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Prabhakar A, Hu S, Tang J, Ghatpande P, Lagna G, Jiang X, Hata A. Essential role of the amino-terminal region of Drosha for the Microprocessor function. iScience 2023; 26:107971. [PMID: 37810246 PMCID: PMC10558778 DOI: 10.1016/j.isci.2023.107971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 03/06/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
Drosha is a core component of the Microprocessor complex that cleaves primary-microRNAs (pri-miRNAs) to generate precursor-miRNA and regulates the expression of ∼80 ribosomal protein (RP) genes. Despite the fact that mutations in the amino-terminal region of Drosha (Drosha-NTR) are associated with a vascular disorder, hereditary hemorrhagic telangiectasia, the precise function of Drosha-NTR remains unclear. By deleting exon 5 from the Drosha gene and generating a Drosha mutant lacking the NTR (ΔN), we demonstrate that ΔN is unable to process pri-miRNAs, which leads to a global miRNA depletion, except for the miR-183/96/182 cluster. We find that Argonaute 2 facilitates the processing of the pri-miR-183/96/182 in ΔN cells. Unlike full-length Drosha, ΔN is not degraded under serum starvation, resulting in unregulated RP biogenesis and protein synthesis in ΔN cells, allowing them to evade growth arrest. This study reveals the essential role of Drosha-NTR in miRNA production and nutrient-dependent translational control.
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Affiliation(s)
- Amit Prabhakar
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Song Hu
- Molecular Cancer Research Center, Sun Yat-Sen University School of Medicine, Guangzhou 511400, P.R.China
| | - Jin Tang
- Molecular Cancer Research Center, Sun Yat-Sen University School of Medicine, Guangzhou 511400, P.R.China
| | - Prajakta Ghatpande
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Giorgio Lagna
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xuan Jiang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
- Molecular Cancer Research Center, Sun Yat-Sen University School of Medicine, Guangzhou 511400, P.R.China
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
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2
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Farhadieh ME, Ghaedi K. Analyzing alternative splicing in Alzheimer's disease postmortem brain: a cell-level perspective. Front Mol Neurosci 2023; 16:1237874. [PMID: 37799732 PMCID: PMC10548223 DOI: 10.3389/fnmol.2023.1237874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/01/2023] [Indexed: 10/07/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease with no effective cure that attacks the brain's cells resulting in memory loss and changes in behavior and language skills. Alternative splicing is a highly regulated process influenced by specific cell types and has been implicated in age-related disorders such as neurodegenerative diseases. A comprehensive detection of alternative splicing events (ASEs) at the cellular level in postmortem brain tissue can provide valuable insights into AD pathology. Here, we provided cell-level ASEs in postmortem brain tissue by employing bioinformatics pipelines on a bulk RNA sequencing study sorted by cell types and two single-cell RNA sequencing studies from the prefrontal cortex. This comprehensive analysis revealed previously overlooked splicing and expression changes in AD patient brains. Among the observed alterations were changed in the splicing and expression of transcripts associated with chaperones, including CLU in astrocytes and excitatory neurons, PTGDS in astrocytes and endothelial cells, and HSP90AA1 in microglia and tauopathy-afflicted neurons, which were associated with differential expression of the splicing factor DDX5. In addition, novel, unknown transcripts were altered, and structural changes were observed in lncRNAs such as MEG3 in neurons. This work provides a novel strategy to identify the notable ASEs at the cell level in neurodegeneration, which revealed cell type-specific splicing changes in AD. This finding may contribute to interpreting associations between splicing and neurodegenerative disease outcomes.
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Affiliation(s)
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
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3
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Son S, Kim B, Yang J, Kim VN. Role of the proline-rich disordered domain of DROSHA in intronic microRNA processing. Genes Dev 2023; 37:383-397. [PMID: 37236670 PMCID: PMC10270192 DOI: 10.1101/gad.350275.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/24/2023] [Indexed: 05/28/2023]
Abstract
DROSHA serves as a gatekeeper of the microRNA (miRNA) pathway by processing primary transcripts (pri-miRNAs). While the functions of structured domains of DROSHA have been well documented, the contribution of N-terminal proline-rich disordered domain (PRD) remains elusive. Here we show that the PRD promotes the processing of miRNA hairpins located within introns. We identified a DROSHA isoform (p140) lacking the PRD, which is produced by proteolytic cleavage. Small RNA sequencing revealed that p140 is significantly impaired in the maturation of intronic miRNAs. Consistently, our minigene constructs demonstrated that PRD enhances the processing of intronic hairpins, but not those in exons. Splice site mutations did not affect the PRD's enhancing effect on intronic constructs, suggesting that the PRD acts independently of splicing reaction by interacting with sequences residing within introns. The N-terminal regions from zebrafish and Xenopus DROSHA can replace the human counterpart, indicating functional conservation despite poor sequence alignment. Moreover, we found that rapidly evolving intronic miRNAs are generally more dependent on PRD than conserved ones, suggesting a role of PRD in miRNA evolution. Our study reveals a new layer of miRNA regulation mediated by a low-complexity disordered domain that senses the genomic contexts of miRNA loci.
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Affiliation(s)
- Soomin Son
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Baekgyu Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea;
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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4
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Xu H, Liu X, Li W, Xi Y, Su P, Meng B, Shao X, Tang B, Yang Q, Mao Z. p38 MAPK-mediated loss of nuclear RNase III enzyme Drosha underlies amyloid beta-induced neuronal stress in Alzheimer's disease. Aging Cell 2021; 20:e13434. [PMID: 34528746 PMCID: PMC8521488 DOI: 10.1111/acel.13434] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/26/2021] [Accepted: 07/03/2021] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs ubiquitously expressed in the brain and regulate gene expression at the post‐transcriptional level. The nuclear RNase III enzyme Drosha initiates the maturation process of miRNAs in the nucleus. Strong evidence suggests that dysregulation of miRNAs is involved in many neurological disorders including Alzheimer's disease (AD). Dysfunction of miRNA biogenesis components may be involved in the processes of those diseases. However, the role of Drosha in AD remains unknown. By using immunohistochemistry, biochemistry, and subcellular fractionation methods, we show here that the level of Drosha protein was significantly lower in the postmortem brain of human AD patients as well as in the transgenic rat model of AD. Interestingly, Drosha level was specifically reduced in neurons of the cortex and hippocampus but not in the cerebellum in the AD brain samples. In primary cortical neurons, amyloid‐beta (Aβ) oligomers caused a p38 MAPK‐dependent phosphorylation of Drosha, leading to its redistribution from the nucleus to the cytoplasm and a decrease in its level. This loss of Drosha function preceded Aβ‐induced neuronal death. Importantly, inhibition of p38 MAPK activity or overexpression of Drosha protected neurons from Aβ oligomers‐induced apoptosis. Taken together, these results establish a role for p38 MAPK‐Drosha pathway in modulating neuronal viability under Aβ oligomers stress condition and implicate loss of Drosha as a key molecular change in the pathogenesis of AD.
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Affiliation(s)
- Haidong Xu
- Department of Pharmacology and Chemical Biology Emory University School of Medicine Atlanta Georgia USA
| | - Xiaolei Liu
- Department of Pharmacology and Chemical Biology Emory University School of Medicine Atlanta Georgia USA
| | - Wenming Li
- Department of Pharmacology and Chemical Biology Emory University School of Medicine Atlanta Georgia USA
| | - Ye Xi
- Department of Pharmacology and Chemical Biology Emory University School of Medicine Atlanta Georgia USA
| | - Peng Su
- Department of Pharmacology and Chemical Biology Emory University School of Medicine Atlanta Georgia USA
| | - Bo Meng
- Department of Pharmacology and Chemical Biology Emory University School of Medicine Atlanta Georgia USA
| | - Xiaoyun Shao
- Department of Pharmacology and Chemical Biology Emory University School of Medicine Atlanta Georgia USA
| | - Beisha Tang
- Department of Neurology Xiangya Hospital Central South University Changsha China
| | - Qian Yang
- Department of Neurosurgery Tangdu Hospital The Fourth Military Medical University Xi'an China
| | - Zixu Mao
- Department of Pharmacology and Chemical Biology Emory University School of Medicine Atlanta Georgia USA
- Department of Neurology Emory University School of Medicine Atlanta Georgia USA
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5
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Nguyen LXT, Zhang B, Hoang DH, Zhao D, Wang H, Wu H, Su YL, Dong H, Rodriguez-Rodriguez S, Armstrong B, Ghoda LY, Perrotti D, Pichiorri F, Chen J, Li L, Kortylewski M, Rockne RC, Kuo YH, Khaled S, Carlesso N, Marcucci G. Cytoplasmic DROSHA and non-canonical mechanisms of MiR-155 biogenesis in FLT3-ITD acute myeloid leukemia. Leukemia 2021; 35:2285-2298. [PMID: 33589748 PMCID: PMC8973317 DOI: 10.1038/s41375-021-01166-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 01/29/2023]
Abstract
We report here on a novel pro-leukemogenic role of FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) that interferes with microRNAs (miRNAs) biogenesis in acute myeloid leukemia (AML) blasts. We showed that FLT3-ITD interferes with the canonical biogenesis of intron-hosted miRNAs such as miR-126, by phosphorylating SPRED1 protein and inhibiting the "gatekeeper" Exportin 5 (XPO5)/RAN-GTP complex that regulates the nucleus-to-cytoplasm transport of pre-miRNAs for completion of maturation into mature miRNAs. Of note, despite the blockage of "canonical" miRNA biogenesis, miR-155 remains upregulated in FLT3-ITD+ AML blasts, suggesting activation of alternative mechanisms of miRNA biogenesis that circumvent the XPO5/RAN-GTP blockage. MiR-155, a BIC-155 long noncoding (lnc) RNA-hosted oncogenic miRNA, has previously been implicated in FLT3-ITD+ AML blast hyperproliferation. We showed that FLT3-ITD upregulates miR-155 by inhibiting DDX3X, a protein implicated in the splicing of lncRNAs, via p-AKT. Inhibition of DDX3X increases unspliced BIC-155 that is then shuttled by NXF1 from the nucleus to the cytoplasm, where it is processed into mature miR-155 by cytoplasmic DROSHA, thereby bypassing the XPO5/RAN-GTP blockage via "non-canonical" mechanisms of miRNA biogenesis.
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Affiliation(s)
- Le Xuan Truong Nguyen
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA.
| | - Bin Zhang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Dinh Hoa Hoang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Dandan Zhao
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Huafeng Wang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Herman Wu
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Yu-Lin Su
- Department of Immuno-Oncology, City of Hope Medical Center, Duarte, CA, USA
| | - Haojie Dong
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Sonia Rodriguez-Rodriguez
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Brian Armstrong
- Light Microscopy Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Lucy Y Ghoda
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Danilo Perrotti
- Department of Medicine, Biochemistry and Molecular Biology and the Marlene and Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Flavia Pichiorri
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Jianjun Chen
- Department of System Biology, City of Hope Medical Center, Duarte, CA, USA
| | - Ling Li
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Marcin Kortylewski
- Department of Immuno-Oncology, City of Hope Medical Center, Duarte, CA, USA
| | - Russell C Rockne
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Ya-Huei Kuo
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Samer Khaled
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Nadia Carlesso
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Guido Marcucci
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, CA, USA.
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6
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Jiang X, Prabhakar A, Van der Voorn SM, Ghatpande P, Celona B, Venkataramanan S, Calviello L, Lin C, Wang W, Black BL, Floor SN, Lagna G, Hata A. Control of ribosomal protein synthesis by the Microprocessor complex. Sci Signal 2021; 14:14/671/eabd2639. [PMID: 33622983 DOI: 10.1126/scisignal.abd2639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribosome biogenesis in eukaryotes requires the coordinated production and assembly of 80 ribosomal proteins and four ribosomal RNAs (rRNAs), and its rate must be synchronized with cellular growth. Here, we showed that the Microprocessor complex, which mediates the first step of microRNA processing, potentiated the transcription of ribosomal protein genes by eliminating DNA/RNA hybrids known as R-loops. Nutrient deprivation triggered the nuclear export of Drosha, a key component of the Microprocessor complex, and its subsequent degradation by the E3 ubiquitin ligase Nedd4, thereby reducing ribosomal protein production and protein synthesis. In mouse erythroid progenitors, conditional deletion of Drosha led to the reduced production of ribosomal proteins, translational inhibition of the mRNA encoding the erythroid transcription factor Gata1, and impaired erythropoiesis. This phenotype mirrored the clinical presentation of human "ribosomopathies." Thus, the Microprocessor complex plays a pivotal role in synchronizing protein synthesis capacity with cellular growth rate and is a potential drug target for anemias caused by ribosomal insufficiency.
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Affiliation(s)
- Xuan Jiang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amit Prabhakar
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie M Van der Voorn
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medical Physiology, University Medical Center Utrecht, Utrecht, 3584 CM, Netherlands
| | - Prajakta Ghatpande
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Barbara Celona
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Srivats Venkataramanan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chuwen Lin
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wanpeng Wang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Giorgio Lagna
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA. .,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
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7
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Dai L, Hallmark L, Bofill De Ros X, Crouch H, Chen S, Shi T, Yang A, Lian C, Zhao Y, Tran B, Gu S. Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells. RNA Biol 2020; 17:1603-1612. [PMID: 32819190 DOI: 10.1080/15476286.2020.1813439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs about 22-nucleotide (nt) in length that collectively regulate more than 60% of coding genes. Aberrant miRNA expression is associated with numerous diseases, including cancer. miRNA biogenesis is licenced by the ribonuclease (RNase) III enzyme Drosha, the regulation of which is critical in determining miRNA levels. We and others have previously revealed that alternative splicing regulates the subcellular localization of Drosha. To further investigate the alternative splicing landscape of Drosha transcripts, we performed PacBio sequencing in different human cell lines. We identified two novel isoforms resulting from partial intron-retention in the region encoding the Drosha catalytic domain. One isoform (AS27a) generates a truncated protein that is unstable in cells. The other (AS32a) produces a full-length Drosha with a 14 amino acid insertion in the RIIID domain. By taking advantage of Drosha knockout cells in combination with a previously established reporter assay, we demonstrated that Drosha-AS32a lacks cleavage activity. Furthermore, neither Drosha-27a nor Drosha-32a were able to rescue miRNA expression in the Drosha knockout cells. Interestingly, both isoforms were abundantly detected in a wide range of cancer cell lines (up to 15% of all Drosha isoforms). Analysis of the RNA-seq data from over 1000 breast cancer patient samples revealed that the AS32a is relatively more abundant in tumours than in normal tissue, suggesting that AS32a may play a role in cancer development.
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Affiliation(s)
- Lisheng Dai
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health , Frederick, MD, USA
| | - Lillian Hallmark
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health , Frederick, MD, USA
| | - Xavier Bofill De Ros
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health , Frederick, MD, USA
| | - Howard Crouch
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health , Frederick, MD, USA
| | - Sean Chen
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health , Frederick, MD, USA
| | - Tony Shi
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health , Frederick, MD, USA
| | - Acong Yang
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health , Frederick, MD, USA
| | - Chuanjiang Lian
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health , Frederick, MD, USA
| | - Yongmei Zhao
- NCI CCR Sequencing Facility, Frederick National Laboratory for Cancer Research , Frederick, MD, USA.,Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer , Frederick, MD, USA
| | - Bao Tran
- NCI CCR Sequencing Facility, Frederick National Laboratory for Cancer Research , Frederick, MD, USA
| | - Shuo Gu
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health , Frederick, MD, USA
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8
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Wang H. MicroRNAs and Apoptosis in Colorectal Cancer. Int J Mol Sci 2020; 21:ijms21155353. [PMID: 32731413 PMCID: PMC7432330 DOI: 10.3390/ijms21155353] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third leading cause of cancer death in the world, and its incidence is rising in developing countries. Treatment with 5-Fluorouracil (5-FU) is known to improve survival in CRC patients. Most anti-cancer therapies trigger apoptosis induction to eliminate malignant cells. However, de-regulated apoptotic signaling allows cancer cells to escape this signaling, leading to therapeutic resistance. Treatment resistance is a major challenge in the development of effective therapies. The microRNAs (miRNAs) play important roles in CRC treatment resistance and CRC progression and apoptosis. This review discusses the role of miRNAs in contributing to the promotion or inhibition of apoptosis in CRC and the role of miRNAs in modulating treatment resistance in CRC cells.
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Affiliation(s)
- Hsiuying Wang
- Institute of Statistics, National Chiao Tung University, Hsinchu 30010, Taiwan
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9
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Barrozo ER, Nakayama S, Singh P, Vanni EAH, Arvin AM, Neumann DM, Bloom DC. Deletion of Herpes Simplex Virus 1 MicroRNAs miR-H1 and miR-H6 Impairs Reactivation. J Virol 2020; 94:e00639-20. [PMID: 32295910 PMCID: PMC7375377 DOI: 10.1128/jvi.00639-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 12/13/2022] Open
Abstract
During all stages of infection, herpes simplex virus 1 (HSV-1) expresses viral microRNAs (miRNAs). There are at least 20 confirmed HSV-1 miRNAs, yet the roles of individual miRNAs in the context of viral infection remain largely uncharacterized. We constructed a recombinant virus lacking the sequences for miR-H1-5p and miR-H6-3p (17dmiR-H1/H6). The seed sequences for these miRNAs are antisense to each other and are transcribed from divergent noncoding RNAs in the latency-associated transcript (LAT) promoter region. Comparing phenotypes exhibited by the recombinant virus lacking these miRNAs to the wild type (17syn+), we found that during acute infection in cell culture, 17dmiR-H1/H6 exhibited a modest increase in viral yields. Analysis of pathogenesis in the mouse following footpad infection revealed a slight increase in virulence for 17dmiR-H1/H6 but no significant difference in the establishment or maintenance of latency. Strikingly, explant of latently infected dorsal root ganglia revealed a decreased and delayed reactivation phenotype. Further, 17dmiR-H1/H6 was severely impaired in epinephrine-induced reactivation in the rabbit ocular model. Finally, we demonstrated that deletion of miR-H1/H6 increased the accumulation of the LAT as well as several of the LAT region miRNAs. These results suggest that miR-H1/H6 plays an important role in facilitating efficient reactivation from latency.IMPORTANCE While HSV antivirals reduce the severity and duration of clinical disease in some individuals, there is no vaccine or cure. Therefore, understanding the mechanisms regulating latency and reactivation as a potential to elucidate targets for better therapeutics is important. There are at least 20 confirmed HSV-1 miRNAs, yet the roles of individual miRNAs in the context of viral infection remain largely uncharacterized. The present study focuses on two of the miRNAs (miR-H1/H6) that are encoded within the latency-associated transcript (LAT) region, a portion of the genome that has been associated with efficient reactivation. Here, we demonstrate that the deletion of the seed sequences of these miRNAs results in a severe reduction in reactivation of HSV-1 in the mouse and rabbit models. These results suggest a linkage between these miRNAs and reactivation.
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Affiliation(s)
- Enrico R Barrozo
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Sanae Nakayama
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Pankaj Singh
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emilia A H Vanni
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Ann M Arvin
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Donna M Neumann
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David C Bloom
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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10
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Coordinated AR and microRNA regulation in prostate cancer. Asian J Urol 2020; 7:233-250. [PMID: 32742925 PMCID: PMC7385519 DOI: 10.1016/j.ajur.2020.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 03/22/2020] [Accepted: 04/17/2020] [Indexed: 12/26/2022] Open
Abstract
The androgen receptor (AR) remains a key driver of prostate cancer (PCa) progression, even in the advanced castrate-resistant stage, where testicular androgens are absent. It is therefore of critical importance to understand the molecular mechanisms governing its activity and regulation during prostate tumourigenesis. MicroRNAs (miRs) are small ∼22 nt non-coding RNAs that regulate target gene, often through association with 3′ untranslated regions (3′UTRs) of transcripts. They display dysregulation during cancer progression, can function as oncogenes or tumour suppressors, and are increasingly recognised as targets or regulators of hormonal action. Thus, understanding factors which modulate miRs synthesis is essential. There is increasing evidence for complex and dynamic bi-directional cross-talk between the multi-step miR biogenesis cascade and the AR signalling axis in PCa. This review summarises the wealth of mechanisms by which miRs are regulated by AR, and conversely, how miRs impact AR's transcriptional activity, including that of AR splice variants. In addition, we assess the implications of the convergence of these pathways on the clinical employment of miRs as PCa biomarkers and therapeutic targets.
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11
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Yu P, Li J, Deng SP, Zhang F, Grozdanov PN, Chin EWM, Martin SD, Vergnes L, Islam MS, Sun D, LaSalle JM, McGee SL, Goh E, MacDonald CC, Jin P. Integrated analysis of a compendium of RNA-Seq datasets for splicing factors. Sci Data 2020; 7:178. [PMID: 32546682 PMCID: PMC7297722 DOI: 10.1038/s41597-020-0514-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/13/2020] [Indexed: 02/05/2023] Open
Abstract
A vast amount of public RNA-sequencing datasets have been generated and used widely to study transcriptome mechanisms. These data offer precious opportunity for advancing biological research in transcriptome studies such as alternative splicing. We report the first large-scale integrated analysis of RNA-Seq data of splicing factors for systematically identifying key factors in diseases and biological processes. We analyzed 1,321 RNA-Seq libraries of various mouse tissues and cell lines, comprising more than 6.6 TB sequences from 75 independent studies that experimentally manipulated 56 splicing factors. Using these data, RNA splicing signatures and gene expression signatures were computed, and signature comparison analysis identified a list of key splicing factors in Rett syndrome and cold-induced thermogenesis. We show that cold-induced RNA-binding proteins rescue the neurite outgrowth defects in Rett syndrome using neuronal morphology analysis, and we also reveal that SRSF1 and PTBP1 are required for energy expenditure in adipocytes using metabolic flux analysis. Our study provides an integrated analysis for identifying key factors in diseases and biological processes and highlights the importance of public data resources for identifying hypotheses for experimental testing.
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Affiliation(s)
- Peng Yu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China.
- Medical Big Data Center, Sichuan University, Chengdu, China.
| | - Jin Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Su-Ping Deng
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu, 215009, China
| | - Feiran Zhang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Petar N Grozdanov
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, 79430, USA
| | - Eunice W M Chin
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, NA, Singapore
| | - Sheree D Martin
- Metabolic Reprogramming Laboratory, Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
| | - Laurent Vergnes
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - M Saharul Islam
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Deqiang Sun
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Sean L McGee
- Metabolic Reprogramming Laboratory, Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, Australia
| | - Eyleen Goh
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, NA, Singapore
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, 79430, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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12
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Fang W, Bartel DP. MicroRNA Clustering Assists Processing of Suboptimal MicroRNA Hairpins through the Action of the ERH Protein. Mol Cell 2020; 78:289-302.e6. [PMID: 32302541 PMCID: PMC7243034 DOI: 10.1016/j.molcel.2020.01.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/02/2020] [Accepted: 01/27/2020] [Indexed: 02/07/2023]
Abstract
Microprocessor initiates the processing of microRNAs (miRNAs) from the hairpin regions of primary transcripts (pri-miRNAs). Pri-miRNAs often contain multiple miRNA hairpins, and this clustered arrangement can assist in the processing of otherwise defective hairpins. We find that miR-451, which derives from a hairpin with a suboptimal terminal loop and a suboptimal stem length, accumulates to 40-fold higher levels when clustered with a helper hairpin. This phenomenon tolerates changes in hairpin order, linker lengths, and the identities of the helper hairpin, the recipient hairpin, the linker-sequence, and the RNA polymerase that transcribes the hairpins. It can act reciprocally and need not occur co-transcriptionally. It requires Microprocessor recognition of the helper hairpin and linkage of the two hairpins, yet predominantly manifests after helper-hairpin processing. It also requires enhancer of rudimentary homolog (ERH), which copurifies with Microprocessor and can dimerize and interact with other proteins that can dimerize, suggesting a model in which one Microprocessor recruits another Microprocessor.
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Affiliation(s)
- Wenwen Fang
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute of Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute of Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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13
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Nair-Menon J, Daulagala AC, Connor DM, Rutledge L, Penix T, Bridges MC, Wellslager B, Spyropoulos DD, Timmers CD, Broome AM, Kourtidis A. Predominant Distribution of the RNAi Machinery at Apical Adherens Junctions in Colonic Epithelia Is Disrupted in Cancer. Int J Mol Sci 2020; 21:E2559. [PMID: 32272708 PMCID: PMC7177752 DOI: 10.3390/ijms21072559] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 12/30/2022] Open
Abstract
The RNA interference (RNAi) machinery is an essential component of the cell, regulating miRNA biogenesis and function. RNAi complexes were thought to localize either in the nucleus, such as the microprocessor, or in the cytoplasm, such as the RNA-induced silencing complex (RISC). We recently revealed that the core microprocessor components DROSHA and DGCR8, as well as the main components of RISC, including Ago2, also associate with the apical adherens junctions of well-differentiated cultured epithelial cells. Here, we demonstrate that the localization of the core RNAi components is specific and predominant at apical areas of cell-cell contact of human normal colon epithelial tissues and normal primary colon epithelial cells. Importantly, the apical junctional localization of RNAi proteins is disrupted or lost in human colon tumors and in poorly differentiated colon cancer cell lines, correlating with the dysregulation of the adherens junction component PLEKHA7. We show that the restoration of PLEKHA7 expression at adherens junctions of aggressively tumorigenic colon cancer cells restores the junctional localization of RNAi components and suppresses cancer cell growth in vitro and in vivo. In summary, this work identifies the apical junctional localization of the RNAi machinery as a key feature of the differentiated colonic epithelium, with a putative tumor suppressing function.
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Affiliation(s)
- Joyce Nair-Menon
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (J.N.-M.); (A.C.D.); (L.R.); (T.P.); (M.C.B.); (B.W.)
| | - Amanda C. Daulagala
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (J.N.-M.); (A.C.D.); (L.R.); (T.P.); (M.C.B.); (B.W.)
| | - Dean M. Connor
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (D.M.C.); (A.-M.B.)
| | - Lauren Rutledge
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (J.N.-M.); (A.C.D.); (L.R.); (T.P.); (M.C.B.); (B.W.)
| | - Trevor Penix
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (J.N.-M.); (A.C.D.); (L.R.); (T.P.); (M.C.B.); (B.W.)
| | - Mary Catherine Bridges
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (J.N.-M.); (A.C.D.); (L.R.); (T.P.); (M.C.B.); (B.W.)
| | - Bridgette Wellslager
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (J.N.-M.); (A.C.D.); (L.R.); (T.P.); (M.C.B.); (B.W.)
| | - Demetri D. Spyropoulos
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA;
| | - Cynthia D. Timmers
- Department of Medicine, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC 29425, USA;
| | - Ann-Marie Broome
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (D.M.C.); (A.-M.B.)
| | - Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (J.N.-M.); (A.C.D.); (L.R.); (T.P.); (M.C.B.); (B.W.)
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14
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DROSHA-Dependent miRNA and AIM2 Inflammasome Activation in Idiopathic Pulmonary Fibrosis. Int J Mol Sci 2020; 21:ijms21051668. [PMID: 32121297 PMCID: PMC7084700 DOI: 10.3390/ijms21051668] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/23/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive interstitial lung disease. Chronic lung inflammation is linked to the pathogenesis of IPF. DROSHA, a class 2 ribonuclease III enzyme, has an important role in the biogenesis of microRNA (miRNA). The function of miRNAs has been identified in the regulation of the target gene or protein related to inflammatory responses via degradation of mRNA or inhibition of translation. The absent-in-melanoma-2 (AIM2) inflammasome is critical for inflammatory responses against cytosolic double stranded DNA (dsDNA) from pathogen-associated molecular patterns (PAMPs) and self-DNA from danger-associated molecular patterns (DAMPs). The AIM2 inflammasome senses double strand DNA (dsDNA) and interacts with the adaptor apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), which recruits pro-caspase-1 and regulates the maturation and secretion of interleukin (IL)-1β and IL-18. A recent study showed that inflammasome activation contributes to lung inflammation and fibrogenesis during IPF. In the current review, we discuss recent advances in our understanding of the DROSHA-miRNA-AIM2 inflammasome axis in the pathogenesis of IPF.
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15
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Ebola Virus Produces Discrete Small Noncoding RNAs Independently of the Host MicroRNA Pathway Which Lack RNA Interference Activity in Bat and Human Cells. J Virol 2020; 94:JVI.01441-19. [PMID: 31852785 DOI: 10.1128/jvi.01441-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
The question as to whether RNA viruses produce bona fide microRNAs (miRNAs) during infection has been the focus of intense research and debate. Recently, several groups using computational prediction methods have independently reported possible miRNA candidates produced by Ebola virus (EBOV). Additionally, efforts to detect these predicted RNA products in samples from infected animals and humans have produced positive results. However, these studies and their conclusions are predicated on the assumption that these RNA products are actually processed through, and function within, the miRNA pathway. In the present study, we performed the first rigorous assessment of the ability of filoviruses to produce miRNA products during infection of both human and bat cells. Using next-generation sequencing, we detected several candidate miRNAs from both EBOV and the closely related Marburg virus (MARV). Focusing our validation efforts on EBOV, we found evidence contrary to the idea that these small RNA products function as miRNAs. The results of our study are important because they highlight the potential pitfalls of relying on computational methods alone for virus miRNA discovery.IMPORTANCE Here, we report the discovery, via deep sequencing, of numerous noncoding RNAs (ncRNAs) derived from both EBOV and MARV during infection of both bat and human cell lines. In addition to identifying several novel ncRNAs from both viruses, we identified two EBOV ncRNAs in our sequencing data that were near-matches to computationally predicted viral miRNAs reported in the literature. Using molecular and immunological techniques, we assessed the potential of EBOV ncRNAs to function as viral miRNAs. Importantly, we found little evidence supporting this hypothesis. Our work is significant because it represents the first rigorous assessment of the potential for EBOV to encode viral miRNAs and provides evidence contrary to the existing paradigm regarding the biological role of computationally predicted EBOV ncRNAs. Moreover, our work highlights further avenues of research regarding the nature and function of EBOV ncRNAs.
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16
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Sano M, Nakasu A, Ohtaka M, Nakanishi M. A Sendai Virus-Based Cytoplasmic RNA Vector as a Novel Platform for Long-Term Expression of MicroRNAs. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 15:371-382. [PMID: 31828179 PMCID: PMC6889074 DOI: 10.1016/j.omtm.2019.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/24/2019] [Indexed: 12/28/2022]
Abstract
Cytoplasmic RNA virus-derived vectors have emerged as attractive vehicles for microRNA (miRNA) delivery as they possess no potential risk of chromosomal insertion. However, their relatively short-term expression limits their use in biological applications that require long-term miRNA manipulation, such as somatic cell reprogramming. Here, we show that a cytoplasmic RNA virus vector based on a replication-defective and persistent Sendai virus (SeVdp) serves as an effective platform for long-term production of miRNAs capable of inducing sequence-specific target suppression. The SeVdp vector was able to simultaneously deliver embryonic stem cell-enriched miRNAs, as well as multiple transcription factors, into fibroblasts, resulting in effective reprogramming into induced pluripotent stem cells. Furthermore, we report that the murine miR-367 hairpin produced elevated levels of mature miRNA when it was incorporated into the SeVdp vector and served as an effective backbone for production of artificial miRNAs. These SeVdp vector-derived artificial miRNAs efficiently inhibited expression of target genes. Our findings provide novel insights into a powerful tool for long-term and targeted gene silencing in areas such as regenerative medicine, gene therapy, and cell therapy.
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Affiliation(s)
- Masayuki Sano
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Asako Nakasu
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Manami Ohtaka
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Mahito Nakanishi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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17
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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: 35] [Impact Index Per Article: 7.0] [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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18
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Ogórek B, Lam HC, Khabibullin D, Liu HJ, Nijmeh J, Triboulet R, Kwiatkowski DJ, Gregory RI, Henske EP. TSC2 regulates microRNA biogenesis via mTORC1 and GSK3β. Hum Mol Genet 2019; 27:1654-1663. [PMID: 29509898 DOI: 10.1093/hmg/ddy073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/26/2018] [Indexed: 12/21/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is an autosomal dominant disease caused by germline inactivating mutations of TSC1 or TSC2. In TSC-associated tumors of the brain, heart, skin, kidney and lung, inactivation of both alleles of TSC1 or TSC2 leads to hyperactivation of the mTORC1 pathway. The TSC/mTORC1 pathway is a key regulator of cellular processes related to growth, proliferation and autophagy. We and others have previously found that mTORC1 regulates microRNA biogenesis, but the mechanisms are not fully understood. Microprocessor, a multi-protein complex including the nuclease Drosha, processes the primary miR transcript. Using a dual-luciferase reporter, we found that inhibition of mTORC1 or downregulation of Raptor decreased Microprocessor activity, while loss of TSC2 led to a striking increase (∼5-fold) in Microprocessor activity. To determine the global impact of TSC2 on microRNAs we quantitatively analyzed 752 microRNAs in Tsc2-expressing and Tsc2-deficient cells. Out of 259 microRNAs expressed in both cell lines, 137 were significantly upregulated and 24 were significantly downregulated in Tsc2-deficient cells, consistent with the increased Microprocessor activity. Microprocessor activity is known to be regulated in part by GSK3β. We found that total GSK3β levels were higher in Tsc2-deficient cells, and the increase in Microprocessor activity associated with Tsc2 loss was reversed by three different GSK3β inhibitors. Furthermore, mTOR inhibition increased the levels of phospho-GSK3β (S9), which negatively affects Microprocessor activity. Taken together these data reveal that TSC2 regulates microRNA biogenesis and Microprocessor activity via GSK3β.
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Affiliation(s)
- Barbara Ogórek
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hilaire C Lam
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Damir Khabibullin
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heng-Jia Liu
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Julie Nijmeh
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Robinson Triboulet
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - David J Kwiatkowski
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth P Henske
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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19
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Bofill-De Ros X, Kasprzak WK, Bhandari Y, Fan L, Cavanaugh Q, Jiang M, Dai L, Yang A, Shao TJ, Shapiro BA, Wang YX, Gu S. Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires. Cell Rep 2019; 26:447-459.e4. [PMID: 30625327 PMCID: PMC6369706 DOI: 10.1016/j.celrep.2018.12.054] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/11/2018] [Accepted: 12/11/2018] [Indexed: 12/16/2022] Open
Abstract
MicroRNA (miRNA) processing begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the maturation of three pri-miR-9 paralogs, which encode the same mature miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its distorted and flexible stem structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Analyses of low-grade glioma patient samples indicate that the alternative-miR-9 has a potential role in tumor progression. Furthermore, we provide evidence that distortion of pri-miRNA stems induced by asymmetric internal loops correlates with Drosha cleavage at non-canonical sites. Our studies reveal that pri-miRNA paralogs can have distinct functions via differential Drosha processing.
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Affiliation(s)
- Xavier Bofill-De Ros
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Wojciech K Kasprzak
- Basic Science Program, RNA Biology Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Yuba Bhandari
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Lixin Fan
- Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Quinn Cavanaugh
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Minjie Jiang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisheng Dai
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Acong Yang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Tie-Juan Shao
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Bruce A Shapiro
- RNA Structure and Design Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Shuo Gu
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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20
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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: 2.2] [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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21
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Li J, Deng SP, Vieira J, Thomas J, Costa V, Tseng CS, Ivankovic F, Ciccodicola A, Yu P. RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5040291. [PMID: 29931156 PMCID: PMC6009576 DOI: 10.1093/database/bay054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/17/2018] [Indexed: 01/03/2023]
Abstract
RNA-binding proteins (RBPs) may play a critical role in gene regulation in various diseases or biological processes by controlling post-transcriptional events such as polyadenylation, splicing and mRNA stabilization via binding activities to RNA molecules. Owing to the importance of RBPs in gene regulation, a great number of studies have been conducted, resulting in a large amount of RNA-Seq datasets. However, these datasets usually do not have structured organization of metadata, which limits their potentially wide use. To bridge this gap, the metadata of a comprehensive set of publicly available mouse RNA-Seq datasets with perturbed RBPs were collected and integrated into a database called RBPMetaDB. This database contains 292 mouse RNA-Seq datasets for a comprehensive list of 187 RBPs. These RBPs account for only ∼10% of all known RBPs annotated in Gene Ontology, indicating that most are still unexplored using high-throughput sequencing. This negative information provides a great pool of candidate RBPs for biologists to conduct future experimental studies. In addition, we found that DNA-binding activities are significantly enriched among RBPs in RBPMetaDB, suggesting that prior studies of these DNA- and RNA-binding factors focus more on DNA-binding activities instead of RNA-binding activities. This result reveals the opportunity to efficiently reuse these data for investigation of the roles of their RNA-binding activities. A web application has also been implemented to enable easy access and wide use of RBPMetaDB. It is expected that RBPMetaDB will be a great resource for improving understanding of the biological roles of RBPs. Database URL: http://rbpmetadb.yubiolab.org
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Affiliation(s)
- Jin Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Su-Ping Deng
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Jacob Vieira
- The Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - James Thomas
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Valerio Costa
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy
| | - Ching-San Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Franjo Ivankovic
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Alfredo Ciccodicola
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy.,Department of Science and Technology, University Parthenope of Naples, 80131 Naples, Italy
| | - Peng Yu
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
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22
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Davis-Vogel C, Van Allen B, Van Hemert JL, Sethi A, Nelson ME, Sashital DG. Identification and comparison of key RNA interference machinery from western corn rootworm, fall armyworm, and southern green stink bug. PLoS One 2018; 13:e0203160. [PMID: 30183751 PMCID: PMC6124762 DOI: 10.1371/journal.pone.0203160] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/15/2018] [Indexed: 12/18/2022] Open
Abstract
RNA interference (RNAi)-based technology shows great potential for use in agriculture, particularly for management of costly insect pests. In the decade since the insecticidal effects of environmentally-introduced RNA were first reported, this treatment has been applied to several types of insect pests. Through the course of those efforts, it has become apparent that different insects exhibit a range of sensitivity to environmentally-introduced RNAs. The variation in responses across insect is not well-understood, with differences in the underlying RNAi mechanisms being one explanation. This study evaluates eight proteins among three agricultural pests whose responses to environmental RNAi are known to differ: western corn rootworm (Diabrotica virgifera virgifera), fall armyworm (Spodoptera frugiperda), and southern green stink bug (Nezara viridula). These proteins have been identified in various organisms as centrally involved in facilitating the microRNA- and small interfering-RNA-mediated interference responses. Various bioinformatics tools, as well as gene expression profiling, were used to identify and evaluate putative homologues for characteristics that may contribute to the differing responses of these insects, such as the absence of critical functional domains within expressed sequences, the absence of entire gene sequences, or unusually low or undetectable expression of critical genes. Though many similarities were observed, the number of isoforms and expression levels of double-stranded RNA-binding and argonaute proteins varied across insect. Differences among key RNAi machinery genes of these three pests may impact the function of their RNAi pathways, and therefore, their respective responses to exogenous RNAs.
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Affiliation(s)
- Courtney Davis-Vogel
- Research and Development, DuPont Pioneer, Johnston, Iowa, United States of America
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Brandon Van Allen
- Research and Development, DuPont Pioneer, Johnston, Iowa, United States of America
| | - John L. Van Hemert
- Research and Development, DuPont Pioneer, Johnston, Iowa, United States of America
| | - Amit Sethi
- Research and Development, DuPont Pioneer, Johnston, Iowa, United States of America
| | - Mark E. Nelson
- Research and Development, DuPont Pioneer, Johnston, Iowa, United States of America
| | - Dipali G. Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
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23
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Monedero Cobeta I, Stadler CB, Li J, Yu P, Thor S, Benito-Sipos J. Specification of Drosophila neuropeptidergic neurons by the splicing component brr2. PLoS Genet 2018; 14:e1007496. [PMID: 30133436 PMCID: PMC6122834 DOI: 10.1371/journal.pgen.1007496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/04/2018] [Accepted: 06/18/2018] [Indexed: 02/07/2023] Open
Abstract
During embryonic development, a number of genetic cues act to generate neuronal diversity. While intrinsic transcriptional cascades are well-known to control neuronal sub-type cell fate, the target cells can also provide critical input to specific neuronal cell fates. Such signals, denoted retrograde signals, are known to provide critical survival cues for neurons, but have also been found to trigger terminal differentiation of neurons. One salient example of such target-derived instructive signals pertains to the specification of the Drosophila FMRFamide neuropeptide neurons, the Tv4 neurons of the ventral nerve cord. Tv4 neurons receive a BMP signal from their target cells, which acts as the final trigger to activate the FMRFa gene. A recent FMRFa-eGFP genetic screen identified several genes involved in Tv4 specification, two of which encode components of the U5 subunit of the spliceosome: brr2 (l(3)72Ab) and Prp8. In this study, we focus on the role of RNA processing during target-derived signaling. We found that brr2 and Prp8 play crucial roles in controlling the expression of the FMRFa neuropeptide specifically in six neurons of the VNC (Tv4 neurons). Detailed analysis of brr2 revealed that this control is executed by two independent mechanisms, both of which are required for the activation of the BMP retrograde signaling pathway in Tv4 neurons: (1) Proper axonal pathfinding to the target tissue in order to receive the BMP ligand. (2) Proper RNA splicing of two genes in the BMP pathway: the thickveins (tkv) gene, encoding a BMP receptor subunit, and the Medea gene, encoding a co-Smad. These results reveal involvement of specific RNA processing in diversifying neuronal identity within the central nervous system. The nervous system displays daunting cellular diversity, largely generated through complex regulatory input operating on stem cells and their neural lineages during development. Most of the reported mechanisms acting to generate neural diversity pertain to transcriptional regulation. In contrast, little is known regarding the post-transcriptional mechanisms involved. Here, we use a specific group of neurons, Apterous neurons, in the ventral nerve cord of Drosophila melanogaster as our model, to analyze the function of two essential components of the spliceosome; Brr2 and Prp8. Apterous neurons require a BMP retrograde signal for terminal differentiation, and we find that brr2 and Prp8 play crucial roles during this process. brr2 is critical for two independent events; axon pathfinding and BMP signaling, both of which are required for the activation of the retrograde signaling pathway necessary for Apterous neurons. These results identify a post-transcriptional mechanism as key for specifying neuronal identity, by ensuring the execution of a retrograde signal.
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Affiliation(s)
- Ignacio Monedero Cobeta
- Dept. of Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Dept. of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | | | - Jin Li
- Department of Electrical and Computer Engineering Texas A&M University, College Station, Texas, United States of America
- TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Peng Yu
- Department of Electrical and Computer Engineering Texas A&M University, College Station, Texas, United States of America
| | - Stefan Thor
- Dept. of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - Jonathan Benito-Sipos
- Dept. of Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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24
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Neuronal activity regulates DROSHA via autophagy in spinal muscular atrophy. Sci Rep 2018; 8:7907. [PMID: 29784949 PMCID: PMC5962575 DOI: 10.1038/s41598-018-26347-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 05/10/2018] [Indexed: 02/06/2023] Open
Abstract
Dysregulated miRNA expression and mutation of genes involved in miRNA biogenesis have been reported in motor neuron diseases including spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Therefore, identifying molecular mechanisms governing miRNA expression is important to understand these diseases. Here, we report that expression of DROSHA, which is a critical enzyme in the microprocessor complex and essential for miRNA biogenesis, is reduced in motor neurons from an SMA mouse model. We show that DROSHA is degraded by neuronal activity induced autophagy machinery, which is also dysregulated in SMA. Blocking neuronal activity or the autophagy-lysosome pathway restores DROSHA levels in SMA motor neurons. Moreover, reducing DROSHA levels enhances axonal growth. As impaired axonal growth is a well described phenotype of SMA motor neurons, these data suggest that DROSHA reduction by autophagy may mitigate the phenotype of SMA. In summary, these findings suggest that autophagy regulates RNA metabolism and neuronal growth via the DROSHA/miRNA pathway and this pathway is dysregulated in SMA.
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25
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Kourtidis A, Anastasiadis PZ. Close encounters of the RNAi kind: the silencing life of the adherens junctions. Curr Opin Cell Biol 2018; 54:30-36. [PMID: 29587176 DOI: 10.1016/j.ceb.2018.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/01/2018] [Accepted: 03/06/2018] [Indexed: 11/19/2022]
Abstract
The adherens junction has been historically considered an essential structural component of epithelial tissues. Although primarily discussed as targets of signaling pathways responsible for cell fate and tissue remodeling, they have also emerged as critical signaling regulators in developmental processes or in disease progression. The recent discovery of a functional localized RNA interference (RNAi) machinery at epithelial adherens junctions revealed a new layer of signaling regulation that is directly associated with the structure itself. This and other findings also indicate that our view of the subcellular localization of RNAi requires revisiting. A number of questions emerge regarding the physiological role and the modes of regulation of the junctional RNAi machinery, pointing towards new directions of investigation.
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Affiliation(s)
- Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA.
| | - Panos Z Anastasiadis
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA.
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26
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Lu WT, Hawley BR, Skalka GL, Baldock RA, Smith EM, Bader AS, Malewicz M, Watts FZ, Wilczynska A, Bushell M. Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair. Nat Commun 2018; 9:532. [PMID: 29416038 PMCID: PMC5803274 DOI: 10.1038/s41467-018-02893-x] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 01/05/2018] [Indexed: 01/08/2023] Open
Abstract
The error-free and efficient repair of DNA double-stranded breaks (DSBs) is extremely important for cell survival. RNA has been implicated in the resolution of DNA damage but the mechanism remains poorly understood. Here, we show that miRNA biogenesis enzymes, Drosha and Dicer, control the recruitment of repair factors from multiple pathways to sites of damage. Depletion of Drosha significantly reduces DNA repair by both homologous recombination (HR) and non-homologous end joining (NHEJ). Drosha is required within minutes of break induction, suggesting a central and early role for RNA processing in DNA repair. Sequencing of DNA:RNA hybrids reveals RNA invasion around DNA break sites in a Drosha-dependent manner. Removal of the RNA component of these structures results in impaired repair. These results show how RNA can be a direct and critical mediator of DNA damage repair in human cells.
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Affiliation(s)
- Wei-Ting Lu
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - Ben R Hawley
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | | | - Robert A Baldock
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15232, PA, USA
| | - Ewan M Smith
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - Aldo S Bader
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | | | - Felicity Z Watts
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | | | - Martin Bushell
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK.
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27
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Kim JO, Bae J, Kim J, Oh SH, An HJ, Han IB, Oh D, Kim OJ, Kim NK. Association of MicroRNA Biogenesis Genes Polymorphisms with Ischemic Stroke Susceptibility and Post-Stroke Mortality. J Stroke 2018; 20:110-121. [PMID: 29402068 PMCID: PMC5836584 DOI: 10.5853/jos.2017.02586] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/30/2017] [Accepted: 01/19/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND AND PURPOSE MicroRNA (miRNA) expression has been examined in multiple conditions, including various cancers, neurological diseases, and cerebrovascular diseases, particularly stroke. Existing evidence indicates that miRNA biosynthesis and function play crucial roles in ischemic stroke physiology and pathology. In this study, we selected six known polymorphisms in miRNA-biogenesis genes; DICER rs13078A>T, rs3742330A>G; DROSHA rs10719T>C, rs6877842G>C; Ran GTPase (RAN) rs14035C>T; exportin 5 (XPO5) rs11077A>C. METHODS We analyzed the associations between these polymorphisms and disease status and clinical factors in 585 ischemic stroke patients and 403 controls. Genotyping was performed with the polymerase chain reaction-restriction fragment length polymorphism method. RESULTS The DICER rs3742330A>G (AA vs. AG+GG: adjusted odds ratio [AOR], 1.360; 95% confidence interval [CI], 1.024 to 1.807; P=0.034) and DROSHA rs10719T>C polymorphisms (TT vs. CC: AOR, 2.038; 95% CI, 1.113 to 3.730; P=0.021) were associated with ischemic stroke prevalence. During a mean follow-up of 4.80±2.11 years, 99 (5.91%) of the stroke patients died. In multivariate Cox proportional hazard regression models, a significant association was found between RAN rs14035 and survival of large artery disease patients with ischemic stroke (CC vs. TT: adjusted hazard ratio, 5.978; P=0.015). CONCLUSIONS An association was identified between the DICER and DROSHA polymorphisms and ischemic stroke. Specifically, polymorphisms (rs3742330 and rs10719) were more common in stroke patients, suggesting that they may be associated with an increased risk of ischemic stroke.
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Affiliation(s)
- Jung Oh Kim
- Department of Biomedical Science, CHA University College of Life Science, Seongnam, Korea
| | - Jinkun Bae
- Department of Emergency Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Jinkwon Kim
- Department of Neurology, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Seung Hun Oh
- Department of Neurology, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Hui Jeong An
- Department of Biomedical Science, CHA University College of Life Science, Seongnam, Korea
| | - In Bo Han
- Department of Neurosurgery, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Doyeun Oh
- Department of Internal Medicine, CHA University, Seongnam, Korea
| | - Ok Joon Kim
- Department of Neurology, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Nam Keun Kim
- Department of Biomedical Science, CHA University College of Life Science, Seongnam, Korea
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28
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Abstract
DROSHA is the catalytic subunit of the Microprocessor complex, which initiates microRNA (miRNA) maturation in the nucleus by recognizing and cleaving hairpin precursors embedded in primary transcripts. However, accumulating evidence suggests that not all hairpin substrates of DROSHA are associated with the generation of functional small RNAs. By targeting those hairpins, DROSHA regulates diverse aspects of RNA metabolism across the transcriptome, serves as a line of defense against the expression of potentially deleterious elements, and permits cell fate determination and differentiation. DROSHA is also versatile in the way that it executes these noncanonical functions, occasionally depending on its RNA-binding activity rather than its catalytic activity. Herein, we discuss the functional and mechanistic diversity of DROSHA beyond the miRNA biogenesis pathway in light of recent findings.
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Affiliation(s)
- Dooyoung Lee
- a Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea
| | - Chanseok Shin
- a Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea.,b Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute , Seoul National University , Seoul , Republic of Korea
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29
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Lee D, Nam JW, Shin C. DROSHA targets its own transcript to modulate alternative splicing. RNA (NEW YORK, N.Y.) 2017; 23:1035-1047. [PMID: 28400409 PMCID: PMC5473138 DOI: 10.1261/rna.059808.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 04/06/2017] [Indexed: 05/23/2023]
Abstract
The nuclear RNase III enzyme DROSHA interacts with its cofactor DGCR8 to form the Microprocessor complex, which initiates microRNA (miRNA) maturation by cleaving hairpin structures embedded in primary transcripts. Apart from its central role in the biogenesis of miRNAs, DROSHA is also known to recognize and cleave miRNA-like hairpins in a subset of transcripts without apparent small RNA production. Here, we report that the human DROSHA transcript is one such noncanonical target of DROSHA. Mammalian DROSHA genes have evolved a conserved hairpin structure spanning a specific exon-intron junction, which serves as a substrate for the Microprocessor in human cells but not in murine cells. We show that it is this hairpin element that decides whether the overlapping exon is alternatively or constitutively spliced. We further demonstrate that DROSHA promotes skipping of the overlapping exon in human cells independently of its cleavage function. Our findings add to the expanding list of noncanonical DROSHA functions.
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Affiliation(s)
- Dooyoung Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
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