1
|
Selective inhibition of miRNA processing by a herpesvirus-encoded miRNA. Nature 2022; 605:539-544. [PMID: 35508655 DOI: 10.1038/s41586-022-04667-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/21/2022] [Indexed: 12/12/2022]
Abstract
Herpesviruses have mastered host cell modulation and immune evasion to augment productive infection, life-long latency and reactivation1,2. A long appreciated, yet undefined relationship exists between the lytic-latent switch and viral non-coding RNAs3,4. Here we identify viral microRNA (miRNA)-mediated inhibition of host miRNA processing as a cellular mechanism that human herpesvirus 6A (HHV-6A) exploits to disrupt mitochondrial architecture, evade intrinsic host defences and drive the switch from latent to lytic virus infection. We demonstrate that virus-encoded miR-aU14 selectively inhibits the processing of multiple miR-30 family members by direct interaction with the respective primary (pri)-miRNA hairpin loops. Subsequent loss of miR-30 and activation of the miR-30-p53-DRP1 axis triggers a profound disruption of mitochondrial architecture. This impairs induction of type I interferons and is necessary for both productive infection and virus reactivation. Ectopic expression of miR-aU14 triggered virus reactivation from latency, identifying viral miR-aU14 as a readily druggable master regulator of the herpesvirus lytic-latent switch. Our results show that miRNA-mediated inhibition of miRNA processing represents a generalized cellular mechanism that can be exploited to selectively target individual members of miRNA families. We anticipate that targeting miR-aU14 will provide new therapeutic options for preventing herpesvirus reactivations in HHV-6-associated disorders.
Collapse
|
2
|
Butterworth MB. Non-coding RNAs and the mineralocorticoid receptor in the kidney. Mol Cell Endocrinol 2021; 521:111115. [PMID: 33301840 PMCID: PMC7796954 DOI: 10.1016/j.mce.2020.111115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
The final steps in the Renin-Angiotensin-Aldosterone signaling System (RAAS) involve binding of the corticosteroid hormone, aldosterone to its mineralocorticoid receptor (MR). The bound MR interacts with response elements to induce or repress the transcription of aldosterone-regulated genes. Along with the classic genomic targets of aldosterone that alter mRNA and protein expression, aldosterone also regulates the expression of non-coding RNAs (ncRNAs). Short ncRNAs termed microRNAs (miRs) have been shown to play a role in transducing aldosterone's actions via MR signaling. The role of miRs in homeostatic regulation of aldosterone signaling, and the potential for aldosterone-regulated miRs to act as feedback regulators of MR have been recently reported. In this review, the role of miRs in RAAS signaling and feedback regulation of MR in kidney epithelial cells will be discussed.
Collapse
Affiliation(s)
- Michael B Butterworth
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| |
Collapse
|
3
|
Logan MK, McLaurin DM, Hebert MD. Synergistic interactions between Cajal bodies and the miRNA processing machinery. Mol Biol Cell 2020; 31:1561-1569. [PMID: 32432989 PMCID: PMC7521794 DOI: 10.1091/mbc.e20-02-0144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cajal bodies (CBs) are subnuclear domains involved in the formation of ribonucleoproteins (RNPs) including small nuclear RNPs (snRNPs). CBs associate with specific gene loci, which impacts expression and provides a platform for the biogenesis of the nascent transcripts emanating from these genes. Here we report that CBs can associate with the C19MC microRNA (miRNA) gene cluster, which suggests a role for CBs in the biogenesis of animal miRNAs. The machinery involved in the formation of miRNAs includes the Drosha/DGCR8 complex, which processes primary-miRNA to precursor miRNA. Further processing of precursor miRNA by Dicer and other components generates mature miRNA. To test if CBs influence the expression and formation of miRNAs, we examined two representative miRNAs (miR-520 h and let-7a) in conditions that disrupt CBs. CB disruption correlates with alterations in the level of primary and mature miRNA and the let-7a mRNA target, HMGA2. We have also found that the processing of some small CB-specific RNAs (scaRNAs) is directly mediated by the Drosha/DGCR8 complex. ScaRNAs form scaRNPs, which play an important role in snRNP formation. Collectively, our results demonstrate that CBs and the miRNA processing machinery functionally interact and together contribute to the biogenesis of miRNAs and snRNPs.
Collapse
Affiliation(s)
- Madelyn K Logan
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216
| | - Douglas M McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216
| | - Michael D Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216
| |
Collapse
|
4
|
Song J, Zhuang Y, Zhu C, Meng H, Lu B, Xie B, Peng J, Li M, Yi C. Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation. Nat Chem Biol 2019; 16:160-169. [PMID: 31819270 DOI: 10.1038/s41589-019-0420-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 10/27/2019] [Indexed: 11/09/2022]
Abstract
Pseudouridine synthases (PUSs) are responsible for installation of pseudouridine (Ψ) modification in RNA. However, the activity and function of the PUS enzymes remain largely unexplored. Here we focus on human PUS10 and find that it co-expresses with the microprocessor (DROSHA-DGCR8 complex). Depletion of PUS10 results in a marked reduction of the expression level of a large number of mature miRNAs and concomitant accumulation of unprocessed primary microRNAs (pri-miRNAs) in multiple human cells. Mechanistically, PUS10 directly binds to pri-miRNAs and interacts with the microprocessor to promote miRNA biogenesis. Unexpectedly, this process is independent of the catalytic activity of PUS10. Additionally, we develop a sequencing method to profile Ψ in the tRNAome and report PUS10-dependent Ψ sites in tRNA. Collectively, our findings reveal differential functions of PUS10 in nuclear miRNA processing and in cytoplasmic tRNA pseudouridylation.
Collapse
Affiliation(s)
- Jinghui Song
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Yuan Zhuang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chenxu Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Bo Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Bingteng Xie
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Mo Li
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China. .,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| |
Collapse
|
5
|
Ouyang H, Zhang K, Fox-Walsh K, Yang Y, Zhang C, Huang J, Li H, Zhou Y, Fu XD. The RNA binding protein EWS is broadly involved in the regulation of pri-miRNA processing in mammalian cells. Nucleic Acids Res 2019; 45:12481-12495. [PMID: 30053258 PMCID: PMC5716145 DOI: 10.1093/nar/gkx912] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 09/27/2017] [Indexed: 12/13/2022] Open
Abstract
The Ewing Sarcoma protein (EWS) is a multifaceted RNA binding protein (RBP) with established roles in transcription, pre-mRNA processing and DNA damage response. By generating high quality EWS-RNA interactome, we uncovered its specific and prevalent interaction with a large subset of primary microRNAs (pri-miRNAs) in mammalian cells. Knockdown of EWS reduced, whereas overexpression enhanced, the expression of its target miRNAs. Biochemical analysis revealed that multiple elements in target pri-miRNAs, including the sequences flanking the stem-loop region, contributed to high affinity EWS binding and sequence swap experiments between target and non-target demonstrated that the flanking sequences provided the specificity for enhanced pri-miRNA processing by the Microprocessor Drosha/DGCR8. Interestingly, while repressing Drosha expression, as reported earlier, we found that EWS was able to enhance the recruitment of Drosha to chromatin. Together, these findings suggest that EWS may positively and negatively regulate miRNA biogenesis via distinct mechanisms, thus providing a new foundation to understand the function of EWS in development and disease.
Collapse
Affiliation(s)
- Huiwu Ouyang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kai Zhang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kristi Fox-Walsh
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yang Yang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Huang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hairi Li
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yu Zhou
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Institue of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xiang-Dong Fu
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| |
Collapse
|
6
|
Stathopoulou A, Chhetri JB, Ambrose JC, Estève PO, Ji L, Erdjument-Bromage H, Zhang G, Neubert TA, Pradhan S, Herrero J, Schmitz RJ, Ooi SK. A novel requirement for DROSHA in maintenance of mammalian CG methylation. Nucleic Acids Res 2017; 45:9398-9412. [PMID: 28934503 PMCID: PMC5766157 DOI: 10.1093/nar/gkx695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/27/2017] [Indexed: 12/18/2022] Open
Abstract
In mammals, faithful inheritance of genomic methylation patterns ensures proper gene regulation and cell behaviour, impacting normal development and fertility. Following establishment, genomic methylation patterns are transmitted through S-phase by the maintenance methyltransferase Dnmt1. Using a protein interaction screen, we identify Microprocessor component DROSHA as a novel DNMT1-interactor. Drosha-deficient embryonic stem (ES) cells display genomic hypomethylation that is not accounted for by changes in the levels of DNMT proteins. DNMT1-mediated methyltransferase activity is also reduced in these cells. We identify two transcripts that are specifically upregulated in Drosha- but not Dicer-deficient ES cells. Regions within these transcripts predicted to form stem-loop structures are processed by Microprocessor and can inhibit DNMT1-mediated methylation in vitro. Our results highlight DROSHA as a novel regulator of mammalian DNA methylation and we propose that DROSHA-mediated processing of RNA is necessary to ensure full DNMT1 activity. This adds to the DROSHA repertoire of non-miRNA dependent functions as well as implicating RNA in regulating DNMT1 activity and correct levels of genomic methylation.
Collapse
Affiliation(s)
| | - Jyoti B. Chhetri
- Department of Cancer Biology, UCL Cancer Institute, London WC1E 6BT, UK
| | - John C. Ambrose
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | | | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA
| | - Hediye Erdjument-Bromage
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Guoqiang Zhang
- New England Biolabs, 240 Country Road, Ipswich, MA 01938, USA
| | - Thomas A. Neubert
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute, NYU School of Medicine, New York, NY 10016, USA
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | - Robert J. Schmitz
- Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA
| | - Steen K.T. Ooi
- Department of Cancer Biology, UCL Cancer Institute, London WC1E 6BT, UK
- To whom correspondence should be addressed. Tel: +44 2076 790717; Fax: +44 2076 796817;
| |
Collapse
|
7
|
Fernandez N, Cordiner RA, Young RS, Hug N, Macias S, Cáceres JF. Genetic variation and RNA structure regulate microRNA biogenesis. Nat Commun 2017; 8:15114. [PMID: 28466845 PMCID: PMC5418625 DOI: 10.1038/ncomms15114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
MiRNA biogenesis is highly regulated at the post-transcriptional level; however, the role of sequence and secondary RNA structure in this process has not been extensively studied. A single G to A substitution present in the terminal loop of pri-mir-30c-1 in breast and gastric cancer patients had been previously described to result in increased levels of mature miRNA. Here, we report that this genetic variant directly affects Drosha-mediated processing of pri-mir-30c-1 in vitro and in cultured cells. Structural analysis of this variant revealed an altered RNA structure that facilitates the interaction with SRSF3, an SR protein family member that promotes pri-miRNA processing. Our results are compatible with a model whereby a genetic variant in pri-mir-30c-1 leads to a secondary RNA structure rearrangement that facilitates binding of SRSF3 resulting in increased levels of miR-30c. These data highlight that primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.
Collapse
Affiliation(s)
- Noemi Fernandez
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ross A. Cordiner
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Robert S. Young
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sara Macias
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Javier F. Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| |
Collapse
|
8
|
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: 2.0] [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.
Collapse
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
| |
Collapse
|
9
|
Rolando C, Erni A, Grison A, Beattie R, Engler A, Gokhale P, Milo M, Wegleiter T, Jessberger S, Taylor V. Multipotency of Adult Hippocampal NSCs In Vivo Is Restricted by Drosha/NFIB. Cell Stem Cell 2016; 19:653-662. [DOI: 10.1016/j.stem.2016.07.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 05/23/2016] [Accepted: 07/06/2016] [Indexed: 11/26/2022]
|
10
|
Panesar S, Neethirajan S. Microfluidics: Rapid Diagnosis for Breast Cancer. NANO-MICRO LETTERS 2016; 8:204-220. [PMID: 30460281 PMCID: PMC6223681 DOI: 10.1007/s40820-015-0079-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 12/04/2015] [Indexed: 05/06/2023]
Abstract
Breast cancer affected 1.7 million people worldwide in 2012 and accounts for approximately 23.3 % of all cancers diagnosed in women. The disease is characterized by a genetic mutation, either inherited or resulting from environmental factors, that causes uncontrollable cellular growth of breast tissue or adjacent tissues. Current means of diagnosing this disease depend on the individual analyzing the results from bulky, highly technical, and expensive equipment that is not globally accessible. As a result, patients can go undiagnosed due to a lack of available equipment or be over-diagnosed due to human error. This review attempts to highlight current means of diagnosing breast cancer and critically analyze their effectiveness and usefulness in terms of patient survival. An alternative means based on microfluidics biomarker detection is then presented. This method can be considered as a primary screening tool for diagnosing breast cancer based on its robustness, high throughput, low energy requirements, and accessibility to the general public.
Collapse
Affiliation(s)
- Satvinder Panesar
- BioNano Laboratory, School of Engineering, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Suresh Neethirajan
- BioNano Laboratory, School of Engineering, University of Guelph, Guelph, ON N1G 2W1 Canada
| |
Collapse
|
11
|
Fang W, Bartel DP. The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes. Mol Cell 2015; 60:131-45. [PMID: 26412306 DOI: 10.1016/j.molcel.2015.08.015] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/13/2015] [Accepted: 08/19/2015] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs processed from stem-loop regions of primary transcripts (pri-miRNAs), with the choice of stem loops for initial processing largely determining what becomes a miRNA. To identify sequence and structural features influencing this choice, we determined cleavage efficiencies of >50,000 variants of three human pri-miRNAs, focusing on the regions intractable to previous high-throughput analyses. Our analyses revealed a mismatched motif in the basal stem region, a preference for maintaining or improving base pairing throughout the remainder of the stem, and a narrow stem-length preference of 35 ± 1 base pairs. Incorporating these features with previously identified features, including three primary-sequence motifs, yielded a unifying model defining mammalian pri-miRNAs in which motifs help orient processing and increase efficiency, with the presence of more motifs compensating for structural defects. This model enables generation of artificial pri-miRNAs, designed de novo, without reference to any natural sequence yet processed more efficiently than natural pri-miRNAs.
Collapse
Affiliation(s)
- Wenwen Fang
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for 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 for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
12
|
Yang Q, Li W, She H, Dou J, Duong DM, Du Y, Yang SH, Seyfried NT, Fu H, Gao G, Mao Z. Stress induces p38 MAPK-mediated phosphorylation and inhibition of Drosha-dependent cell survival. Mol Cell 2015; 57:721-734. [PMID: 25699712 DOI: 10.1016/j.molcel.2015.01.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 07/14/2014] [Accepted: 12/29/2014] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) regulate the translational potential of their mRNA targets and control many cellular processes. The key step in canonical miRNA biogenesis is the cleavage of the primary transcripts by the nuclear RNase III enzyme Drosha. Emerging evidence suggests that the miRNA biogenic cascade is tightly controlled. However, little is known whether Drosha is regulated. Here, we show that Drosha is targeted by stress. Under stress, p38 MAPK directly phosphorylates Drosha at its N terminus. This reduces its interaction with DiGeorge syndrome critical region gene 8 and promotes its nuclear export and degradation by calpain. This regulatory mechanism mediates stress-induced inhibition of Drosha function. Reduction of Drosha sensitizes cells to stress and increases death. In contrast, increase in Drosha attenuates stress-induced death. These findings reveal a critical regulatory mechanism by which stress engages p38 MAPK pathway to destabilize Drosha and inhibit Drosha-mediated cellular survival.
Collapse
Affiliation(s)
- Qian Yang
- Department of Neurosurgery, Tangdu Hospital, the Fourth Military Medical University, Xi'an, Shaanxi 710038, China; Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Wenming Li
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hua She
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Juan Dou
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Duc M Duong
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yuhong Du
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shao-Hua Yang
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Guodong Gao
- Department of Neurosurgery, Tangdu Hospital, the Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Zixu Mao
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| |
Collapse
|
13
|
Alarcón CR, Lee H, Goodarzi H, Halberg N, Tavazoie SF. N6-methyladenosine marks primary microRNAs for processing. Nature 2015; 519:482-5. [PMID: 25799998 DOI: 10.1038/nature14281] [Citation(s) in RCA: 961] [Impact Index Per Article: 106.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 02/02/2015] [Indexed: 12/21/2022]
Abstract
The first step in the biogenesis of microRNAs is the processing of primary microRNAs (pri-miRNAs) by the microprocessor complex, composed of the RNA-binding protein DGCR8 and the type III RNase DROSHA. This initial event requires recognition of the junction between the stem and the flanking single-stranded RNA of the pri-miRNA hairpin by DGCR8 followed by recruitment of DROSHA, which cleaves the RNA duplex to yield the pre-miRNA product. While the mechanisms underlying pri-miRNA processing have been determined, the mechanism by which DGCR8 recognizes and binds pri-miRNAs, as opposed to other secondary structures present in transcripts, is not understood. Here we find in mammalian cells that methyltransferase-like 3 (METTL3) methylates pri-miRNAs, marking them for recognition and processing by DGCR8. Consistent with this, METTL3 depletion reduced the binding of DGCR8 to pri-miRNAs and resulted in the global reduction of mature miRNAs and concomitant accumulation of unprocessed pri-miRNAs. In vitro processing reactions confirmed the sufficiency of the N(6)-methyladenosine (m(6)A) mark in promoting pri-miRNA processing. Finally, gain-of-function experiments revealed that METTL3 is sufficient to enhance miRNA maturation in a global and non-cell-type-specific manner. Our findings reveal that the m(6)A mark acts as a key post-transcriptional modification that promotes the initiation of miRNA biogenesis.
Collapse
Affiliation(s)
- Claudio R Alarcón
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Hyeseung Lee
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Hani Goodarzi
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Nils Halberg
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| |
Collapse
|
14
|
Chen T, Xiang JF, Zhu S, Chen S, Yin QF, Zhang XO, Zhang J, Feng H, Dong R, Li XJ, Yang L, Chen LL. ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner. Cell Res 2015; 25:459-76. [PMID: 25708366 DOI: 10.1038/cr.2015.24] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/09/2014] [Accepted: 12/01/2014] [Indexed: 02/08/2023] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) are involved in adenosine-to-inosine RNA editing and are implicated in development and diseases. Here we observed that ADAR1 deficiency in human embryonic stem cells (hESCs) significantly affected hESC differentiation and neural induction with widespread changes in mRNA and miRNA expression, including upregulation of self-renewal-related miRNAs, such as miR302s. Global editing analyses revealed that ADAR1 editing activity contributes little to the altered miRNA/mRNA expression in ADAR1-deficient hESCs upon neural induction. Genome-wide iCLIP studies identified that ADAR1 binds directly to pri-miRNAs to interfere with miRNA processing by acting as an RNA-binding protein. Importantly, aberrant expression of miRNAs and phenotypes observed in ADAR1-depleted hESCs upon neural differentiation could be reversed by an enzymatically inactive ADAR1 mutant, but not by the RNA-binding-null ADAR1 mutant. These findings reveal that ADAR1, but not its editing activity, is critical for hESC differentiation and neural induction by regulating miRNA biogenesis via direct RNA interaction.
Collapse
Affiliation(s)
- Tian Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jian-Feng Xiang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shanshan Zhu
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Siye Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qing-Fei Yin
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao-Ou Zhang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jun Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hua Feng
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rui Dong
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xue-Jun Li
- Department of Neuroscience, University of Connecticut Stem Cell Institute, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Li Yang
- 1] CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China [2] School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Ling-Ling Chen
- 1] State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China [2] School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| |
Collapse
|
15
|
Eadon MT, Jacob A, Cunningham PN, Quigg RJ, Garcia JGN, Alexander JJ. Transcriptional profiling reveals that C5a alters microRNA in brain endothelial cells. Immunology 2014; 143:363-73. [PMID: 24801999 DOI: 10.1111/imm.12314] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 04/11/2014] [Accepted: 05/01/2014] [Indexed: 01/10/2023] Open
Abstract
Blood-brain barrier (BBB) disturbance is a crucial occurrence in many neurological diseases, including systemic lupus erythematosus (SLE). Our previous studies showed that experimental lupus serum altered the integrity of the mouse brain endothelial layer, an important constituent of the BBB. Complement activation occurs in lupus with increased circulating complement components. Using a genomics approach, we identified the microRNA (miRNA) altered in mouse brain endothelial cells (bEnd3) by lupus serum and the complement protein, C5a. Of the 318 miRNA evaluated, 23 miRNAs were altered by lupus serum and 32 were altered by C5a alone compared with controls. Seven miRNAs (P < 0 · 05) were differentially expressed by both treatments: mmu-miR-133a*, mmu-miR-193*, mmu-miR-26b, mmu-miR-28*, mmu-miR-320a, mmu-miR-423-3p and mmu-miR-509-5p. The microarray results were validated by quantitative RT-PCR. In line with the in vitro results, expression of miR-26b and miR-28* were also significantly up-regulated in lupus mouse brain which was reduced by C5a receptor inhibition. Target prediction analysis revealed miR gene targets encoding components involved in inflammation, matrix arrangement, and apoptosis, pathways known to play important roles in central nervous system lupus. Our findings suggest that the miRNAs reported in this study may represent novel therapeutic targets in central nervous system lupus and other similar neuroinflammatory settings.
Collapse
Affiliation(s)
- Michael T Eadon
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | | | | | | |
Collapse
|
16
|
Abstract
In animals, the Microprocessor complex cleaves primary transcripts of microRNAs (pri-miRNAs) to produce precursor microRNAs in the nucleus. The core components of Microprocessor include the Drosha ribonuclease and its RNA-binding partner protein DiGeorge critical region 8 (DGCR8). DGCR8 has been shown to tightly bind an Fe(III) heme cofactor, which activates its pri-miRNA processing activity. Here we describe how to reconstitute pri-miRNA processing using recombinant human Drosha and DGCR8 proteins. In particular, we present the procedures for expressing and purifying DGCR8 as an Fe(III) heme-bound dimer, the most active form of this protein, and for estimating its heme content.
Collapse
|
17
|
Han SJ, Marshall V, Barsov E, Quiñones O, Ray A, Labo N, Trivett M, Ott D, Renne R, Whitby D. Kaposi's sarcoma-associated herpesvirus microRNA single-nucleotide polymorphisms identified in clinical samples can affect microRNA processing, level of expression, and silencing activity. J Virol 2013; 87:12237-48. [PMID: 24006441 PMCID: PMC3807933 DOI: 10.1128/jvi.01202-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/29/2013] [Indexed: 12/24/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) encodes 12 pre-microRNAs that can produce 25 KSHV mature microRNAs. We previously reported single-nucleotide polymorphisms (SNPs) in KSHV-encoded pre-microRNA and mature microRNA sequences from clinical samples (V. Marshall et al., J. Infect. Dis., 195:645-659, 2007). To determine whether microRNA SNPs affect pre-microRNA processing and, ultimately, mature microRNA expression levels, we performed a detailed comparative analysis of (i) mature microRNA expression levels, (ii) in vitro Drosha/Dicer processing, and (iii) RNA-induced silencing complex-dependent targeting of wild-type (wt) and variant microRNA genes. Expression of pairs of wt and variant pre-microRNAs from retroviral vectors and measurement of KSHV mature microRNA expression by real-time reverse transcription-PCR (RT-PCR) revealed differential expression levels that correlated with the presence of specific sequence polymorphisms. Measurement of KSHV mature microRNA expression in a panel of primary effusion lymphoma cell lines by real-time RT-PCR recapitulated some observed expression differences but suggested a more complex relationship between sequence differences and expression of mature microRNA. Furthermore, in vitro maturation assays demonstrated significant SNP-associated changes in Drosha/DGCR8 and/or Dicer processing. These data demonstrate that SNPs within KSHV-encoded pre-microRNAs are associated with differential microRNA expression levels. Given the multiple reports on the involvement of microRNAs in cancer, the biological significance of these phenotypic and genotypic variants merits further studies in patients with KSHV-associated malignancies.
Collapse
MESH Headings
- Cells, Cultured
- Gene Expression Regulation, Viral
- HEK293 Cells
- Herpesviridae Infections/genetics
- Herpesviridae Infections/virology
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/pathogenicity
- Humans
- Luciferases/metabolism
- Lymphoma, Primary Effusion/genetics
- Lymphoma, Primary Effusion/virology
- MicroRNAs/genetics
- MicroRNAs/physiology
- Polymorphism, Single Nucleotide/genetics
- RNA Processing, Post-Transcriptional/genetics
- RNA, Messenger/genetics
- RNA, Viral/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
Collapse
Affiliation(s)
- Soo-Jin Han
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Vickie Marshall
- AIDS and Cancer Virus Program, SAIC—Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Eugene Barsov
- AIDS and Cancer Virus Program, SAIC—Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Octavio Quiñones
- Computer and Statistical Services, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alex Ray
- AIDS and Cancer Virus Program, SAIC—Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Nazzarena Labo
- AIDS and Cancer Virus Program, SAIC—Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Matthew Trivett
- AIDS and Cancer Virus Program, SAIC—Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David Ott
- AIDS and Cancer Virus Program, SAIC—Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Denise Whitby
- AIDS and Cancer Virus Program, SAIC—Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| |
Collapse
|
18
|
Kaposi's sarcoma-associated herpesvirus encodes a mimic of cellular miR-23. J Virol 2013; 87:11821-30. [PMID: 23986579 DOI: 10.1128/jvi.01692-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) expresses ∼20 viral microRNAs (miRNAs) in latently infected cells. We have previously shown that two of these miRNAs function as mimics of the cellular miRNAs miR-155 and miR-142-3p. Two additional KSHV miRNAs, miR-K3+1 and miR-K3, share perfect and offset 5' homology with cellular miR-23, respectively. Here, we report a single nucleotide polymorphism that causes miR-K3+1 expression in a subset of KSHV-infected primary effusion lymphoma cell lines as a consequence of altered processing of the primary transcript by the Microprocessor complex. We confirm that miR-K3+1 regulates miR-23 targets, which is expected because these miRNAs share the entire seed region (nucleotides 2 to 8). Surprisingly, we found that miR-K3 also regulates miR-23 targets, despite offset seed sequences. In addition, the offset homology of miR-K3 to miR-23 likely allows this viral miRNA to expand its target repertoire beyond the targets of miR-23. Because miR-23 is highly expressed in endothelial cells but expressed at only low levels in B cells, we hypothesize that miR-K3 may function to introduce miR-23-like activities into KSHV-infected B cells. Together, our data demonstrate that KSHV has evolved at least three distinct viral miRNAs to tap into evolutionarily conserved cellular miRNA-regulatory networks. Furthermore, our data allow fundamental insights into the generation and functional impact of miRNA 5' end variation.
Collapse
|
19
|
Roth BM, Ishimaru D, Hennig M. The core microprocessor component DiGeorge syndrome critical region 8 (DGCR8) is a nonspecific RNA-binding protein. J Biol Chem 2013; 288:26785-99. [PMID: 23893406 DOI: 10.1074/jbc.m112.446880] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MicroRNA (miRNA) biogenesis follows a conserved succession of processing steps, beginning with the recognition and liberation of an miRNA-containing precursor miRNA hairpin from a large primary miRNA transcript (pri-miRNA) by the Microprocessor, which consists of the nuclear RNase III Drosha and the double-stranded RNA-binding domain protein DGCR8 (DiGeorge syndrome critical region protein 8). Current models suggest that specific recognition is driven by DGCR8 detection of single-stranded elements of the pri-miRNA stem-loop followed by Drosha recruitment and pri-miRNA cleavage. Because countless RNA transcripts feature single-stranded-dsRNA junctions and DGCR8 can bind hundreds of mRNAs, we explored correlations between RNA binding properties of DGCR8 and specific pri-miRNA substrate processing. We found that DGCR8 bound single-stranded, double-stranded, and random hairpin transcripts with similar affinity. Further investigation of DGCR8/pri-mir-16 interactions by NMR detected intermediate exchange regimes over a wide range of stoichiometric ratios. Diffusion analysis of DGCR8/pri-mir-16 interactions by pulsed field gradient NMR lent further support to dynamic complex formation involving free components in exchange with complexes of varying stoichiometry, although in vitro processing assays showed exclusive cleavage of pri-mir-16 variants bearing single-stranded flanking regions. Our results indicate that DGCR8 binds RNA nonspecifically. Therefore, a sequential model of DGCR8 recognition followed by Drosha recruitment is unlikely. Known RNA substrate requirements are broad and include 70-nucleotide hairpins with unpaired flanking regions. Thus, specific RNA processing is likely facilitated by preformed DGCR8-Drosha heterodimers that can discriminate between authentic substrates and other hairpins.
Collapse
Affiliation(s)
- Braden M Roth
- From the Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | | | | |
Collapse
|
20
|
Auyeung VC, Ulitsky I, McGeary SE, Bartel DP. Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell 2013; 152:844-58. [PMID: 23415231 DOI: 10.1016/j.cell.2013.01.031] [Citation(s) in RCA: 309] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 10/28/2012] [Accepted: 01/14/2013] [Indexed: 12/26/2022]
Abstract
To use microRNAs to downregulate mRNA targets, cells must first process these ~22 nt RNAs from primary transcripts (pri-miRNAs). These transcripts form RNA hairpins important for processing, but additional determinants must distinguish pri-miRNAs from the many other hairpin-containing transcripts expressed in each cell. Illustrating the complexity of this recognition, we show that most Caenorhabditis elegans pri-miRNAs lack determinants required for processing in human cells. To find these determinants, we generated many variants of four human pri-miRNAs, sequenced millions that retained function, and compared them with the starting variants. Our results confirmed the importance of pairing in the stem and revealed three primary-sequence determinants, including an SRp20-binding motif (CNNC) found downstream of most pri-miRNA hairpins in bilaterian animals, but not in nematodes. Adding this and other determinants to C. elegans pri-miRNAs imparted efficient processing in human cells, thereby confirming the importance of primary-sequence determinants for distinguishing pri-miRNAs from other hairpin-containing transcripts.
Collapse
Affiliation(s)
- Vincent C Auyeung
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | | | | |
Collapse
|
21
|
Ryu I, Park JH, An S, Kwon OS, Jang SK. eIF4GI facilitates the MicroRNA-mediated gene silencing. PLoS One 2013; 8:e55725. [PMID: 23409027 PMCID: PMC3567085 DOI: 10.1371/journal.pone.0055725] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 12/29/2012] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene silencing by binding to complementary target mRNAs and recruiting the miRNA-containing ribonucleoprotein complexes to the mRNAs. However, the molecular basis of this silencing is unclear. Here, we show that human Ago2 associates with the cap-binding protein complex and this association is mediated by human eIF4GI, a scaffold protein required for the translation initiation. Using a cap photo-crosslinking method, we show that Ago2 closely associates with the cap structure. Taken together, these data suggest that eIF4GI participates in the miRNA-mediated post-transcriptional gene silencing by promoting the association of Ago2 with the cap-binding complex.
Collapse
Affiliation(s)
- Incheol Ryu
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Ji Hoon Park
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Sihyeon An
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Oh Sung Kwon
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Sung Key Jang
- Molecular Virology Laboratory, POSTECH Biotech Center, Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
- Biotechnology Research Center, Pohang University of Science and Technology, Pohang, Korea
- * E-mail:
| |
Collapse
|
22
|
Pickering BF, Yu D, Van Dyke MW. Nucleolin protein interacts with microprocessor complex to affect biogenesis of microRNAs 15a and 16. J Biol Chem 2011; 286:44095-44103. [PMID: 22049078 PMCID: PMC3243533 DOI: 10.1074/jbc.m111.265439] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 10/22/2011] [Indexed: 01/09/2023] Open
Abstract
MicroRNAs (miRNA) are endogenous, short, non-coding RNA that undergo a multistep biogenesis before generating the functional, mature sequence. The core components of the microprocessor complex, consisting of Drosha and DGCR8, are both necessary and sufficient for this process, although accessory proteins have been found that modulate the biogenesis of a subset of miRNA. Curiously, many of the proteins involved in miRNA biogenesis are also needed for ribosomal RNA processing. Here we show that nucleolin, another protein critical for rRNA processing, is involved in the biogenesis of microRNA 15a/16 (miR-15a/16), specifically at the primary to precursor stage of processing. Through overexpression and knockdown studies, we show that miR-15a/16 levels are directly correlated to nucleolin expression. Furthermore, we found that cellular localization is critical for the proper functioning of nucleolin in this pathway and that nucleolin directly interacts with DGCR8 and Drosha in the nucleus. Nucleolin can bind to the primary miRNA both directly and specifically. Finally, we show that in the absence of nucleolin, cell extracts are unable to process miR-15a/16 in vitro and that this can be rescued by the addition of nucleolin. Our findings offer a new protein component in the microRNA biogenesis pathway and lend insight into miRNA dysregulation in certain cancers.
Collapse
Affiliation(s)
- Brian F Pickering
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030; Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030.
| | - Dihua Yu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030; Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030.
| | - Michael W Van Dyke
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina 28723
| |
Collapse
|
23
|
Kim YJ, Park SJ, Choi EY, Kim S, Kwak HJ, Yoo BC, Yoo H, Lee SH, Kim D, Park JB, Kim JH. PTEN modulates miR-21 processing via RNA-regulatory protein RNH1. PLoS One 2011; 6:e28308. [PMID: 22162762 PMCID: PMC3230587 DOI: 10.1371/journal.pone.0028308] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 11/05/2011] [Indexed: 01/01/2023] Open
Abstract
Aberrant miR-21 expression is closely associated with cell proliferation, anti-apoptosis, migration, invasion, and metastasis in various cancers. However, the regulatory mechanism of miR-21 biogenesis is largely unknown. Here, we demonstrated that the tumor suppressor PTEN negatively regulates the expression of oncogenic miR-21 at the post-transcriptional level. Moreover, our results suggest that PTEN plays such a role through the indirect interaction with the Drosha complex. To elucidate how PTEN regulates pri- to pre-miR-21 processing, we attempted to find PTEN-interacting proteins and identified an RNA-regulatory protein, RNH1. Using the sensor to monitor pri-miR-21 processing, we demonstrated that RNH1 is necessary and sufficient for pri-miR-21 processing. Moreover, our results propose that the nuclear localization of RNH1 is important for this function. Further analysis showed that RNH1 directly interacts with the Drosha complex and that PTEN blocks this interaction. Taken together, these results suggest that the PTEN-mediated miR-21 regulation is achieved by inhibiting the interaction between the Drosha complex and RNH1, revealing previously unidentified role of PTEN in the oncogenic miR-21 biogenesis.
Collapse
Affiliation(s)
- Youn-Jae Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
- Specific Organs Cancer Branch, Research Institute, National Cancer Center, Ilsan, Korea
| | - Se-Jeong Park
- Carcinogenesis Branch, Research Institute, National Cancer Center, Ilsan, Korea
| | - Eun Young Choi
- Specific Organs Cancer Branch, Research Institute, National Cancer Center, Ilsan, Korea
| | - Sol Kim
- Carcinogenesis Branch, Research Institute, National Cancer Center, Ilsan, Korea
| | - Hee Jin Kwak
- Specific Organs Cancer Branch, Research Institute, National Cancer Center, Ilsan, Korea
| | - Byong Chul Yoo
- Colorectal Cancer Branch, Research Institute, National Cancer Center, Ilsan, Korea
| | - Heon Yoo
- Specific Organs Cancer Branch, Research Institute, National Cancer Center, Ilsan, Korea
| | - Seung-Hoon Lee
- Specific Organs Cancer Branch, Research Institute, National Cancer Center, Ilsan, Korea
| | - Daesoo Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jong Bae Park
- Specific Organs Cancer Branch, Research Institute, National Cancer Center, Ilsan, Korea
- * E-mail: (JHK); (JBP)
| | - Jong Heon Kim
- Carcinogenesis Branch, Research Institute, National Cancer Center, Ilsan, Korea
- * E-mail: (JHK); (JBP)
| |
Collapse
|
24
|
Kawahara H, Okada Y, Imai T, Iwanami A, Mischel PS, Okano H. Musashi1 cooperates in abnormal cell lineage protein 28 (Lin28)-mediated let-7 family microRNA biogenesis in early neural differentiation. J Biol Chem 2011; 286:16121-30. [PMID: 21378162 DOI: 10.1074/jbc.m110.199166] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Musashi1 (Msi1) is an RNA-binding protein that is highly expressed in neural stem/progenitor cells (NS/PCs) as well as in other tissue stem cells. Msi1 binds to the 3'-UTR of its target mRNAs in NS/PCs, prevents their translation, and interferes with NS/PC differentiation. We previously showed that Msi1 competes with eIF4G to bind poly(A)-binding protein and inhibits assembly of the 80 S ribosome. Here we show that Msi1 works in concert with Lin28 to regulate post-transcriptional microRNA (miRNA) biogenesis in the cropping step, which occurs in the nucleus. Lin28 and its binding partner terminal uridylyltransferase 4 (TUT4) are known to maintain embryonic stem cell pluripotency by blocking let-7 miRNA biogenesis at the dicing step. Interestingly, we found that during early neural differentiation of embryonic stem cells, Msi1 enhanced the localization of Lin28 to the nucleus and also inhibited the nuclear cropping step of another let-7 family miRNA, miR98. These results suggest that Msi1 can influence stem cell maintenance and differentiation by controlling the subcellular localization of proteins involved in miRNA biogenesis, as well as by regulating the translation of its target mRNA.
Collapse
Affiliation(s)
- Hironori Kawahara
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | | | | | | | | | | |
Collapse
|
25
|
Beisel CL, Chen YY, Culler SJ, Hoff KG, Smolke CD. Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing. Nucleic Acids Res 2010; 39:2981-94. [PMID: 21149259 PMCID: PMC3074164 DOI: 10.1093/nar/gkq954] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are prevalent regulatory RNAs that mediate gene silencing and play key roles in diverse cellular processes. While synthetic RNA-based regulatory systems that integrate regulatory and sensing functions have been demonstrated, the lack of detail on miRNA structure–function relationships has limited the development of integrated control systems based on miRNA silencing. Using an elucidated relationship between Drosha processing and the single-stranded nature of the miRNA basal segments, we developed a strategy for designing ligand-responsive miRNAs. We demonstrate that ligand binding to an aptamer integrated into the miRNA basal segments inhibits Drosha processing, resulting in titratable control over gene silencing. The generality of this control strategy was shown for three aptamer–small molecule ligand pairs. The platform can be extended to the design of synthetic miRNAs clusters, cis-acting miRNAs and self-targeting miRNAs that act both in cis and trans, enabling fine-tuning of the regulatory strength and dynamics. The ability of our ligand-responsive miRNA platform to respond to user-defined inputs, undergo regulatory performance tuning and display scalable combinatorial control schemes will help advance applications in biological research and applied medicine.
Collapse
Affiliation(s)
- Chase L Beisel
- Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | | | | |
Collapse
|
26
|
Chong MMW, Zhang G, Cheloufi S, Neubert TA, Hannon GJ, Littman DR. Canonical and alternate functions of the microRNA biogenesis machinery. Genes Dev 2010; 24:1951-60. [PMID: 20713509 DOI: 10.1101/gad.1953310] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The canonical microRNA (miRNA) biogenesis pathway requires two RNaseIII enzymes: Drosha and Dicer. To understand their functions in mammals in vivo, we engineered mice with germline or tissue-specific inactivation of the genes encoding these two proteins. Changes in proteomic and transcriptional profiles that were shared in Dicer- and Drosha-deficient mice confirmed the requirement for both enzymes in canonical miRNA biogenesis. However, deficiency in Drosha or Dicer did not always result in identical phenotypes, suggesting additional functions. We found that, in early-stage thymocytes, Drosha recognizes and directly cleaves many protein-coding messenger RNAs (mRNAs) with secondary stem-loop structures. In addition, we identified a subset of miRNAs generated by a Dicer-dependent but Drosha-independent mechanism. These were distinct from previously described mirtrons. Thus, in mammalian cells, Dicer is required for the biogenesis of multiple classes of miRNAs. Together, these findings extend the range of function of RNaseIII enzymes beyond canonical miRNA biogenesis, and help explain the nonoverlapping phenotypes caused by Drosha and Dicer deficiency.
Collapse
Affiliation(s)
- Mark M W Chong
- Molecular Pathogenesis Program, Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York 10016, USA.
| | | | | | | | | | | |
Collapse
|
27
|
Abstract
MicroRNAs (miRNAs) are 18- to 24-nt RNA molecules that regulate messenger RNAs (mRNAs). Posttranscriptional mechanisms regulate miRNA abundance during development as well as in cancer cells where miRNAs frequently exhibit dysregulated expression. The molecular mechanisms that govern the global efficiency of miRNA biogenesis in these settings remain incompletely understood, and experimental systems for the biochemical dissection of these pathways are currently lacking. Here, we demonstrate that miRNAs are subject to dynamic posttranscriptional regulation in widely used cell culture systems. As diverse mammalian and Drosophila cell lines are grown to increasing density, miRNA biogenesis is globally activated, leading to elevated mature miRNA levels and stronger repression of target constructs. This broad increase in miRNA abundance is associated with enhanced processing of miRNAs by Drosha and more efficient formation of RNA-induced silencing complexes. These findings uncover a critical parameter necessary for accurate analysis of miRNAs in cell culture settings, establish a tractable system for the study of regulated miRNA biogenesis, and may provide insight into mechanisms that influence miRNA expression in physiologic and pathophysiologic states.
Collapse
|
28
|
Meng W, Nicholson RH, Nathania L, Pertzev AV, Nicholson AW. New approaches to understanding double-stranded RNA processing by ribonuclease III purification and assays of homodimeric and heterodimeric forms of RNase III from bacterial extremophiles and mesophiles. Methods Enzymol 2009; 447:119-29. [PMID: 19161841 DOI: 10.1016/s0076-6879(08)02207-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Ribonuclease III (RNase III) is a double-stranded (ds)-RNA-specific endonuclease that plays essential roles in the maturation and decay of coding and noncoding RNAs. Bacterial RNases III are structurally the simplest members of the RNase III family, which includes the eukaryotic orthologs Dicer and Drosha. High-resolution crystal structures of RNase III of the hyperthermophilic bacteria Aquifex aeolicus and Thermotoga maritima are available. A. aeolicus RNase III also has been cocrystallized with dsRNA or specific hairpin substrates. These structures have provided essential structural insight to the mechanism of dsRNA recognition and cleavage. However, comparatively little is known about the catalytic behaviors of A. aeolicus or T. maritima RNases III. This chapter provides protocols for the purification of A. aeolicus and T. maritima RNases III and also describes the preparation of artificial heterodimers of Escherichia coli RNase III, which are providing new insight on the subunit and domain interactions involved in dsRNA recognition and cleavage.
Collapse
Affiliation(s)
- Wenzhao Meng
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, USA
| | | | | | | | | |
Collapse
|
29
|
Establishment of cells to monitor Microprocessor through fusion genes of microRNA and GFP. Biochem Biophys Res Commun 2008; 372:856-61. [PMID: 18533106 DOI: 10.1016/j.bbrc.2008.05.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 05/23/2008] [Indexed: 01/07/2023]
Abstract
Microprocessor, the complex of Drosha and DGCR8, promotes the processing of primary microRNA to precursor microRNA, which is a crucial step for microRNA maturation. So far, no convenient assay systems have been developed for observing this step in vivo. Here we report the establishment of highly sensitive cellular systems where we can visually monitor the function of Microprocessor. During a series of screening of transfectants with fusion genes of the EGFP cDNA and primary microRNA genes, we have obtained certain cell lines where introduction of siRNA against DGCR8 or Drosha strikingly augments GFP signals. In contrast, these cells have not responded to Dicer siRNA; thus they have a unique character that GFP signals should be negatively and specifically correlated to the action of Microprocessor among biogenesis of microRNA. These cell lines can be useful tools for real-time analysis of Microprocessor action in vivo and identifying its novel modulators.
Collapse
|