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Piasecka A, Szcześniak M, Sekrecki M, Kajdasz A, Sznajder Ł, Baud A, Sobczak K. MBNL splicing factors regulate the microtranscriptome of skeletal muscles. Nucleic Acids Res 2024; 52:12055-12073. [PMID: 39258536 PMCID: PMC11514471 DOI: 10.1093/nar/gkae774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 08/07/2024] [Accepted: 08/23/2024] [Indexed: 09/12/2024] Open
Abstract
Muscleblind like splicing regulators (MBNLs) govern various RNA-processing steps, including alternative splicing, polyadenylation, RNA stability and mRNA intracellular localization. In myotonic dystrophy type 1 (DM1), the most common muscular dystrophy in adults, MBNLs are sequestered on toxic RNA containing expanded CUG repeats, which leads to disruption of MBNL-regulated processes and disease features of DM1. Herein, we show the significance of MBNLs in regulating microtranscriptome dynamics during the postnatal development of skeletal muscles and in microRNA (miRNA) misregulation observed in mouse models and patients with DM1. We identify multiple miRNAs sensitive to MBNL proteins insufficiency and reveal that many of them were postnatally regulated, which correlates with increases in the activity of these proteins during this process. In adult Mbnl1-knockout mice, miRNA expression exhibited an adult-to-newborn shift. We hypothesize that Mbnl1 deficiency influences miRNA levels through a combination of mechanisms. First, the absence of Mbnl1 protein results in alterations to the levels of pri-miRNAs. Second, MBNLs affect miRNA biogenesis by regulating the alternative splicing of miRNA primary transcripts. We propose that the expression of miR-23b, miR-27b and miR-24-1, produced from the same cluster, depends on the MBNL-sensitive inclusion of alternative exons containing miRNA sequences. Our findings suggest that MBNL sequestration in DM1 is partially responsible for altered miRNA activity. This study provides new insights into the biological roles and functions of MBNL proteins as regulators of miRNA expression in skeletal muscles.
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Affiliation(s)
- Agnieszka Piasecka
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
| | - Michał W Szcześniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
| | - Michał Sekrecki
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
| | - Arkadiusz Kajdasz
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704Poznań, Poland
| | - Łukasz J Sznajder
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV 89154, USA
| | - Anna Baud
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
| | - Krzysztof Sobczak
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
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Xu S, Wang G, Feng Y, Zheng J, Huang L, Liu J, Jiang Y, Wang Y, Liu N. PNA-Functionalized, Silica Nanowires-Filled Glass Microtube for Ultrasensitive and Label-Free Detection of miRNA-21. Anal Chem 2024; 96:7470-7478. [PMID: 38696229 DOI: 10.1021/acs.analchem.3c05839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
MicroRNAs (miRNAs) are endogenous and noncoding single-stranded RNA molecules with a length of approximately 18-25 nucleotides, which play an undeniable role in early cancer screening. Therefore, it is very important to develop an ultrasensitive and highly specific method for detecting miRNAs. Here, we present a bottom-up assembly approach for modifying glass microtubes with silica nanowires (SiNWs) and develop a label-free sensing platform for miRNA-21 detection. The three-dimensional (3D) networks formed by SiNWs make them abundant and highly accessible sites for binding with peptide nucleic acid (PNA). As a receptor, PNA has no phosphate groups and exhibits an overall electrically neutral state, resulting in a relatively small repulsion between PNA and RNA, which can improve the hybridization efficiency. The SiNWs-filled glass microtube (SiNWs@GMT) sensor enables ultrasensitive, label-free detection of miRNA-21 with a detection limit as low as 1 aM at a detection range of 1 aM-100 nM. Noteworthy, the sensor can still detect miRNA-21 in the range of 102-108 fM in complex solutions containing 1000-fold homologous interference of miRNAs. The high anti-interference performance of the sensor enables it to specifically recognize target miRNA-21 in the presence of other miRNAs and distinguish 1-, 3-mismatch nucleotide sequences. Significantly, the sensor platform is able to detect miRNA-21 in the lysate of breast cancer cell lines (e.g., MCF-7 cells and MDA-MB-231 cells), indicating that it has good potential in the screening of early breast cancers.
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Affiliation(s)
- Shiwei Xu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Guofeng Wang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yueyue Feng
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Juanjuan Zheng
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Liying Huang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Jiahao Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yisha Jiang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yajun Wang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Nannan Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
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3
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Gu K, Mok L, Wakefield MJ, Chong MMW. Non-canonical RNA substrates of Drosha lack many of the conserved features found in primary microRNA stem-loops. Sci Rep 2024; 14:6713. [PMID: 38509178 PMCID: PMC10954719 DOI: 10.1038/s41598-024-57330-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
The RNase III enzyme Drosha has a central role in microRNA (miRNA) biogenesis, where it is required to release the stem-loop intermediate from primary (pri)-miRNA transcripts. However, it can also cleave stem-loops embedded within messenger (m)RNAs. This destabilizes the mRNA causing target gene repression and appears to occur primarily in stem cells. While pri-miRNA stem-loops have been extensively studied, such non-canonical substrates of Drosha have yet to be characterized in detail. In this study, we employed high-throughput sequencing to capture all polyA-tailed RNAs that are cleaved by Drosha in mouse embryonic stem cells (ESCs) and compared the features of non-canonical versus miRNA stem-loop substrates. mRNA substrates are less efficiently processed than miRNA stem-loops. Sequence and structural analyses revealed that these mRNA substrates are also less stable and more likely to fold into alternative structures than miRNA stem-loops. Moreover, they lack the sequence and structural motifs found in miRNA stem-loops that are required for precise cleavage. Notably, we discovered a non-canonical Drosha substrate that is cleaved in an inverse manner, which is a process that is normally inhibited by features in miRNA stem-loops. Our study thus provides valuable insights into the recognition of non-canonical targets by Drosha.
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Affiliation(s)
- Karen Gu
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Lawrence Mok
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mark M W Chong
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia.
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia.
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Singh K, Sharma D, Bhagat PK, Tayyeba S, Noryang S, Sinha AK. Phosphorylation of AGO1a by MAP kinases is required for miRNA mediated resistance against Xanthomonas oryzae pv. oryzae infection in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111967. [PMID: 38154578 DOI: 10.1016/j.plantsci.2023.111967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023]
Abstract
Bacterial leaf blight is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo) which causes severe crop loss in rice. The molecular mechanism that initiates defense against such pathogens remains unexplored. Reports have suggested crucial role of several miRNAs in regulating immune responses in plants. Argonaute (AGO) proteins have been implicated in imparting immunity against pathogens by using small RNAs as guide molecules. Here, we show that phosphorylation of rice AGO1a by MAP kinases is required for miRNA expression regulation during Xoo infection. AGO1a is induced in response to pathogen infection and is under the control of SA signaling pathway. The pathogen responsive MAP kinases MPK3, MPK4 and MPK6, interact with AGO1a in planta and can phosphorylate the protein in vitro. Overexpression of AGO1a extends disease resistance against Xoo in rice and leads to a higher accumulation of miRNAs. Conversely, overexpression of a non phosphorylatable mutant protein aggravates disease susceptibility and remarkably suppresses the miRNA expression levels. At a molecular level, phosphorylation of AGO1a by MAP kinase is required for increased accumulation of miRNAs during pathogen challenge. Taken together, the data suggests that OsAGO1a is a direct phosphorylation target of MAP kinases and this phosphorylation is crucial for its role in imparting disease resistance.
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Affiliation(s)
- Kirti Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepika Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Prakash Kumar Bhagat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Sumaira Tayyeba
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
| | - Stanzin Noryang
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; Biochemistry Department, Elizer Joldan Memorial College, UT Ladakh 194101, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Lett KE, McLaurin DM, Tucker SK, Hebert MD. The Cajal body marker protein coilin is SUMOylated and possesses SUMO E3 ligase-like activity. FRONTIERS IN RNA RESEARCH 2023; 1:1197990. [PMID: 39703804 PMCID: PMC11656447 DOI: 10.3389/frnar.2023.1197990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
Cajal bodies (CBs) are subnuclear domains that contribute to the biogenesis of several different classes of ribonucleoproteins (RNPs) including small nuclear RNPs. Only some cell types contain abundant CBs, such as neuronal cells and skeletal muscle, but CBs are invariant features of transformed cells. In contrast, coilin, the CB marker protein, is a ubiquitously expressed nuclear protein but the function of coilin in cell types that lack CBs is not well understood. We have previously shown that coilin promotes microRNA biogenesis by promoting phosphorylation of DGCR8, a component of the Microprocessor. Here we identify 7 additional residues of DGCR8 with decreased phosphorylation upon coilin knockdown. In addition to phosphorylation, the addition of a small ubiquitin-like modifier (SUMO) to DGCR8 also increases its stability. Because of coilin's role in the promotion of DGCR8 phosphorylation, we investigated whether coilin is involved in DGCR8 SUMOylation. We show that coilin knockdown results in global decrease of protein SUMOylation, including decreased DGCR8 and Sp100 (a PML body client protein) SUMOylation and decreased SMN expression. Alternatively, we found that coilin expression rescued Sp100 SUMOylation and increased DGCR8 and SMN levels in a coilin knockout cell line. Furthermore, we found that coilin facilitates RanGAP1 SUMOylation, interacts directly with components of the SUMOylation machinery (Ubc9 and SUMO2), and itself is SUMOylated in vitro and in vivo. In summary, we have identified coilin as a regulator of DGCR8 phosphorylation and a promotor of protein SUMOylation with SUMO E3 ligase-like activity.
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Affiliation(s)
- Katheryn E. Lett
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Douglas M. McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Sara K. Tucker
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Michael D. Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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Li Y, Carey TS, Feng CH, Zhu HM, Sun XX, Dai MS. The Ubiquitin-specific Protease USP36 Associates with the Microprocessor Complex and Regulates miRNA Biogenesis by SUMOylating DGCR8. CANCER RESEARCH COMMUNICATIONS 2023; 3:459-470. [PMID: 36950067 PMCID: PMC10026737 DOI: 10.1158/2767-9764.crc-22-0344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/19/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
miRNA biogenesis is a cellular process that produces mature miRNAs from their primary transcripts, pri-miRNAs, via two RNAse III enzyme complexes: the Drosha-DGCR8 microprocessor complex in the nucleus and the Dicer-TRBP complex in the cytoplasm. Emerging evidence suggests that miRNA biogenesis is tightly regulated by posttranscriptional and posttranslational modifications and aberrant miRNA biogenesis is associated with various human diseases including cancer. DGCR8 has been shown to be modified by SUMOylation. Yet, the SUMO ligase mediating DGCR8 SUMOylation is currently unknown. Here, we report that USP36, a nucleolar ubiquitin-specific protease essential for ribosome biogenesis, is a novel regulator of DGCR8. USP36 interacts with the microprocessor complex and promotes DGCR8 SUMOylation, specifically modified by SUMO2. USP36-mediated SUMOylation does not affect the levels of DGCR8 and the formation of the Drosha-DGCR8 complex, but promotes the binding of DGCR8 to pri-miRNAs. Consistently, abolishing DGCR8 SUMOylation significantly attenuates its binding to pri-miRNAs and knockdown of USP36 attenuates pri-miRNA processing, resulting in marked reduction of tested mature miRNAs. Induced expression of a SUMOylation-defective mutant of DGCR8 inhibits cell proliferation. Together, these results suggest that USP36 plays an important role in regulating miRNA biogenesis by SUMOylating DGCR8. Significance This study identifies that USP36 mediates DGCR8 SUMOylation by SUMO2 and is critical for miRNA biogenesis. As USP36 is frequently overexpressed in various human cancers, our study suggests that deregulated USP36-miRNA biogenesis pathway may contribute to tumorigenesis.
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Affiliation(s)
- Yanping Li
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Timothy S. Carey
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Catherine H. Feng
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Hong-Ming Zhu
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Xiao-Xin Sun
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Mu-Shui Dai
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, Oregon
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de Rooij LA, Mastebroek DJ, ten Voorde N, van der Wall E, van Diest PJ, Moelans CB. The microRNA Lifecycle in Health and Cancer. Cancers (Basel) 2022; 14:cancers14235748. [PMID: 36497229 PMCID: PMC9736740 DOI: 10.3390/cancers14235748] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs of ~22 nucleotides that regulate gene expression at the post-transcriptional level. They can bind to around 60% of all protein-coding genes with an average of 200 targets per miRNA, indicating their important function within physiological and pathological cellular processes. miRNAs can be quickly produced in high amounts through canonical and non-canonical pathways that involve a multitude of steps and proteins. In cancer, miRNA biogenesis, availability and regulation of target expression can be altered to promote tumour progression. This can be due to genetic causes, such as single nucleotide polymorphisms, epigenetic changes, differences in host gene expression, or chromosomal remodelling. Alternatively, post-transcriptional changes in miRNA stability, and defective or absent components and mediators of the miRNA-induced silencing complex can lead to altered miRNA function. This review provides an overview of the current knowledge on the lifecycle of miRNAs in health and cancer. Understanding miRNA function and regulation is fundamental prior to potential future application of miRNAs as cancer biomarkers.
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Affiliation(s)
- Laura Adriana de Rooij
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-887-556-557
| | - Dirk Jan Mastebroek
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Nicky ten Voorde
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Elsken van der Wall
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Paul Joannes van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Cathy Beatrice Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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Arabidopsis AAR2, a conserved splicing factor in eukaryotes, acts in microRNA biogenesis. Proc Natl Acad Sci U S A 2022; 119:e2208415119. [PMID: 36191209 PMCID: PMC9565372 DOI: 10.1073/pnas.2208415119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In yeast and humans, AAR2 is involved in pre-messenger RNA (pre-mRNA) splicing through regulating U5 snRNP assembly. This study shows that Arabidopsis AAR2 promotes microRNA (miRNA) accumulation in addition to its conserved role in pre-mRNA splicing. AAR2 is associated with the microprocessor component HYL1 and promotes its dephosphorylation to produce the active form in miRNA biogenesis. The study also reveals a previously unknown role of HYL1 in causing the degradation of the primary precursors to miRNAs (pri-miRNAs) and a role of AAR2 in protecting pri-miRNAs from HYL1-depedent degradation. Taken together, our findings provide insights into the role of a conserved splicing factor in miRNA biogenesis in plants. MicroRNAs (miRNAs) play an essential role in plant growth and development, and as such, their biogenesis is fine-tuned via regulation of the core microprocessor components. Here, we report that Arabidopsis AAR2, a homolog of a U5 snRNP assembly factor in yeast and humans, not only acts in splicing but also promotes miRNA biogenesis. AAR2 interacts with the microprocessor component hyponastic leaves 1 (HYL1) in the cytoplasm, nucleus, and dicing bodies. In aar2 mutants, abundance of nonphosphorylated HYL1, the active form of HYL1, and the number of HYL1-labeled dicing bodies are reduced. Primary miRNA (pri-miRNA) accumulation is compromised despite normal promoter activities of MIR genes in aar2 mutants. RNA decay assays show that the aar2-1 mutation leads to faster degradation of pri-miRNAs in a HYL1-dependent manner, which reveals a previously unknown and negative role of HYL1 in miRNA biogenesis. Taken together, our findings reveal a dual role of AAR2 in miRNA biogenesis and pre-messenger RNA splicing.
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Beyond controlling cell size: functional analyses of S6K in tumorigenesis. Cell Death Dis 2022; 13:646. [PMID: 35879299 PMCID: PMC9314331 DOI: 10.1038/s41419-022-05081-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 01/21/2023]
Abstract
As a substrate and major effector of the mammalian target of rapamycin complex 1 (mTORC1), the biological functions of ribosomal protein S6 kinase (S6K) have been canonically assigned for cell size control by facilitating mRNA transcription, splicing, and protein synthesis. However, accumulating evidence implies that diverse stimuli and upstream regulators modulate S6K kinase activity, leading to the activation of a plethora of downstream substrates for distinct pathobiological functions. Beyond controlling cell size, S6K simultaneously plays crucial roles in directing cell apoptosis, metabolism, and feedback regulation of its upstream signals. Thus, we comprehensively summarize the emerging upstream regulators, downstream substrates, mouse models, clinical relevance, and candidate inhibitors for S6K and shed light on S6K as a potential therapeutic target for cancers.
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10
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Wang C, Sun H, Jiang X, Guan X, Gao F, Shi B. Maternal Oxidized Soybean Oil Administration in Rats during Pregnancy and Lactation Alters the Intestinal DNA Methylation in Offspring. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6224-6238. [PMID: 35549255 DOI: 10.1021/acs.jafc.2c01100] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As a food contaminant, oxidized oil or lipid oxidative products have been proven to exert toxicological effects on the growth and development of animals and humans. Research shows that maternal oxidative stress damage might transmit to another generation by epigenetic modulation. However, current evidence is still not clear on the mechanism of the effects of dietary oxidized oil during pregnancy on the two generations. This study employed a rat model fed with oxidized soybean oil (OSO) during pregnancy and lactation to explore the effects of the oxidative degree (0, 200, 400, and 800 mequiv of O2/kg) on the placental RNA methylation and DNA methylation in offspring jejunum. The results showed that following the ingestion of OSO, the placental genes of different m6A methylation were significantly enriched to nutrient metabolic processes and hormone activity. In addition, the intestine in offspring hypofunctioned observably, such as reducing the height of villi and the level of anti-inflammatory cytokine. Furthermore, maternal intake of OSO during pregnancy can damage the intestinal barrier function of offspring by inhibiting the proliferation and differentiation of intestinal epithelial cells and reducing the activity of intestinal DNA methyltransferase. In conclusion, this study reinforces the assertion that maternal OSO consumption during gestation and lactation negatively affects the placental health and intestinal development of suckling pups.
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Affiliation(s)
- Chuanqi Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Haoyang Sun
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Xu Jiang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Xin Guan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Feng Gao
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Baoming Shi
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
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11
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Wang L, Yan X, Li Y, Wang Z, Chhajed S, Shang B, Wang Z, Choi SW, Zhao H, Chen S, Zhang X. PRP4KA phosphorylates SERRATE for degradation via 20 S proteasome to fine-tune miRNA production in Arabidopsis. SCIENCE ADVANCES 2022; 8:eabm8435. [PMID: 35333566 PMCID: PMC8956257 DOI: 10.1126/sciadv.abm8435] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/02/2022] [Indexed: 05/13/2023]
Abstract
Phosphorylation can quickly switch on/off protein functions. Here, we reported pre-mRNA processing 4 kinase A (PRP4KA), and its paralogs interact with Serrate (SE), a key factor in RNA processing. PRP4KA phosphorylates at least five residues of SE in vitro and in vivo. Hypophosphorylated, but not hyperphosphorylated, SE variants could readily rescue se phenotypes in vivo. Moreover, hypophosphorylated SE variants had stronger binding affinity to microprocessor component HYL1 and were more resistant to degradation by 20S proteasome than hyperphosphorylated counterparts. Knockdown of the kinases enhanced the accumulation of hypophosphorylated SE. However, the excessive SE interfered with the assembly and function of SE-scaffolded macromolecule complexes, causing the se-like defects in the mutant and wild-type backgrounds. Thus, phosphorylation of SE via PRP4KA can quickly clear accumulated SE to secure its proper amount. This study provides new insight into how protein phosphorylation regulates miRNA metabolism through controlling homeostasis of SE accumulation in plants.
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Affiliation(s)
- Lin Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Laboratory of Bio-interactions and Crop Health, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shweta Chhajed
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zhen Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Suk Won Choi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Hongwei Zhao
- Laboratory of Bio-interactions and Crop Health, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Sixue Chen
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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12
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Abstract
MicroRNAs are RNAs of about 18-24 nucleotides in lengths, which are found in the small noncoding RNA class and have a crucial role in the posttranscriptional regulation of gene expression, cellular metabolic pathways, and developmental events. These small but essential molecules are first processed by Drosha and DGCR8 in the nucleus and then released into the cytoplasm, where they cleaved by Dicer to form the miRNA duplex. These duplexes are bound by the Argonaute (AGO) protein to form the RNA-induced silencing complex (RISC) in a process called RISC loading. Transcription of miRNAs, processing with Drosha and DGCR8 in the nucleus, cleavage by Dicer, binding to AGO proteins and forming RISC are the most critical steps in miRNA biogenesis. Additional molecules involved in biogenesis at these stages can enhance or inhibit these processes, which can radically change the fate of the cell. Biogenesis is regulated by many checkpoints at every step, primarily at the transcriptional level, in the nucleus, cytoplasm, with RNA regulation, RISC loading, miRNA strand selection, RNA methylation/uridylation, and turnover rate. Moreover, in recent years, different regulation mechanisms have been discovered in noncanonical Drosha or Dicer-independent pathways. This chapter seeks answers to how miRNA biogenesis and function are regulated through both canonical and non-canonical pathways.
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13
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Mirahmadi Y, Nabavi R, Taheri F, Samadian MM, Ghale-Noie ZN, Farjami M, Samadi-khouzani A, Yousefi M, Azhdari S, Salmaninejad A, Sahebkar A. MicroRNAs as Biomarkers for Early Diagnosis, Prognosis, and Therapeutic Targeting of Ovarian Cancer. JOURNAL OF ONCOLOGY 2021; 2021:3408937. [PMID: 34721577 PMCID: PMC8553480 DOI: 10.1155/2021/3408937] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023]
Abstract
Ovarian cancer is the major cause of gynecologic cancer-related mortality. Regardless of outstanding advances, which have been made for improving the prognosis, diagnosis, and treatment of ovarian cancer, the majority of the patients will die of the disease. Late-stage diagnosis and the occurrence of recurrent cancer after treatment are the most important causes of the high mortality rate observed in ovarian cancer patients. Unraveling the molecular mechanisms involved in the pathogenesis of ovarian cancer may help find new biomarkers and therapeutic targets for ovarian cancer. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression, mostly at the posttranscriptional stage, through binding to mRNA targets and inducing translational repression or degradation of target via the RNA-induced silencing complex. Over the last two decades, the role of miRNAs in the pathogenesis of various human cancers, including ovarian cancer, has been documented in multiple studies. Consequently, these small RNAs could be considered as reliable markers for prognosis and early diagnosis. Furthermore, given the function of miRNAs in various cellular pathways, including cell survival and differentiation, targeting miRNAs could be an interesting approach for the treatment of human cancers. Here, we review our current understanding of the most updated role of the important dysregulation of miRNAs and their roles in the progression and metastasis of ovarian cancer. Furthermore, we meticulously discuss the significance of miRNAs as prognostic and diagnostic markers. Lastly, we mention the opportunities and the efforts made for targeting ovarian cancer through inhibition and/or stimulation of the miRNAs.
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Affiliation(s)
- Yegane Mirahmadi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Fourough Taheri
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Mahdi Samadian
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zari Naderi Ghale-Noie
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Farjami
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Samadi-khouzani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Meysam Yousefi
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sara Azhdari
- Department of Anatomy and Embryology, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Guilan University of Medical Sciences, Guilan, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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14
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Lett KE, Logan MK, McLaurin DM, Hebert MD. Coilin enhances phosphorylation and stability of DGCR8 and promotes miRNA biogenesis. Mol Biol Cell 2021; 32:br4. [PMID: 34319763 PMCID: PMC8684749 DOI: 10.1091/mbc.e21-05-0225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 11/11/2022] Open
Abstract
MicroRNAs (miRNAs) are ∼22 nt small noncoding RNAs that control gene expression at the posttranscriptional level through translational inhibition and destabilization of their target mRNAs. The biogenesis of miRNAs involves a series of processing steps beginning with cropping of the primary miRNA transcript by the Microprocessor complex, which is composed of Drosha and DGCR8. Here we report a novel regulatory interaction between the Microprocessor components and coilin, the Cajal body (CB) marker protein. Coilin knockdown causes alterations in the level of primary and mature miRNAs, let-7a and miR-34a, and their miRNA targets, HMGA2 and Notch1, respectively. We also found that coilin knockdown affects the levels of DGCR8 and Drosha in cells with (HeLa) and without (WI-38) CBs. To further explore the role of coilin in miRNA biogenesis, we conducted a series of coimmunoprecipitation experiments using coilin and DGCR8 constructs, which revealed that coilin and DGCR8 can form a complex. Additionally, our results indicate that phosphorylation of DGCR8, which has been shown to increase protein stability, is impacted by coilin knockdown. Collectively, our results implicate coilin as a member of the regulatory network governing miRNA biogenesis.
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Affiliation(s)
- Katheryn E. Lett
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216-4505
| | - Madelyn K. Logan
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216-4505
| | - Douglas M. McLaurin
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216-4505
| | - Michael D. Hebert
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216-4505
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15
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Shi C, Jin J, Xu H, Ma J, Li T, Xie Y, Li Z. CCR1 enhances SUMOylation of DGCR8 by up-regulating ERK phosphorylation to promote spinal nerve ligation-induced neuropathic pain. Gene Ther 2021; 29:379-389. [PMID: 34413501 DOI: 10.1038/s41434-021-00285-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 11/09/2022]
Abstract
Neuropathic pain is a somatosensory nervous system dysfunction that remains a threatening health problem globally. Recent studies have highlighted the involvement of C-C motif chemokine receptor 1 (CCR1) in neuropathic pain. Herein, the current study set out to explore the modulatory role of CCR1 in spinal nerve ligation (SNL)-induced neuropathic pain and its underlying molecular mechanism. First, it was found that CCR1 was highly expressed in spinal cord tissues and microglial cells of SNL rats. On the other hand, CCR1 knockdown attenuated nerve pain in SNL rats and repressed microglial cell activation in SNL rats and also in the LPS-induced microglial cell model of nerve injury, as evidenced by elevated microglial cell markers OX-42 and IL-1β, IL-6 and TNF-α. Mechanistically, CCR1 enhanced small ubiquitin-like modifier 1 (SUMO1) modification of DiGeorge syndrome critical region gene 8 (DGCR8) in LPS-treated microglial cells by phosphorylating ERK. Moreover, CCR1 silencing brought about elevations in mechanical withdrawal threshold and thermal withdrawal latency. To conclude, our findings indicated that CCR1 enhanced the modification of DGCR8 by SUMO1 through phosphorylation of ERK, thereby promoting the activation and inflammatory response of spinal cord microglial cells and increasing the sensitivity of SNL rats to pain. Thus, this study offers a promising therapeutic target for the management of neuropathic pain.
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Affiliation(s)
- Cunxian Shi
- Department of Anesthesiology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Jin Jin
- Department of Anesthesiology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Hongyu Xu
- Department of Anesthesiology, Central Hospital of Zibo City, Zibo, China
| | - Jiahai Ma
- Department of Anesthesiology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Tao Li
- Department of Anesthesiology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Yonggang Xie
- Department of Anesthesiology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China.
| | - Zhen Li
- Department of Otorhinolaryngology, Yantaishan Hospital, Yantai, China.
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16
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Non-canonical function of DGCR8 in DNA double-strand break repair signaling and tumor radioresistance. Nat Commun 2021; 12:4033. [PMID: 34188037 PMCID: PMC8242032 DOI: 10.1038/s41467-021-24298-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), repair proteins are recruited to the damaged sites. Ubiquitin signaling plays a critical role in coordinating protein recruitment during the DNA damage response. Here, we find that the microRNA biogenesis factor DGCR8 promotes tumor resistance to X-ray radiation independently of its Drosha-binding ability. Upon radiation, the kinase ATM and the deubiquitinase USP51 mediate the activation and stabilization of DGCR8 through phosphorylation and deubiquitination. Specifically, radiation-induced ATM-dependent phosphorylation of DGCR8 at serine 677 facilitates USP51 to bind, deubiquitinate, and stabilize DGCR8, which leads to the recruitment of DGCR8 and DGCR8’s binding partner RNF168 to MDC1 and RNF8 at DSBs. This, in turn, promotes ubiquitination of histone H2A, repair of DSBs, and radioresistance. Altogether, these findings reveal the non-canonical function of DGCR8 in DSB repair and suggest that radiation treatment may result in therapy-induced tumor radioresistance through ATM- and USP51-mediated activation and upregulation of DGCR8. The molecular mechanisms underlying cancer cell radioresistance need to be elucidated. In this study, the authors show that the microRNA biogenesis factor DGCR8 is stabilized by USP51 and ATM upon irradiation and by consequence it promotes the repair of DNA double-strand breaks and radioresistance by recruiting RNF168 to sites of damage.
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17
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Souza VDGPD, Souza GTD, Lemos DRD, Guimarães JMDO, Quintão CCR, Munk M, Saraiva NZ, Camargo LSDA. Heat shock during in vitro maturation of bovine oocytes disturbs bta-miR-19b and DROSHA transcripts abundance after in vitro fertilization. Reprod Domest Anim 2021; 56:1128-1136. [PMID: 34021645 DOI: 10.1111/rda.13956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/18/2021] [Indexed: 11/28/2022]
Abstract
While microRNAs (miRNAs) are a class of non-coding RNAs important for embryo development, the relationship between them and heat stress during oocyte maturation has not yet been established. This study investigated the effect of heat shock during in vitro maturation (IVM) on the abundance of bta-miR-20a, -27b, -103, -21-5p, -19b, -1246 miRNAs and DROSHA and DICER1 mRNAs, previously reported for being involved in oocyte maturation, response to heat stress and miRNA biogenesis. Oocytes were exposed for 12h to heat shock during IVM, fertilized in vitro and the presumptive zygotes cultured for eight days. The relative quantification of miRNAs and mRNAs was performed by real-time PCR in vitro-matured oocytes and 8-cell stage embryos. Progression of meiosis, embryonic development and apoptotic indices was also evaluated. Heat shock compromised (p < .05) oocyte nuclear maturation, cleavage and embryo development, with a higher (p < .05) embryonic apoptotic index than the control group. The abundance of bta-miR-19b increased (p < .05) whereas the abundance of DROSHA transcripts decreased (p < .05) in embryos derived from heat-shocked oocytes. In conclusion, heat shock during IVM influences the abundance of bta-miR-19b and DROSHA in pre-implantation embryos, indicating a persistent effect of heat shock that can be associated with impaired embryo development.
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Affiliation(s)
- Vanessa das Graças Pereira de Souza
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil.,Biology Department, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Gustavo Torres de Souza
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil.,Biology Department, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Diana Rangel de Lemos
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil.,Federal University of Viçosa, UFV, Viçosa, Minas Gerais, Brazil
| | - Judith Maria de Oliveira Guimarães
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil.,Biology Department, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | | | - Michele Munk
- Biology Department, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Naiara Zoccal Saraiva
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil
| | - Luiz Sérgio de Almeida Camargo
- Reproduction and Biotechnology Laboratory, Brazilian Agricultural Research Corporation (Embrapa), Juiz de Fora, Minas Gerais, Brazil
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18
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Spatiotemporal 22q11.21 Protein Network Implicates DGCR8-Dependent MicroRNA Biogenesis as a Risk for Late-Fetal Cortical Development in Psychiatric Diseases. Life (Basel) 2021; 11:life11060514. [PMID: 34073122 PMCID: PMC8227527 DOI: 10.3390/life11060514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022] Open
Abstract
The chromosome 22q11.21 copy number variant (CNV) is a vital risk factor that can be a genetic predisposition to neurodevelopmental disorders (NDD). As the 22q11.21 CNV affects multiple genes, causal disease genes and mechanisms affected are still poorly understood. Thus, we aimed to identify the most impactful 22q11.21 CNV genes and the potential impacted human brain regions, developmental stages and signaling pathways. We constructed the spatiotemporal dynamic networks of 22q11.21 CNV genes using the brain developmental transcriptome and physical protein–protein interactions. The affected brain regions, developmental stages, driver genes and pathways were subsequently investigated via integrated bioinformatics analysis. As a result, we first identified that 22q11.21 CNV genes affect the cortical area mainly during late fetal periods. Interestingly, we observed that connections between a driver gene, DGCR8, and its interacting partners, MECP2 and CUL3, also network hubs, only existed in the network of the late fetal period within the cortical region, suggesting their functional specificity during brain development. We also confirmed the physical interaction result between DGCR8 and CUL3 by liquid chromatography-tandem mass spectrometry. In conclusion, our results could suggest that the disruption of DGCR8-dependent microRNA biogenesis plays a vital role in NDD for late fetal cortical development.
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19
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Mao QY, Xie S, Wu LL, Xiang RL, Cai ZG. MicroRNA-mRNA expression profiles and functional network after injection of botulinum toxin type A into submandibular glands. Toxicon 2021; 199:31-40. [PMID: 34052235 DOI: 10.1016/j.toxicon.2021.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Botulinum toxin type A (BTXA) is effective for the treatment of sialorrhea. MicroRNAs (miRNAs) have significant functions in salivary diseases, but the role of miRNAs during BTXA-inhibited salivary secretion is not yet clear. A total of 19 differentially expressed (DE) miRNAs and 1072 DE mRNAs were identified following BTXA injected into submandibular glands of rats (n = 4) through miRNA sequencing and microarray analysis. Bioinformatic analysis identified that several pathways may be associated with the inhibition of salivary secretion, such as the MAPK signalling pathway, tight junctions, and cytokine-cytokine receptor interaction. We predicted the target genes of DE miRNAs and established the miRNA-mRNA interaction network. The intersection of DE mRNAs and target genes of DE miRNAs was performed and seven mRNAs were obtained: Egr2, Paqr9, Zkscan1, Usp6n, Cyb561a3, Zfhx4, and Clic5. These findings explore the mechanism of BTXA in inhibiting salivary secretion and probably will provide new ideas for clinical application.
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Affiliation(s)
- Qian-Ying Mao
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Shang Xie
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Li-Ling Wu
- Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, 100191, China
| | - Ruo-Lan Xiang
- Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, 100191, China.
| | - Zhi-Gang Cai
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China.
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20
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Zhang F, Yong L, Hua X, You F, Wang B, Feng YL, Mao L. Noble-metal nanoparticle labelling multiplex miRNAs by ICP-MS readout with internal standard isotopes of 115In and 209Bi. Analyst 2021; 146:2074-2082. [PMID: 33566037 DOI: 10.1039/d0an01975e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Inductively coupled plasma-mass spectrometry (ICP-MS) is one of the most powerful techniques for multiplex nucleotide assay owing to the virtue of the high resolution of multiple-elements' mass to charge ratio, in a mass spectrum. Here, a small sized (less than 20 nm) noble-metal nanoparticle labelled ICP-MS (NP-ICP-MS) is proposed for high-throughput microRNA (miRNA) determination. Three miRNA targets - miR-486-5p, miR-221, and miR-21 - in serum, were distinguished by single-stranded DNA (ssDNA) probes labelled with a small sized noble-metal nanoparticle - silver nanoparticles (AgNPs), platinum nanoparticles (PtNPs), and gold nanoparticles (AuNPs). The counting isotopes ion intensity per second (CPS) of the noble-metal label versus internal standard isotope intensity of 115In and 209Bi, exhibited good linearity in the range 0.25 pM to 100 pM with correlation coefficients (R2) of 0.9680, 0.9305, and 0.9418. The specific sandwich-type miRNA assay using the sensitive NP-ICP-MS readout pushed the detection limits down to 0.18 pM for miR-221, 0.23 pM for miR-486-5p, and 0.22 pM for miR-21. And the relative standard deviations (RSDs) for 10 pM target miRNA were less than 3.7%. This work promises a potential ultrasensitive ICP-MS bioassay of multiplex miRNA biomarkers for clinical serum diagnosis.
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Affiliation(s)
- Fei Zhang
- Institute of Physicochemical Detection, Sichuan Centre for Disease Control and Prevention, Chengdu, Sichuan 610041, China
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21
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Pawlick JS, Zuzic M, Pasquini G, Swiersy A, Busskamp V. MiRNA Regulatory Functions in Photoreceptors. Front Cell Dev Biol 2021; 8:620249. [PMID: 33553155 PMCID: PMC7858257 DOI: 10.3389/fcell.2020.620249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/31/2020] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression. These small, non-coding RNAs post-transcriptionally silence messenger RNAs (mRNAs) in a sequence-specific manner. In this way, miRNAs control important regulatory functions, also in the retina. If dysregulated, these molecules are involved in several retinal pathologies. For example, several miRNAs have been linked to essential photoreceptor functions, including light sensitivity, synaptic transmission, and modulation of inflammatory responses. Mechanistic miRNA knockout and knockdown studies further linked their functions to degenerative retinal diseases. Of note, the type and timing of genetic manipulation before, during, or after retinal development, is important when studying specific miRNA knockout effects. Within this review, we focus on miR-124 and the miR-183/96/182 cluster, which have assigned functions in photoreceptors in health and disease. As a single miRNA can regulate hundreds of mRNAs, we will also discuss the experimental validation and manipulation approaches to study complex miRNA/mRNA regulatory networks. Revealing these networks is essential to understand retinal pathologies and to harness miRNAs as precise therapeutic and diagnostic tools to stabilize the photoreceptors’ transcriptomes and, thereby, function.
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Affiliation(s)
- Julia Sophie Pawlick
- Universitäts-Augenklinik Bonn, Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Marta Zuzic
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Giovanni Pasquini
- Universitäts-Augenklinik Bonn, Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Anka Swiersy
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Volker Busskamp
- Universitäts-Augenklinik Bonn, Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
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22
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Good KV, Vincent JB, Ausió J. MeCP2: The Genetic Driver of Rett Syndrome Epigenetics. Front Genet 2021; 12:620859. [PMID: 33552148 PMCID: PMC7859524 DOI: 10.3389/fgene.2021.620859] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Mutations in methyl CpG binding protein 2 (MeCP2) are the major cause of Rett syndrome (RTT), a rare neurodevelopmental disorder with a notable period of developmental regression following apparently normal initial development. Such MeCP2 alterations often result in changes to DNA binding and chromatin clustering ability, and in the stability of this protein. Among other functions, MeCP2 binds to methylated genomic DNA, which represents an important epigenetic mark with broad physiological implications, including neuronal development. In this review, we will summarize the genetic foundations behind RTT, and the variable degrees of protein stability exhibited by MeCP2 and its mutated versions. Also, past and emerging relationships that MeCP2 has with mRNA splicing, miRNA processing, and other non-coding RNAs (ncRNA) will be explored, and we suggest that these molecules could be missing links in understanding the epigenetic consequences incurred from genetic ablation of this important chromatin modifier. Importantly, although MeCP2 is highly expressed in the brain, where it has been most extensively studied, the role of this protein and its alterations in other tissues cannot be ignored and will also be discussed. Finally, the additional complexity to RTT pathology introduced by structural and functional implications of the two MeCP2 isoforms (MeCP2-E1 and MeCP2-E2) will be described. Epigenetic therapeutics are gaining clinical popularity, yet treatment for Rett syndrome is more complicated than would be anticipated for a purely epigenetic disorder, which should be taken into account in future clinical contexts.
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Affiliation(s)
- Katrina V. Good
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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23
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Annese T, Tamma R, De Giorgis M, Ribatti D. microRNAs Biogenesis, Functions and Role in Tumor Angiogenesis. Front Oncol 2020; 10:581007. [PMID: 33330058 PMCID: PMC7729128 DOI: 10.3389/fonc.2020.581007] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/27/2020] [Indexed: 12/19/2022] Open
Abstract
microRNAs (miRNAs) are small non-coding RNA molecules, evolutionary conserved. They target more than one mRNAs, thus influencing multiple molecular pathways, but also mRNAs may bind to a variety of miRNAs, either simultaneously or in a context-dependent manner. miRNAs biogenesis, including miRNA transcription, processing by Drosha and Dicer, transportation, RISC biding, and miRNA decay, are finely controlled in space and time. miRNAs are critical regulators in various biological processes, such as differentiation, proliferation, apoptosis, and development in both health and disease. Their dysregulation is involved in tumor initiation and progression. In tumors, they can act as onco-miRNAs or oncosuppressor-miRNA participating in distinct cellular pathways, and the same miRNA can perform both activities depending on the context. In tumor progression, the angiogenic switch is fundamental. miRNAs derived from tumor cells, endothelial cells, and cells of the surrounding microenvironment regulate tumor angiogenesis, acting as pro-angiomiR or anti-angiomiR. In this review, we described miRNA biogenesis and function, and we update the non-classical aspects of them. The most recent role in the nucleus, as transcriptional gene regulators and the different mechanisms by which they could be dysregulated, in tumor initiation and progression, are treated. In particular, we describe the role of miRNAs in sprouting angiogenesis, vessel co-option, and vasculogenic mimicry. The role of miRNAs in lymphoma angiogenesis is also discussed despite the scarcity of data. The information presented in this review reveals the need to do much more to discover the complete miRNA network regulating angiogenesis, not only using high-throughput computational analysis approaches but also morphological ones.
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Affiliation(s)
- Tiziana Annese
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Section of Human Anatomy and Histology, University of Bari Medical School, Bari, Italy
| | - Roberto Tamma
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Section of Human Anatomy and Histology, University of Bari Medical School, Bari, Italy
| | - Michelina De Giorgis
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Section of Human Anatomy and Histology, University of Bari Medical School, Bari, Italy
| | - Domenico Ribatti
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Section of Human Anatomy and Histology, University of Bari Medical School, Bari, Italy
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24
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Nandan D, Rath CT, Reiner NE. Leishmania regulates host macrophage miRNAs expression by engaging transcription factor c-Myc. J Leukoc Biol 2020; 109:999-1007. [PMID: 33211335 DOI: 10.1002/jlb.4ru0920-614r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/19/2022] Open
Abstract
Parasites of Leishmania genus have developed sophisticated strategies allowing them to deactivate their host macrophage to promote their survival. It has become clear that miRNAs play important roles in shaping innate and adaptive immune responses toward pathogens. It is not surprising that several pathogens including Leishmania have evolved the ability to regulate host macrophage miRNA expression in order to manipulate host cell phenotypes to their advantage. However, very little is known about the mechanisms used by intracellular pathogens to drive changes in host cell miRNA abundance. In this review, Leishmania exploitation of macrophage transcription factor c-Myc as a critical proxy virulence factor to regulate abundance of macrophage miRNAs influencing macrophage physiology to promote its survival will be discussed.
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Affiliation(s)
- Devki Nandan
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolina Torturella Rath
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, British Columbia, Canada
| | - Neil E Reiner
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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25
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Samanta T, Kar S. Fine-tuning Nanog expression heterogeneity in embryonic stem cells by regulating a Nanog transcript-specific microRNA. FEBS Lett 2020; 594:4292-4306. [PMID: 32969052 DOI: 10.1002/1873-3468.13936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 12/24/2022]
Abstract
In embryonic stem cells (ESCs), the transcription factor Nanog maintains the stemness of ESCs despite exhibiting heterogeneous expression patterns under varied culture conditions. Efficient fine-tuning of Nanog expression heterogeneity could enable ESC proliferation and differentiation along specific lineages to be regulated. Herein, by employing a stochastic modeling approach, we show that Nanog expression heterogeneity can be controlled by modulating the regulatory features of a Nanog transcript-specific microRNA, mir-296. We demonstrate how and why the extent of origin-dependent fluctuations in Nanog expression level can be altered by varying either the binding efficiency of the microRNA-mRNA complex or the expression level of mir-296. Moreover, our model makes experimentally feasible and insightful predictions to maneuver Nanog expression heterogeneity explicitly to achieve cell-type-specific differentiation of ESCs.
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Affiliation(s)
| | - Sandip Kar
- Department of Chemistry, IIT Bombay, Mumbai, India
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26
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Tan C, Dai Y, Liu X, Zhao G, Wang W, Li J, Qi L. STAT5A induced LINC01198 promotes proliferation of glioma cells through stabilizing DGCR8. Aging (Albany NY) 2020; 12:5675-5692. [PMID: 32246817 PMCID: PMC7185146 DOI: 10.18632/aging.102938] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/27/2020] [Indexed: 01/03/2023]
Abstract
Background: LINC01198 has been suggested to be able to predict overall prognosis for glioma; however, it has been little described in glioma. Results: It was shown that LINC01198 was markedly enriched in neoplasmic tissues relative to normal controls; and that elevated LINC01198 significantly correlated with unfavorable overall prognosis. Moreover, activation of STAT5A, identified as transcription factor (TF), can induce the expression of LINC01198. DGCR8, a kind of RNA-binding proteins (RBPs), was identified to be able to bind with LINC01198 that can stabilize the DGCR8. Five differential miRNAs with most significant difference, including miR-21-5p, miR-34-5p, miR-1246, miR-4488 and miR-494, were obtainable after silencing of DGCR8. Conclusions: Together, the data we presented here suggested that STAT5 induced LINC01198 promotes proliferation and motility of glioma cells through stabilizing DGCR8 in glioma cells. Methods: Expression of LINC01198 was appraised by quantitative PCR (qPCR) and in situ hybridization (ISH) in glioma clinical specimens, totaling 100 cases. Post hoc statistical analysis was conducted. In vitro, LINC01198 was stably silenced or re-expressed by transfection with lentiviral-based vectors. Chromatin-immunoprecipitation (CHIP) was applied to identify the relevant TFs that can bind with LINC01198, which was corroborated with electrophoretic mobility shift (EMSA) assay. RNA-immunoprecipitation (RIP) was used to identify the RNA-binding protein that can bind with LINC01198. Moreover, miRNA microarray was used to screen out differential miRNAs after silencing of DGCR8.
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Affiliation(s)
- Cheng Tan
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, P.R. China
| | - Yimeng Dai
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, P.R. China
| | - Xiaoyang Liu
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, P.R. China
| | - Guifang Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, P.R. China.,Department of Pathophysiology, Jilin Medical University, Jilin 132013, P.R. China
| | - Weiyao Wang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, P.R. China.,Department of Pathophysiology, Jilin Medical University, Jilin 132013, P.R. China
| | - Jia Li
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, P.R. China
| | - Ling Qi
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, P.R. China.,Department of Pathophysiology, Jilin Medical University, Jilin 132013, P.R. China
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27
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Spadotto V, Giambruno R, Massignani E, Mihailovich M, Maniaci M, Patuzzo F, Ghini F, Nicassio F, Bonaldi T. PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis. Nucleic Acids Res 2020; 48:96-115. [PMID: 31777917 PMCID: PMC6943135 DOI: 10.1093/nar/gkz1051] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 10/04/2019] [Accepted: 11/22/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNA (miRNA) biogenesis is a tightly controlled multi-step process operated in the nucleus by the activity of the Microprocessor and its associated proteins. Through high resolution mass spectrometry (MS)- proteomics we discovered that this complex is extensively methylated, with 84 methylated sites associated to 19 out of its 24 subunits. The majority of the modifications occurs on arginine (R) residues (61), leading to 81 methylation events, while 30 lysine (K)-methylation events occurs on 23 sites of the complex. Interestingly, both depletion and pharmacological inhibition of the Type-I Protein Arginine Methyltransferases (PRMTs) lead to a widespread change in the methylation state of the complex and induce global decrease of miRNA expression, as a consequence of the impairment of the pri-to-pre-miRNA processing step. In particular, we show that the reduced methylation of the Microprocessor subunit ILF3 is linked to its diminished binding to the pri-miRNAs miR-15a/16, miR-17-92, miR-301a and miR-331. Our study uncovers a previously uncharacterized role of R-methylation in the regulation of miRNA biogenesis in mammalian cells.
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Affiliation(s)
- Valeria Spadotto
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Roberto Giambruno
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marianna Maniaci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesca Patuzzo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Ghini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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28
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Burger K, Ketley RF, Gullerova M. Beyond the Trinity of ATM, ATR, and DNA-PK: Multiple Kinases Shape the DNA Damage Response in Concert With RNA Metabolism. Front Mol Biosci 2019; 6:61. [PMID: 31428617 PMCID: PMC6688092 DOI: 10.3389/fmolb.2019.00061] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/11/2019] [Indexed: 12/22/2022] Open
Abstract
Our genome is constantly exposed to endogenous and exogenous sources of DNA damage resulting in various alterations of the genetic code. DNA double-strand breaks (DSBs) are considered one of the most cytotoxic lesions. Several types of repair pathways act to repair DNA damage and maintain genome stability. In the canonical DNA damage response (DDR) DSBs are recognized by the sensing kinases Ataxia-telangiectasia mutated (ATM), Ataxia-telangiectasia and Rad3-related (ATR), and DNA-dependent protein kinase (DNA-PK), which initiate a cascade of kinase-dependent amplification steps known as DSB signaling. Recent evidence suggests that efficient recognition and repair of DSBs relies on the transcription and processing of non-coding (nc)RNA molecules by RNA polymerase II (RNAPII) and the RNA interference (RNAi) factors Drosha and Dicer. Multiple kinases influence the phosphorylation status of both the RNAPII carboxy-terminal domain (CTD) and Dicer in order to regulate RNA-dependent DSBs repair. The importance of kinase signaling and RNA processing in the DDR is highlighted by the regulation of p53-binding protein (53BP1), a key regulator of DSB repair pathway choice between homologous recombination (HR) and non-homologous end joining (NHEJ). Additionally, emerging evidence suggests that RNA metabolic enzymes also play a role in the repair of other types of DNA damage, including the DDR to ultraviolet radiation (UVR). RNAi factors are also substrates for mitogen-activated protein kinase (MAPK) signaling and mediate the turnover of ncRNA during nucleotide excision repair (NER) in response to UVR. Here, we review kinase-dependent phosphorylation events on RNAPII, Drosha and Dicer, and 53BP1 that modulate the key steps of the DDR to DSBs and UVR, suggesting an intimate link between the DDR and RNA metabolism.
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Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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29
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Long-term impact of maternal high-fat diet on offspring cardiac health: role of micro-RNA biogenesis. Cell Death Discov 2019; 5:71. [PMID: 30854230 PMCID: PMC6397280 DOI: 10.1038/s41420-019-0153-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/08/2019] [Accepted: 02/13/2019] [Indexed: 12/25/2022] Open
Abstract
Heart failure is a worldwide leading cause of death. Diet and obesity are particularly of high concern in heart disease etiology. Gravely, altered nutrition during developmental windows of vulnerability can have long-term impact on heart health; however, the underlying mechanisms are poorly understood. In the understanding of the initiation of chronic diseases related to developmental exposure to environmental challenges, deregulations in epigenetic mechanisms including micro-RNAs have been proposed as key events. In this context, we aimed at delineating the role of micro-RNAs in the programming of cardiac alterations induced by early developmental exposure to nutritional imbalance. To reach our aim, we developed a human relevant model of developmental exposure to nutritional imbalance by maternally exposing rat to high-fat diet during gestation and lactation. In this model, offspring exposed to maternal high-fat diet developed cardiac hypertrophy and increased extracellular matrix depot compared to those exposed to chow diet. Microarray approach performed on cardiac tissue allowed the identification of a micro-RNA subset which was down-regulated in high-fat diet-exposed animals and which were predicted to regulate transforming growth factor-beta (TGFβ)-mediated remodeling. As indicated by in vitro approaches and gene expression measurement in the heart of our animals, decrease in DiGeorge critical region 8 (DGCR8) expression, involved in micro-RNA biogenesis, seems to be a critical point in the alterations of the micro-RNA profile and the TGFβ-mediated remodeling induced by maternal exposure to high-fat diet. Finally, increasing DGCR8 activity and/or expression through hemin treatment in vitro revealed its potential in the rescue of the pro-fibrotic phenotype in cardiomyocytes driven by DGCR8 decrease. These findings suggest that cardiac alterations induced by maternal exposure to high-fat diet is related to abnormalities in TGFβ pathway and associated with down-regulated micro-RNA processing. Our study highlighted DGCR8 as a potential therapeutic target for heart diseases related to early exposure to dietary challenge.
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30
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Zhao C, Zhang Y, Popel AS. Mechanistic Computational Models of MicroRNA-Mediated Signaling Networks in Human Diseases. Int J Mol Sci 2019; 20:E421. [PMID: 30669429 PMCID: PMC6358731 DOI: 10.3390/ijms20020421] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRs) are endogenous non-coding RNA molecules that play important roles in human health and disease by regulating gene expression and cellular processes. In recent years, with the increasing scientific knowledge and new discovery of miRs and their gene targets, as well as the plentiful experimental evidence that shows dysregulation of miRs in a wide variety of human diseases, the computational modeling approach has emerged as an effective tool to help researchers identify novel functional associations between differential miR expression and diseases, dissect the phenotypic expression patterns of miRs in gene regulatory networks, and elucidate the critical roles of miRs in the modulation of disease pathways from mechanistic and quantitative perspectives. Here we will review the recent systems biology studies that employed different kinetic modeling techniques to provide mechanistic insights relating to the regulatory function and therapeutic potential of miRs in human diseases. Some of the key computational aspects to be discussed in detail in this review include (i) models of miR-mediated network motifs in the regulation of gene expression, (ii) models of miR biogenesis and miR⁻target interactions, and (iii) the incorporation of such models into complex disease pathways in order to generate mechanistic, molecular- and systems-level understanding of pathophysiology. Other related bioinformatics tools such as computational platforms that predict miR-disease associations will also be discussed, and we will provide perspectives on the challenges and opportunities in the future development and translational application of data-driven systems biology models that involve miRs and their regulatory pathways in human diseases.
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Affiliation(s)
- Chen Zhao
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Yu Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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31
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Nguyen HM, Nguyen TD, Nguyen TL, Nguyen TA. Orientation of Human Microprocessor on Primary MicroRNAs. Biochemistry 2018; 58:189-198. [DOI: 10.1021/acs.biochem.8b00944] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Huong Minh Nguyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Trung Duc Nguyen
- Division of Life Science, Hong Kong University of Science & Technology, Hong Kong, China
| | - Thuy Linh Nguyen
- Division of Life Science, Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, Hong Kong University of Science & Technology, Hong Kong, China
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32
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Giambruno R, Mihailovich M, Bonaldi T. Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Front Mol Biosci 2018; 5:90. [PMID: 30467545 PMCID: PMC6236024 DOI: 10.3389/fmolb.2018.00090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
The interaction between non-coding RNAs (ncRNAs) and proteins is crucial for the stability, localization and function of the different classes of ncRNAs. Although ncRNAs, when embedded in various ribonucleoprotein (RNP) complexes, control the fundamental processes of gene expression, their biological functions and mechanisms of action are still largely unexplored. Mass Spectrometry (MS)-based proteomics has emerged as powerful tool to study the ncRNA world: on the one hand, by identifying the proteins interacting with distinct ncRNAs; on the other hand, by measuring the impact of ncRNAs on global protein levels. Here, we will first provide a concise overview on the basic principles of MS-based proteomics for systematic protein identification and quantification; then, we will recapitulate the main approaches that have been implemented for the screening of ncRNA interactors and the dissection of ncRNA-protein complex composition. Finally, we will describe examples of various proteomics strategies developed to characterize the effect of ncRNAs on gene expression, with a focus on the systematic identification of microRNA (miRNA) targets.
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Affiliation(s)
| | | | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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33
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Treiber T, Treiber N, Meister G. Regulation of microRNA biogenesis and its crosstalk with other cellular pathways. Nat Rev Mol Cell Biol 2018; 20:5-20. [DOI: 10.1038/s41580-018-0059-1] [Citation(s) in RCA: 904] [Impact Index Per Article: 129.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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34
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Label-free ultrasensitive detection of breast cancer miRNA-21 biomarker employing electrochemical nano-genosensor based on sandwiched AgNPs in PANI and N-doped graphene. Biosens Bioelectron 2018; 120:129-136. [PMID: 30172235 DOI: 10.1016/j.bios.2018.08.025] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small, endogenous, noncoding RNAs, shown to be expressed abnormally in many tumors and identified as predictive biomarkers for early diagnosis of several cancers including the breast. Therefore, the label-free and highly sensitive detection of miRNAs is of critical significance. In this work, a highly sensitive and label-free nano-genosensor is developed for the detection of miRNA-21, a known breast cancer biomarker, based on a specific architecture of nitrogen-doped functionalized graphene (NFG), silver nanoparticles (AgNPs), and polyaniline (PANI) that resulted in a remarkable effect on signal amplification. Following the successful functionalization of the nanocomposite and immobilization of the specific sequence of the aminated complementary oligonucleotide of miRNA-21, the detection was performed using differential pulse voltammetry (DPV). The oxidation peak current of the redox probe under optimal conditions was determined to monitor the event hybridization of miRNA-21 biomarker. Applying this highly sensitive and optimized nano-biosensor enabled detection of a wide dynamic range of 10 fM-10 µM with a sensitivity of 2.5 µA cm-2 and a low detection limit of 0.2 fM. This nano-biosensor also demonstrated highly reproducible results in the analysis of blood samples, with recoveries between 94% and 107%, and could be used for early detection of breast cancer by direct detection of the miRNA-21 in real clinical samples without any need to sample preparation, RNA extraction and/or amplification.
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35
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Achkar NP, Cho SK, Poulsen C, Arce AL, Re DA, Giudicatti AJ, Karayekov E, Ryu MY, Choi SW, Harholt J, Casal JJ, Yang SW, Manavella PA. A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation. Dev Cell 2018; 46:236-247.e6. [PMID: 30016624 DOI: 10.1016/j.devcel.2018.06.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 03/14/2018] [Accepted: 06/19/2018] [Indexed: 12/31/2022]
Abstract
Light is the most influential environmental stimulus for plant growth. In response to deficient light, plants reprogram their development to adjust their growth in search for a light source. A fine reprogramming of gene expression orchestrates this adaptive trait. Here we show that plants alter microRNA (miRNA) biogenesis in response to light transition. When plants suffer an unusual extended period of light deprivation, the miRNA biogenesis factor HYPONASTIC LEAVES 1 (HYL1) is degraded but an inactive pool of phosphorylated protein remains stable inside the nucleus. Degradation of HYL1 leads to the release of gene silencing, triggering a proper response to dark and shade. Upon light restoration, a quick dephosphorylation of HYL1 leads to the reactivation of miRNA biogenesis and a switch toward a developmental program that maximizes the light uptake. Our findings define a unique and fast regulatory mechanism controlling the plant silencing machinery during plant light response.
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Affiliation(s)
- Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Seok Keun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | | | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Delfina A Re
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Elizabeth Karayekov
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina
| | - Moon Young Ryu
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Suk Won Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Jesper Harholt
- Carlsberg Research Laboratory, Copenhagen V 1799, Denmark
| | - Jorge J Casal
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina; Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires 1405, Argentina
| | - Seong Wook Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina.
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36
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Zhou L, Lim MYT, Kaur P, Saj A, Bortolamiol-Becet D, Gopal V, Tolwinski N, Tucker-Kellogg G, Okamura K. Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development. eLife 2018; 7:e38389. [PMID: 30024380 PMCID: PMC6066331 DOI: 10.7554/elife.38389] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/04/2018] [Indexed: 12/19/2022] Open
Abstract
Mature microRNAs (miRNAs) are processed from primary transcripts (pri-miRNAs), and their expression is controlled at transcriptional and post-transcriptional levels. However, how regulation at multiple levels achieves precise control remains elusive. Using published and new datasets, we profile a time course of mature and pri-miRNAs in Drosophila embryos and reveal the dynamics of miRNA production and degradation as well as dynamic changes in pri-miRNA isoform selection. We found that 5' nucleotides influence stability of mature miRNAs. Furthermore, distinct half-lives of miRNAs from the mir-309 cluster shape their temporal expression patterns, and the importance of rapid degradation of the miRNAs in gene regulation is detected as distinct evolutionary signatures at the target sites in the transcriptome. Finally, we show that rapid degradation of miR-3/-309 may be important for regulation of the planar cell polarity pathway component Vang. Altogether, the results suggest that complex mechanisms regulate miRNA expression to support normal development.
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Affiliation(s)
- Li Zhou
- Temasek Life Sciences LaboratorySingaporeSingapore
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| | - Mandy Yu Theng Lim
- Temasek Life Sciences LaboratorySingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Prameet Kaur
- Division of ScienceYale-NUS CollegeSingaporeSingapore
| | - Abil Saj
- Cancer Therapeutics and Stratified OncologyGenome Institute of SingaporeSingaporeSingapore
| | | | - Vikneswaran Gopal
- Department of Statistics and Applied Probability, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| | - Nicholas Tolwinski
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
- Division of ScienceYale-NUS CollegeSingaporeSingapore
| | - Greg Tucker-Kellogg
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| | - Katsutomo Okamura
- Temasek Life Sciences LaboratorySingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
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37
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Creugny A, Fender A, Pfeffer S. Regulation of primary microRNA processing. FEBS Lett 2018; 592:1980-1996. [PMID: 29683487 DOI: 10.1002/1873-3468.13067] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRNAs) are evolutionarily conserved small regulatory RNAs that participate in the adjustment of many, if not all, fundamental biological processes. Molecular mechanisms involved in miRNA biogenesis and mode of action have been elucidated in the past two decades. Similar to many cellular pathways, miRNA processing and function can be globally or specifically regulated at several levels and by numerous proteins and RNAs. Given their role as fine-tuning molecules, it is essential for miRNA expression to be tightly regulated in order to maintain cellular homeostasis. Here, we review our current knowledge of the first step of their maturation occurring in the nucleus and how it can be specifically and dynamically modulated.
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Affiliation(s)
- Antoine Creugny
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
| | - Aurélie Fender
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
| | - Sébastien Pfeffer
- Architecture and Reactivity of RNA, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, France
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38
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Calses PC, Dhillon KK, Tucker N, Chi Y, Huang JW, Kawasumi M, Nghiem P, Wang Y, Clurman BE, Jacquemont C, Gafken PR, Sugasawa K, Saijo M, Taniguchi T. DGCR8 Mediates Repair of UV-Induced DNA Damage Independently of RNA Processing. Cell Rep 2017; 19:162-174. [PMID: 28380355 DOI: 10.1016/j.celrep.2017.03.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/24/2016] [Accepted: 03/03/2017] [Indexed: 12/20/2022] Open
Abstract
Ultraviolet (UV) radiation is a carcinogen that generates DNA lesions. Here, we demonstrate an unexpected role for DGCR8, an RNA binding protein that canonically functions with Drosha to mediate microRNA processing, in the repair of UV-induced DNA lesions. Treatment with UV induced phosphorylation on serine 153 (S153) of DGCR8 in both human and murine cells. S153 phosphorylation was critical for cellular resistance to UV, the removal of UV-induced DNA lesions, and the recovery of RNA synthesis after UV exposure but not for microRNA expression. The RNA-binding and Drosha-binding activities of DGCR8 were not critical for UV resistance. DGCR8 depletion was epistatic to defects in XPA, CSA, and CSB for UV sensitivity. DGCR8 physically interacted with CSB and RNA polymerase II. JNKs were involved in the UV-induced S153 phosphorylation. These findings suggest that UV-induced S153 phosphorylation mediates transcription-coupled nucleotide excision repair of UV-induced DNA lesions in a manner independent of microRNA processing.
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Affiliation(s)
- Philamer C Calses
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific, HSB T-466, Seattle, WA 98195-7275, USA
| | - Kiranjit K Dhillon
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Nyka Tucker
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Yong Chi
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Jen-Wei Huang
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific, HSB T-466, Seattle, WA 98195-7275, USA
| | - Masaoki Kawasumi
- Division of Dermatology, Department of Medicine, University of Washington, 850 Republican St., Seattle, WA 98109-4714, USA
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, 850 Republican St., Seattle, WA 98109-4714, USA
| | - Yemin Wang
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Bruce E Clurman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Celine Jacquemont
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA
| | - Philip R Gafken
- Proteomics Core Facility, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., DE-352, Seattle, WA 98109-1024, USA
| | - Kaoru Sugasawa
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Masafumi Saijo
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
| | - Toshiyasu Taniguchi
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., C1-015, Seattle, WA 98109-1024, USA; Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
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39
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Su C, Li Z, Cheng J, Li L, Zhong S, Liu L, Zheng Y, Zheng B. The Protein Phosphatase 4 and SMEK1 Complex Dephosphorylates HYL1 to Promote miRNA Biogenesis by Antagonizing the MAPK Cascade in Arabidopsis. Dev Cell 2017; 41:527-539.e5. [PMID: 28586645 DOI: 10.1016/j.devcel.2017.05.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/03/2017] [Accepted: 05/08/2017] [Indexed: 01/12/2023]
Abstract
Phosphorylation plays an essential role in microRNA (miRNA) processing by regulating co-factors of the miRNA biogenesis machinery. HYL1 (Hyponastic Leaves 1), a core co-factor in plant miRNA biogenesis, is a short-lived phosphoprotein. However, the precise balance and regulatory mechanism of the stability and phosphorylation of HYL1 remain unclear. Here, we show that a highly conserved PP4 (Protein Phosphatase 4) and SMEK1 (Suppressor of MEK 1) complex dephosphorylates HYL1 to promote miRNA biogenesis, by antagonizing the MAPK cascade in Arabidopsis. The smek1 mutants exhibit defective miRNA biogenesis due to accelerated degradation of HYL1. SMEK1 stabilizes HYL1 in a dual manner: SMEK1, as a suppressor, inhibits MAPK activation to attenuate HYL1 phosphorylation; SMEK1 assembles a functional PP4 to target HYL1 for dephosphorylation. Moreover, the protein level of SMEK1 is increased in response to abscisic acid. Our results provide insights into the delicate balance between a protein kinase and a phosphatase during miRNA biogenesis.
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Affiliation(s)
- Chuanbin Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ziwei Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinping Cheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lei Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Songxiao Zhong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Li Liu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
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40
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Abstract
MicroRNAs (miRNAs or miRs) are small 19-22 nucleotide long, noncoding, single-stranded, and multifunctional RNAs that regulate a diverse assortment of gene and protein functions that impact on a vast network of pathways. Lin-4, a noncoding transcript discovered in 1993 and named miRNA, initiated the exploration of research into these intriguing molecules identified in almost all organisms. miRNAs interfere with translation or posttranscriptional regulation of their target gene and regulate multiple biological actions exerted by these target genes. In cancer, they function as both oncogenes and tumor suppressor genes displaying differential activity in various cellular contexts. Although the role of miRNAs on target gene functions has been extensively investigated, less is currently known about the upstream regulatory molecules that regulate miRNAs. This chapter focuses on the factors and processes involved in miRNA regulation.
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Affiliation(s)
- Anjan K Pradhan
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Luni Emdad
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Swadesh K Das
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Devanand Sarkar
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Paul B Fisher
- Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
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41
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González-Villagra J, Kurepin LV, Reyes-Díaz MM. Evaluating the involvement and interaction of abscisic acid and miRNA156 in the induction of anthocyanin biosynthesis in drought-stressed plants. PLANTA 2017; 246:299-312. [PMID: 28534253 DOI: 10.1007/s00425-017-2711-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/13/2017] [Indexed: 05/11/2023]
Abstract
ABA is involved in anthocyanin synthesis through the regulation of microRNA156, augmenting the level of expression of anthocyanin synthesis-related genes and, therefore, increasing anthocyanin level. Drought stress is the main cause of agricultural crop loss in the world. However, plants have developed mechanisms that allow them to tolerate drought stress conditions. At cellular level, drought stress induces changes in metabolite accumulation, including increases in anthocyanin levels due to upregulation of the anthocyanin biosynthetic pathway. Recent studies suggest that the higher anthocyanin content observed under drought stress conditions could be a consequence of a rise in the abscisic acid (ABA) concentration. This plant hormone crosses the plasma membrane by specific transporters, and it is recognized at the cytosolic level by receptors known as pyrabactin resistance (PYR)/regulatory component of ABA receptors (PYR/RCARs) that regulate downstream components. In this review, we discuss the hypothesis regarding the involvement of ABA in the regulation of microRNA156 (miRNA156), which is upregulated as part of dehydration stress responsiveness in different species. The miRNA156 upregulation produces a greater level of anthocyanin gene expression, forming the multienzyme complex that will synthesize an increased level of anthocyanins at the cytosolic face of the rough endoplasmic reticulum (RER). After synthesis, anthocyanins are transported from the RER to the vacuole by two possible models of transport: (1) membrane vesicle-mediated transport, or (2) membrane transporter-mediated transport. Thus, the aim was to analyze the recent findings on synthesis, transport and the possible mechanism by which ABA could increase anthocyanin synthesis under drought stress conditions potentially throughout microRNA156 (miRNA156).
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Affiliation(s)
- Jorge González-Villagra
- Doctoral Program in Science of Natural Resources, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile
| | - Leonid V Kurepin
- Department of Biology and The Biotron Centre for Experimental Climate Change Research, Western University, London, ON, N6A 5B7, Canada
| | - Marjorie M Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile.
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile.
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42
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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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43
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Fletcher CE, Godfrey JD, Shibakawa A, Bushell M, Bevan CL. A novel role for GSK3β as a modulator of Drosha microprocessor activity and MicroRNA biogenesis. Nucleic Acids Res 2017; 45:2809-2828. [PMID: 27907888 PMCID: PMC5389555 DOI: 10.1093/nar/gkw938] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 09/13/2016] [Accepted: 10/19/2016] [Indexed: 01/13/2023] Open
Abstract
Regulation of microRNA (miR) biogenesis is complex and stringently controlled. Here, we identify the kinase GSK3β as an important modulator of miR biogenesis at Microprocessor level. Repression of GSK3β activity reduces Drosha activity toward pri-miRs, leading to accumulation of unprocessed pri-miRs and reduction of pre-miRs and mature miRs without altering levels or cellular localisation of miR biogenesis proteins. Conversely, GSK3β activation increases Drosha activity and mature miR accumulation. GSK3β achieves this through promoting Drosha:cofactor and Drosha:pri-miR interactions: it binds to DGCR8 and p72 in the Microprocessor, an effect dependent upon presence of RNA. Indeed, GSK3β itself can immunoprecipitate pri-miRs, suggesting possible RNA-binding capacity. Kinase assays identify the mechanism for GSK3β-enhanced Drosha activity, which requires GSK3β nuclear localisation, as phosphorylation of Drosha at S300 and/or S302; confirmed by enhanced Drosha activity and association with cofactors, and increased abundance of mature miRs in the presence of phospho-mimic Drosha. Functional implications of GSK3β-enhanced miR biogenesis are illustrated by increased levels of GSK3β-upregulated miR targets following GSK3β inhibition. These data, the first to link GSK3β with the miR cascade in humans, highlight a novel pro-biogenesis role for GSK3β in increasing miR biogenesis as a component of the Microprocessor complex with wide-ranging functional consequences.
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Affiliation(s)
- Claire E Fletcher
- Imperial Centre for Translational and Experimental Medicine, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Jack D Godfrey
- Medical Research Council Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Akifumi Shibakawa
- Imperial Centre for Translational and Experimental Medicine, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Martin Bushell
- Medical Research Council Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Charlotte L Bevan
- Imperial Centre for Translational and Experimental Medicine, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
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44
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Affiliation(s)
- D Cirera-Salinas
- a Swiss Federal Institute of Technology Zurich, Department of Biology , Institute of Molecular Health Sciences, RNAi and Genome Integrity , Zurich , Switzerland
| | - M Bodak
- a Swiss Federal Institute of Technology Zurich, Department of Biology , Institute of Molecular Health Sciences, RNAi and Genome Integrity , Zurich , Switzerland.,b Life Science Zurich Graduate School, University of Zurich , Zurich , Switzerland
| | - C Ciaudo
- a Swiss Federal Institute of Technology Zurich, Department of Biology , Institute of Molecular Health Sciences, RNAi and Genome Integrity , Zurich , Switzerland
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45
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Progranulin and Its Related MicroRNAs after Status Epilepticus: Possible Mechanisms of Neuroprotection. Int J Mol Sci 2017; 18:ijms18030490. [PMID: 28245590 PMCID: PMC5372506 DOI: 10.3390/ijms18030490] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 02/09/2017] [Accepted: 02/15/2017] [Indexed: 12/31/2022] Open
Abstract
The current knowledge about neuroprotective mechanisms in humans after status epilepticus is scarce. One reason is the difficulty to measure possible mediators of these neuroprotective mechanisms. The dawn of microRNA detection in the cerebrospinal fluid (CSF) and the recent advancements in measuring proteins in the CSF such as progranulin, which is, e.g., responsible for neurite outgrowth and limiting exceeding neuroinflammatory responses, have given us new insights into putative neuroprotective mechanisms following status epilepticus. This should complement the animal data. In this review, we cover what is known about the role of progranulin as well as the links between microRNA changes and the progranulin pathway following status epilepticus in humans and animals hypothesizing neuroprotective and neurorehabilitative effects. Progranulin has also been found to feature prominently in the neuroprotective processes under hypoxic conditions and initiating neurorehabilitative processes. These properties may be used therapeutically, e.g., through drugs that raise the progranulin levels and therefore the cerebral progranulin levels as well with the goal of improving the outcome after status epilepticus.
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46
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Dalgaard LT, Eliasson L. An 'alpha-beta' of pancreatic islet microribonucleotides. Int J Biochem Cell Biol 2017; 88:208-219. [PMID: 28122254 DOI: 10.1016/j.biocel.2017.01.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/16/2017] [Accepted: 01/18/2017] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) are cellular, short, non-coding ribonucleotides acting as endogenous posttranscriptional repressors following incorporation in the RNA-induced silencing complex. Despite being chemically and mechanistically very similar, miRNAs exert a multitude of different cellular effects by acting on mRNA species, whose gene-products partake in a wide array of processes. Here, the aim was to review the knowledge of miRNA expression and action in the islet of Langerhans. We have focused on: 1) physiological consequences of islet or beta cell specific inhibition of miRNA processing, 2) mechanisms regulating processing of miRNAs in islet cells, 3) presence and function of miRNAs in alpha versus beta cells - the two main cell types of islets, and 4) miRNA mediators of beta cell decompensation. It is clear that miRNAs regulate pancreatic islet development, maturation, and function in vivo. Moreover, processing of miRNAs appears to be altered by obesity, diabetes, and aging. A number of miRNAs (such as miR-7, miR-21, miR-29, miR-34a, miR-212/miR-132, miR-184, miR-200 and miR-375) are involved in mediating beta cell dysfunction and/or compensation induced by hyperglycemia, oxidative stress, cytotoxic cytokines, and in rodent models of fetal metabolic programming prediabetes and overt diabetes. Studies of human type 2 diabetic islets underline that these miRNA families could have important roles also in human type 2 diabetes. Furthermore, there is a genuine gap of knowledge regarding miRNA expression and function in pancreatic alpha cells. Progress in this area would be enhanced by improved in vitro alpha cell models and better tools for islet cell sorting.
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Affiliation(s)
| | - Lena Eliasson
- Lund University Diabetes Center, Department of Clinical Sciences Malmö, CRC, SUS, Malmö, Sweden.
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47
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The Role of RNA Interference in Stem Cell Biology: Beyond the Mutant Phenotypes. J Mol Biol 2017; 429:1532-1543. [PMID: 28118980 DOI: 10.1016/j.jmb.2017.01.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 01/01/2023]
Abstract
Complex gene regulation systems ensure the maintenance of cellular identity during early development in mammals. Eukaryotic small RNAs have emerged as critical players in RNA interference (RNAi) by mediating gene silencing during embryonic stem cell self-renewal. Most of the proteins involved in the biogenesis of small RNAs are essential for proliferation and differentiation into the three germ layers of mouse embryonic stem cells. In the last decade, new functions for some RNAi proteins, independent of their roles in RNAi pathways, have been demonstrated in different biological systems. In parallel, new concepts in stem cell biology have emerged. Here, we review and integrate the current understanding of how RNAi proteins regulate stem cell identity with the new advances in the stem cell field and the recent non-canonical functions of the RNAi proteins. Finally, we propose a reevaluation of all RNAi mutant phenotypes, as non-canonical (small non-coding RNA independent) functions may contribute to the molecular mechanisms governing mouse embryonic stem cells commitment.
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48
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Cirera-Salinas D, Yu J, Bodak M, Ngondo RP, Herbert KM, Ciaudo C. Noncanonical function of DGCR8 controls mESC exit from pluripotency. J Cell Biol 2017; 216:355-366. [PMID: 28100686 PMCID: PMC5294780 DOI: 10.1083/jcb.201606073] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/14/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022] Open
Abstract
DGCR8 is essential for mouse early development and microRNA biogenesis. Cirera-Salinas et al. report a new noncanonical function of DGCR8 essential for the exit from pluripotency of mouse embryonic stem cells. Mouse embryonic stem cells (mESCs) deficient for DGCR8, a key component of the microprocessor complex, present strong differentiation defects. However, the exact reasons impairing their commitment remain elusive. The analysis of newly generated mutant mESCs revealed that DGCR8 is essential for the exit from the pluripotency state. To dissociate canonical versus noncanonical functions of DGCR8, we complemented the mutant mESCs with a phosphomutant DGCR8, which restored microRNA levels but did not rescue the exit from pluripotency defect. Integration of omics data and RNA immunoprecipitation experiments established DGCR8 as a direct interactor of Tcf7l1 mRNA, a core component of the pluripotency network. Finally, we found that DGCR8 facilitated the splicing of Tcf7l1, an event necessary for the differentiation of mESCs. Our data reveal a new noncanonical function of DGCR8 in the modulation of the alternative splicing of Tcf7l1 mRNA in addition to its established function in microRNA biogenesis.
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Affiliation(s)
- Daniel Cirera-Salinas
- Department of Biology, Institute of Molecular Health Sciences, RNAi and Genome Integrity, Swiss Federal Institute of Technology Zurich, Zurich 8093, Switzerland
| | - Jian Yu
- Department of Biology, Institute of Molecular Health Sciences, RNAi and Genome Integrity, Swiss Federal Institute of Technology Zurich, Zurich 8093, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich 8093, Switzerland
| | - Maxime Bodak
- Department of Biology, Institute of Molecular Health Sciences, RNAi and Genome Integrity, Swiss Federal Institute of Technology Zurich, Zurich 8093, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich 8093, Switzerland
| | - Richard P Ngondo
- Department of Biology, Institute of Molecular Health Sciences, RNAi and Genome Integrity, Swiss Federal Institute of Technology Zurich, Zurich 8093, Switzerland
| | - Kristina M Herbert
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, San Diego, CA 92037
| | - Constance Ciaudo
- Department of Biology, Institute of Molecular Health Sciences, RNAi and Genome Integrity, Swiss Federal Institute of Technology Zurich, Zurich 8093, Switzerland
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49
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Sun HL, Cui R, Zhou J, Teng KY, Hsiao YH, Nakanishi K, Fassan M, Luo Z, Shi G, Tili E, Kutay H, Lovat F, Vicentini C, Huang HL, Wang SW, Kim T, Zanesi N, Jeon YJ, Lee TJ, Guh JH, Hung MC, Ghoshal K, Teng CM, Peng Y, Croce CM. ERK Activation Globally Downregulates miRNAs through Phosphorylating Exportin-5. Cancer Cell 2016; 30:723-736. [PMID: 27846390 PMCID: PMC5127275 DOI: 10.1016/j.ccell.2016.10.001] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 04/01/2016] [Accepted: 10/03/2016] [Indexed: 02/05/2023]
Abstract
MicroRNAs (miRNA) are mostly downregulated in cancer. However, the mechanism underlying this phenomenon and the precise consequence in tumorigenesis remain obscure. Here we show that ERK suppresses pre-miRNA export from the nucleus through phosphorylation of exportin-5 (XPO5) at T345/S416/S497. After phosphorylation by ERK, conformation of XPO5 is altered by prolyl isomerase Pin1, resulting in reduction of pre-miRNA loading. In liver cancer, the ERK-mediated XPO5 suppression reduces miR-122, increases microtubule dynamics, and results in tumor development and drug resistance. Analysis of clinical specimens further showed that XPO5 phosphorylation is associated with poor prognosis for liver cancer patients. Our study reveals a function of ERK in miRNA biogenesis and suggests that modulation of miRNA export has potential clinical implications.
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Affiliation(s)
- Hui-Lung Sun
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA; Pharmacological Institute, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ri Cui
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - JianKang Zhou
- Department of Thoracic Surgery, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Kun-Yu Teng
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA
| | - Yung-Hsuan Hsiao
- Department of Human Sciences, Human Nutrition Program, College of Education and Human Ecology, Ohio State University, Columbus, OH 43210, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Matteo Fassan
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA; ARC-NET Research Centre, University and Hospital Trust of Verona, Verona 37126, Italy
| | - Zhenghua Luo
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Guqin Shi
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Esmerina Tili
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA; Department of Anesthesiology, Ohio State University, Columbus, OH 43210, USA
| | - Huban Kutay
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA
| | - Francesca Lovat
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Caterina Vicentini
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona 37126, Italy
| | - Han-Li Huang
- The Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Shih-Wei Wang
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
| | - Taewan Kim
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicola Zanesi
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Young-Jun Jeon
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Tae Jin Lee
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Jih-Hwa Guh
- School of Pharmacy, National Taiwan University, Taipei 10051, Taiwan
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 40402, Taiwan; Department of Biotechnology, Asia University, Taichung 41354, Taiwan
| | - Kalpana Ghoshal
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA
| | - Che-Ming Teng
- Pharmacological Institute, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yong Peng
- Department of Thoracic Surgery, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, PR China.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA.
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Woldemichael BT, Jawaid A, Kremer EA, Gaur N, Krol J, Marchais A, Mansuy IM. The microRNA cluster miR-183/96/182 contributes to long-term memory in a protein phosphatase 1-dependent manner. Nat Commun 2016; 7:12594. [PMID: 27558292 PMCID: PMC5007330 DOI: 10.1038/ncomms12594] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/13/2016] [Indexed: 12/24/2022] Open
Abstract
Memory formation is a complex cognitive function regulated by coordinated synaptic and nuclear processes in neurons. In mammals, it is controlled by multiple molecular activators and suppressors, including the key signalling regulator, protein phosphatase 1 (PP1). Here, we show that memory control by PP1 involves the miR-183/96/182 cluster and its selective regulation during memory formation. Inhibiting nuclear PP1 in the mouse brain, or training on an object recognition task similarly increases miR-183/96/182 expression in the hippocampus. Mimicking this increase by miR-183/96/182 overexpression enhances object memory, while knocking-down endogenous miR-183/96/182 impairs it. This effect involves the modulation of several plasticity-related genes, with HDAC9 identified as an important functional target. Further, PP1 controls miR-183/96/182 in a transcription-independent manner through the processing of their precursors. These findings provide novel evidence for a role of miRNAs in memory formation and suggest the implication of PP1 in miRNAs processing in the adult brain.
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Affiliation(s)
- Bisrat T Woldemichael
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
| | - Ali Jawaid
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
| | - Eloïse A Kremer
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
| | - Niharika Gaur
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
| | - Jacek Krol
- Friedrich Miescher Institute for Biomedical Research, Basel CH-4048, Switzerland
| | - Antonin Marchais
- Institute of Agricultural Sciences, Swiss Federal Institute of Technology, Zurich CH-8092, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
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