-immunotherapeutics and hence, increasing survival, reducing toxicity, and improving quality of life.
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Fang Y, Zhang L, Li Z, Li Y, Huang C, Lu X. MicroRNAs in DNA Damage Response, Carcinogenesis, and Chemoresistance. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 333:1-49. [DOI: 10.1016/bs.ircmb.2017.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Stage-Specific Timing of the microRNA Regulation of lin-28 by the Heterochronic Gene lin-14 in Caenorhabditis elegans. Genetics 2016; 205:251-262. [PMID: 27815363 DOI: 10.1534/genetics.116.195040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/20/2016] [Indexed: 01/01/2023] Open
Abstract
In normal development, the order and synchrony of diverse developmental events must be explicitly controlled. In the nematode Caenorhabditis elegans, the timing of larval events is regulated by hierarchy of proteins and microRNAs (miRNAs) known as the heterochronic pathway. These regulators are organized in feedforward and feedback interactions to form a robust mechanism for specifying the timing and execution of cell fates at successive stages. One member of this pathway is the RNA binding protein LIN-28, which promotes pluripotency and cell fate decisions in successive stages. Two genetic circuits control LIN-28 abundance: it is negatively regulated by the miRNA lin-4, and positively regulated by the transcription factor LIN-14 through a mechanism that was previously unknown. In this report, we used animals that lack lin-4 to elucidate LIN-14's activity in this circuit. We demonstrate that three let-7 family miRNAs-miR-48, miR-84, and miR-241-inhibit lin-28 expression. Furthermore, we show genetically that these miRNAs act between lin-14 and lin-28, and that they comprise the pathway by which lin-14 positively regulates lin-28 We also show that the lin-4 family member mir-237, also regulates early cell fates. Finally, we show that the expression of these miRNAs is directly inhibited by lin-14 activity, making them the first known targets of lin-14 that act in the heterochronic pathway.
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Faunes F, Larraín J. Conservation in the involvement of heterochronic genes and hormones during developmental transitions. Dev Biol 2016; 416:3-17. [DOI: 10.1016/j.ydbio.2016.06.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 06/03/2016] [Accepted: 06/09/2016] [Indexed: 01/26/2023]
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Maldotti M, Incarnato D, Neri F, Krepelova A, Rapelli S, Anselmi F, Parlato C, Basile G, Dettori D, Calogero R, Oliviero S. The long intergenic non-coding RNA CCR492 functions as a let-7 competitive endogenous RNA to regulate c-Myc expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1322-32. [PMID: 27344374 DOI: 10.1016/j.bbagrm.2016.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/06/2016] [Accepted: 06/22/2016] [Indexed: 02/03/2023]
Abstract
In mammals the cell-cycle progression through the G1 phase is a tightly regulated process mediated by the transcriptional activation of early genes in response to mitogenic stimuli, whose dysregulation often leads to tumorigenesis. We here report the discovery by RNA-seq of cell-cycle regulated (CCR) long intergenic non-coding RNAs (lincRNAs), potentially involved in the control of the cell-cycle progression. We identified 10 novel lincRNAs expressed in response to serum treatment in mouse embryonic fibroblasts (MEFs) and in BALB/c fibroblasts, comparably to early genes. By loss-of-function experiments we found that lincRNA CCR492 is required for G1/S progression, localizes in the cell cytoplasm and contains 4 let-7 microRNA recognition elements (MREs). Mechanistically, CCR492 functions as a competing endogenous RNA (ceRNA) to antagonize the function of let-7 microRNAs, leading to the de-repression of c-Myc. Moreover, we show that ectopic expression of CCR492 along with a constitutively active H-Ras promotes cell transformation. Thus, we identified a new lincRNA expressed as an early gene in mammalian cells to regulate the cell-cycle progression by upregulating c-Myc expression.
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Affiliation(s)
- Mara Maldotti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy; Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy
| | - Danny Incarnato
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy; Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy
| | - Francesco Neri
- Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy
| | - Anna Krepelova
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy; Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy
| | - Stefania Rapelli
- Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy
| | - Francesca Anselmi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy; Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy
| | - Caterina Parlato
- Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy
| | - Giulia Basile
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy; Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy
| | - Daniela Dettori
- Dipartimento di Biotecnologie Molecolari e Scienze per la Salute, Università di Torino, Via Nizza 52, Torino, Italy
| | - Raffaele Calogero
- Dipartimento di Biotecnologie Molecolari e Scienze per la Salute, Università di Torino, Via Nizza 52, Torino, Italy
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy; Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy.
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Mullany LE, Herrick JS, Wolff RK, Buas MF, Slattery ML. Impact of polymorphisms in microRNA biogenesis genes on colon cancer risk and microRNA expression levels: a population-based, case-control study. BMC Med Genomics 2016; 9:21. [PMID: 27107574 PMCID: PMC4841949 DOI: 10.1186/s12920-016-0181-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/10/2016] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) have been implicated in the incidence and progression of cancer. It has been proposed that single nucleotide polymorphisms (SNPs) influence cancer risk due to their position within genes involved in miRNA synthesis and regulation. Methods Genes directly and indirectly involved in miRNA biogenesis were identified from the literature. We then identified SNPs within these regions. Using genome-wide association study data we evaluated associations between biogenesis-related SNPs with colon cancer risk and their corresponding mRNA expression in normal colonic mucosa and carcinoma and difference in expression between the two tissues. SNPs that were associated with either altered colon cancer risk or with mRNA expression were evaluated for associations with altered miRNA expression. Results Eleven SNPs were associated (P < 0.05) with colon cancer risk, and two of these variants remained significant after correction for multiple comparisons (PHolm < 0.05): rs1967327 (PRKRA) (ORdom = 0.78, 95 % CI 0.66–0.92) and rs4548444 (MAPKAP2) (ORrec = 1.67, 95 % CI 1.12–2.48). Of these two SNPs, rs4548444 (MAPKAP2), was associated with significantly altered miRNA expression levels in normal colonic mucosa, with nine miRNAs upregulated among individuals homozygous rare (GG) for rs4548444. One SNP associated with cancer prior to adjustment for multiple comparisons, rs11089328 (DGCR8), was associated with altered levels of hsa-miR-645 in differential tissue under the dominant model. Three SNPs, rs2740349 (GEMIN4) in carcinoma tissue, and rs235768 (BMP2) and rs2059691 (PRKRA) in normal mucosa, were significantly associated with altered mRNA expression levels across genotypes after multiple comparison adjustment. Rs2740349 (GEMIN4) and rs235768 (BMP2) were significantly associated with the upregulation of six and nine individual miRNAs in normal colonic mucosa, respectively. Conclusion Our data suggest that few of the SNPs in biogenesis genes we evaluated alter levels of mRNA transcription or colon cancer risk. As only one SNP both alters colon cancer risk and miRNA expression it is likely that SNPs influencing cancer do not do so through miRNAs. Because the significant SNPs were associated with downregulated mRNAs and upregulated miRNAs, and because each SNP was associated with unique miRNAs, it is possible that other mechanisms influence mature miRNA levels.
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Affiliation(s)
- Lila E Mullany
- Department of Internal Medicine, University of Utah, School of Medicine, Salt Lake City, UT, USA.
| | - Jennifer S Herrick
- Department of Internal Medicine, University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Roger K Wolff
- Department of Internal Medicine, University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Matthew F Buas
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, School of Medicine, Salt Lake City, UT, USA
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Kim S, Lee HJ, Hahm JH, Jeong SK, Park DH, Hancock WS, Paik YK. Quantitative Profiling Identifies Potential Regulatory Proteins Involved in Development from Dauer Stage to L4 Stage in Caenorhabditis elegans. J Proteome Res 2016; 15:531-9. [DOI: 10.1021/acs.jproteome.5b00884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunhee Kim
- Department
of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Hyoung-Joo Lee
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
| | - Jeong-Hoon Hahm
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
| | - Seul-Ki Jeong
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
| | - Don-Ha Park
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
| | - William S. Hancock
- Department
of Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States,
| | - Young-Ki Paik
- Department
of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
- Yonsei
Proteome Research Center, Yonsei University, Seoul, Korea
- Department
of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
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Lee YT, de Vasconcellos JF, Byrnes C, Kaushal M, Rabel A, Tumburu L, Allwardt JM, Miller JL. Erythroid-Specific Expression of LIN28A Is Sufficient for Robust Gamma-Globin Gene and Protein Expression in Adult Erythroblasts. PLoS One 2015; 10:e0144977. [PMID: 26675483 PMCID: PMC4684222 DOI: 10.1371/journal.pone.0144977] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/25/2015] [Indexed: 01/10/2023] Open
Abstract
Increasing fetal hemoglobin (HbF) levels in adult humans remains an active area in hematologic research. Here we explored erythroid-specific LIN28A expression for its effect in regulating gamma-globin gene expression and HbF levels in cultured adult erythroblasts. For this purpose, lentiviral transduction vectors were produced with LIN28A expression driven by erythroid-specific gene promoter regions of the human KLF1 or SPTA1 genes. Transgene expression of LIN28A with a linked puromycin resistance marker was restricted to the erythroid lineage as demonstrated by selective survival of erythroid colonies (greater than 95% of all colonies). Erythroblast LIN28A over-expression (LIN28A-OE) did not significantly affect proliferation or inhibit differentiation. Greater than 70% suppression of total let-7 microRNA levels was confirmed in LIN28A-OE cells. Increases in gamma-globin mRNA and protein expression with HbF levels reaching 30-40% were achieved. These data suggest that erythroblast targeting of LIN28A expression is sufficient for increasing fetal hemoglobin expression in adult human erythroblasts.
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Affiliation(s)
- Y. Terry Lee
- Molecular Genomics and Therapeutics Section, Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jaira F. de Vasconcellos
- Molecular Genomics and Therapeutics Section, Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Colleen Byrnes
- Molecular Genomics and Therapeutics Section, Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Megha Kaushal
- Molecular Genomics and Therapeutics Section, Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Antoinette Rabel
- Molecular Genomics and Therapeutics Section, Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Laxminath Tumburu
- Molecular Genomics and Therapeutics Section, Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joshua M. Allwardt
- Molecular Genomics and Therapeutics Section, Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffery L. Miller
- Molecular Genomics and Therapeutics Section, Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Abstract
LIN28 is an RNA-binding protein that is best known for its roles in promoting pluripotency via regulation of the microRNA let-7. However, recent studies have uncovered new roles for LIN28 and have revealed how it functions, suggesting that it is more than just a regulator of miRNA biogenesis. Together, these findings imply a new paradigm for LIN28 - as a gatekeeper molecule that regulates the transition between pluripotency and committed cell lineages, in both let-7-dependent and let-7-independent manners. Here, we provide an overview of LIN28 function in development and disease.
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Affiliation(s)
- Jennifer Tsialikas
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Jennifer Romer-Seibert
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
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Mondol V, Ahn BC, Pasquinelli AE. Splicing remodels the let-7 primary microRNA to facilitate Drosha processing in Caenorhabditis elegans. RNA (NEW YORK, N.Y.) 2015; 21:1396-1403. [PMID: 26081559 PMCID: PMC4509930 DOI: 10.1261/rna.052118.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/11/2015] [Indexed: 06/04/2023]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that use partial base-pairing to recognize and regulate the expression of messenger RNAs (mRNAs). Mature miRNAs arise from longer primary transcripts (pri-miRNAs) that are processed to a shorter hairpin precursor miRNA (pre-miRNA) by the Microprocessor complex. In Caenorhabditis elegans the primary let-7 (pri-let-7) transcript undergoes trans-splicing, where pri-let-7 is cleaved at a 3' splice site and the splice-leader-1 (SL1) sequence is appended at the 5' end. Here we investigate the role of this splicing event in the biogenesis of let-7 miRNA. We hypothesized that splicing changes the secondary structure of the pri-let-7 transcript, creating a more favorable substrate for recognition by the Microprocessor. Supporting this idea, we detected conspicuous structural differences between unspliced and SL1-spliced pri-let-7 transcripts using in vitro ribonuclease (RNase) assays. Through the generation of transgenic worm strains, we found that the RNA secondary structure produced by splicing, as opposed to the act of splicing itself, optimizes processing of pri-let-7 by the Microprocessor in vivo. We also observed that the endogenous spliced, but not the unspliced, pri-let-7 transcripts bind to the Microprocessor and accumulate upon its depletion. We conclude that splicing is a key step in generating pri-let-7 transcripts with a structure that enables downstream processing events to produce appropriate levels of mature let-7.
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Affiliation(s)
- Vanessa Mondol
- Division of Biology, University of California, San Diego, La Jolla, California 92093-0349, USA
| | - Byoung Chan Ahn
- Division of Biology, University of California, San Diego, La Jolla, California 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, California 92093-0349, USA
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