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Zhou X, Wen M, Zhang J, Long K, Lu L, Jin L, Sun J, Ge L, Li X, Li M, Ma J. Unveiling the Regulatory Role of LncRNA MYU in Hypoxia-Induced Angiogenesis via the miR-23a-3p Axis in Endothelial Cells. Cells 2024; 13:1198. [PMID: 39056780 PMCID: PMC11275003 DOI: 10.3390/cells13141198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/08/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Background: Angiogenesis is essential for various physiological and pathological processes, such as embryonic development and cancer cell proliferation, migration, and invasion. Long noncoding RNAs (lncRNAs) play pivotal roles in normal homeostasis and disease processes by regulating gene expression through various mechanisms, including competing endogenous RNAs (ceRNAs) of target microRNAs (miRNAs). The lncRNA MYU is known to promote prostate cancer proliferation via the miR-184/c-Myc regulatory axis and to be upregulated in vascular endothelial cells under hypoxic conditions, which often occurs in solid tumors. In the present study, we investigated whether MYU might affect cancer growth by regulating angiogenesis in vascular endothelial cells under hypoxia. Methods: The expression of MYU-regulated miR-23a-3p and interleukin-8 (IL-8) in HUVEC cell lines was examined using qRT-PCR. The CCK-8 assay, EdU assay, wound-healing assay, and tube-formation assay were used to assess the effects of MYU on cell proliferation, migration, and tube formation of HUVEC cells in vitro. The dual-luciferase reporter assay was performed to examine the effects of miR-23a-3p on MYU and IL-8 expression. Results: We found that the overexpression of MYU and knockdown of miR-23a-3p in human umbilical vein endothelial cells (HUVECs) under hypoxia promoted cell proliferation, migration, and tube formation. Mechanistically, MYU was shown to bind competitively to miR-23a-3p, thereby preventing miR-23a-3p binding to the 3' untranslated region of IL-8 mRNA. In turn, increased production of pro-angiogenic IL-8 promoted HUVEC proliferation, migration, and tube formation under hypoxia. Conclusion: This study identified a new role for lncRNA MYU as a ceRNA for miR-23a-3p and uncovered a novel MYU-miR-23a-3p-IL-8 regulatory axis for angiogenesis. MYU and/or miR-23a-3p may thus represent new targets for the treatment of hypoxia-related diseases by promoting angiogenesis.
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Affiliation(s)
- Xiankun Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (M.W.); (K.L.); (L.L.); (L.J.); (X.L.); (M.L.)
| | - Mingxing Wen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (M.W.); (K.L.); (L.L.); (L.J.); (X.L.); (M.L.)
| | - Jinwei Zhang
- Chongqing Academy of Animal Sciences, Chongqing 402460, China; (J.Z.); (J.S.); (L.G.)
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing 402460, China
- Chongqing Key Laboratory of Pig Industry Sciences, Chongqing 402460, China
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (M.W.); (K.L.); (L.L.); (L.J.); (X.L.); (M.L.)
| | - Lu Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (M.W.); (K.L.); (L.L.); (L.J.); (X.L.); (M.L.)
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (M.W.); (K.L.); (L.L.); (L.J.); (X.L.); (M.L.)
| | - Jing Sun
- Chongqing Academy of Animal Sciences, Chongqing 402460, China; (J.Z.); (J.S.); (L.G.)
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing 402460, China
- Chongqing Key Laboratory of Pig Industry Sciences, Chongqing 402460, China
| | - Liangpeng Ge
- Chongqing Academy of Animal Sciences, Chongqing 402460, China; (J.Z.); (J.S.); (L.G.)
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing 402460, China
- Chongqing Key Laboratory of Pig Industry Sciences, Chongqing 402460, China
| | - Xuewei Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (M.W.); (K.L.); (L.L.); (L.J.); (X.L.); (M.L.)
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (M.W.); (K.L.); (L.L.); (L.J.); (X.L.); (M.L.)
| | - Jideng Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (M.W.); (K.L.); (L.L.); (L.J.); (X.L.); (M.L.)
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2
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Brown SD, Klimi E, Bakker WAM, Beqqali A, Baker AH. Non-coding RNAs to treat vascular smooth muscle cell dysfunction. Br J Pharmacol 2024. [PMID: 38773733 DOI: 10.1111/bph.16409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/19/2024] [Accepted: 03/14/2024] [Indexed: 05/24/2024] Open
Abstract
Vascular smooth muscle cell (vSMC) dysfunction is a critical contributor to cardiovascular diseases, including atherosclerosis, restenosis and vein graft failure. Recent advances have unveiled a fascinating range of non-coding RNAs (ncRNAs) that play a pivotal role in regulating vSMC function. This review aims to provide an in-depth analysis of the mechanisms underlying vSMC dysfunction and the therapeutic potential of various ncRNAs in mitigating this dysfunction, either preventing or reversing it. We explore the intricate interplay of microRNAs, long-non-coding RNAs and circular RNAs, shedding light on their roles in regulating key signalling pathways associated with vSMC dysfunction. We also discuss the prospects and challenges associated with developing ncRNA-based therapies for this prevalent type of cardiovascular pathology.
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Affiliation(s)
- Simon D Brown
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Eftychia Klimi
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Abdelaziz Beqqali
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew H Baker
- BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht, The Netherlands
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3
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Fantone S, Piani F, Olivieri F, Rippo MR, Sirico A, Di Simone N, Marzioni D, Tossetta G. Role of SLC7A11/xCT in Ovarian Cancer. Int J Mol Sci 2024; 25:587. [PMID: 38203758 PMCID: PMC10779187 DOI: 10.3390/ijms25010587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Ovarian cancer is one of the most dangerous gynecologic cancers worldwide and has a high fatality rate due to diagnosis at an advanced stage of the disease as well as a high recurrence rate due to the occurrence of chemotherapy resistance. In fact, chemoresistance weakens the therapeutic effects, worsening the outcome of this pathology. Solute Carrier Family 7 Member 11 (SLC7A11, also known as xCT) is the functional subunit of the Xc- system, an anionic L-cystine/L-glutamate antiporter expressed on the cell surface. SLC7A11 expression is significantly upregulated in several types of cancers in which it can inhibit ferroptosis and favor cancer cell proliferation, invasion and chemoresistance. SLC7A11 expression is also increased in ovarian cancer tissues, suggesting a possible role of this protein as a therapeutic target. In this review, we provide an overview of the current literature regarding the role of SLC7A11 in ovarian cancer to provide new insights on SLC7A11 modulation and evaluate the potential role of SLC7A11 as a therapeutic target.
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Affiliation(s)
- Sonia Fantone
- Scientific Direction, IRCCS INRCA, 60124 Ancona, Italy; (S.F.); (F.O.)
| | - Federica Piani
- Hypertension and Cardiovascular Risk Research Center, Medical and Surgical Sciences Department, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy;
| | - Fabiola Olivieri
- Scientific Direction, IRCCS INRCA, 60124 Ancona, Italy; (S.F.); (F.O.)
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, 60126 Ancona, Italy;
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, 60126 Ancona, Italy;
| | - Angelo Sirico
- Obstetrics and Gynecology Unit, Sant’Anna e San Sebastiano Hospital, 81100 Caserta, Italy;
| | - Nicoletta Di Simone
- Department of Biomedical Sciences, Humanitas University, 20072 Milan, Italy;
- IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Daniela Marzioni
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60126 Ancona, Italy;
| | - Giovanni Tossetta
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60126 Ancona, Italy;
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4
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Sivasankar C, Hewawaduge C, Muthuramalingam P, Lee JH. Tumor-targeted delivery of lnc antisense RNA against RCAS1 by live-attenuated tryptophan-auxotrophic Salmonella inhibited 4T1 breast tumors and metastasis in mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102053. [PMID: 37941832 PMCID: PMC10628790 DOI: 10.1016/j.omtn.2023.102053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
Abstract
Emerging chemo- and radiotherapy resistance exacerbated the cancer risk and necessitated novel treatment strategies. Although RNA therapeutics against pro-oncogenic genes are highly effective, tumor-specific delivery remains a barrier to the implementation of this valuable tool. In this study, we report a tryptophan-auxotrophic Salmonella typhimurium strain as an onco-therapeutic delivery system with tumor-targeting ability using 4T1 mice breast-cancer model. The receptor-binding cancer antigen expressed on SiSo cell (RCAS1) is a cancer-specific protein that induces the apoptosis of peripheral lymphocytes and confers tumor immune evasion. We designed a long non-coding antisense-RNA against RCAS1 (asRCAS1) and delivered by Salmonella using a non-antibiotic, auxotrophic-selective, eukaryotic expression plasmid, pJHL204. After in vivo tumor-to-tumor passaging, the JOL2888 (ΔtrpA, ΔtrpE, Δasd + asRCAS1) strain exhibited high sustainability in tumors, but did not last in healthy organs, thereby demonstrating tumor specificity and safety. RCAS1 inhibition in the tumor was confirmed by western blotting and qPCR. In mice, JOL2888 treatment reduced tumor-associated macrophages, improved the T cell population, elicited cell-mediated immunity, and suppressed cancer-promoting genes. Consequently, the JOL2888 treatment significantly decreased the tumor volume by 80%, decreased splenomegaly by 30%, and completely arrested lung metastasis. These findings highlight the intrinsic tumor-targeting ability of tryptophan-auxotrophic Salmonella for delivering onco-therapeutic macromolecules.
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Affiliation(s)
- Chandran Sivasankar
- College of Veterinary Medicine, Jeonbuk National University, Iksan Campus 54596, Republic of Korea
| | - Chamith Hewawaduge
- College of Veterinary Medicine, Jeonbuk National University, Iksan Campus 54596, Republic of Korea
| | | | - John Hwa Lee
- College of Veterinary Medicine, Jeonbuk National University, Iksan Campus 54596, Republic of Korea
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5
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Bravo‐Estupiñan DM, Aguilar‐Guerrero K, Quirós S, Acón M, Marín‐Müller C, Ibáñez‐Hernández M, Mora‐Rodríguez RA. Gene dosage compensation: Origins, criteria to identify compensated genes, and mechanisms including sensor loops as an emerging systems-level property in cancer. Cancer Med 2023; 12:22130-22155. [PMID: 37987212 PMCID: PMC10757140 DOI: 10.1002/cam4.6719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
The gene dosage compensation hypothesis presents a mechanism through which the expression of certain genes is modulated to compensate for differences in the dose of genes when additional chromosomes are present. It is one of the means through which cancer cells actively cope with the potential damaging effects of aneuploidy, a hallmark of most cancers. Dosage compensation arises through several processes, including downregulation or overexpression of specific genes and the relocation of dosage-sensitive genes. In cancer, a majority of compensated genes are generally thought to be regulated at the translational or post-translational level, and include the basic components of a compensation loop, including sensors of gene dosage and modulators of gene expression. Post-translational regulation is mostly undertaken by a general degradation or aggregation of remaining protein subunits of macromolecular complexes. An increasingly important role has also been observed for transcriptional level regulation. This article reviews the process of targeted gene dosage compensation in cancer and other biological conditions, along with the mechanisms by which cells regulate specific genes to restore cellular homeostasis. These mechanisms represent potential targets for the inhibition of dosage compensation of specific genes in aneuploid cancers. This article critically examines the process of targeted gene dosage compensation in cancer and other biological contexts, alongside the criteria for identifying genes subject to dosage compensation and the intricate mechanisms by which cells orchestrate the regulation of specific genes to reinstate cellular homeostasis. Ultimately, our aim is to gain a comprehensive understanding of the intricate nature of a systems-level property. This property hinges upon the kinetic parameters of regulatory motifs, which we have termed "gene dosage sensor loops." These loops have the potential to operate at both the transcriptional and translational levels, thus emerging as promising candidates for the inhibition of dosage compensation in specific genes. Additionally, they represent novel and highly specific therapeutic targets in the context of aneuploid cancer.
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Affiliation(s)
- Diana M. Bravo‐Estupiñan
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Programa de Doctorado en Ciencias, Sistema de Estudios de Posgrado (SEP)Universidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Karol Aguilar‐Guerrero
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Maestría académica en Microbiología, Programa de Posgrado en Microbiología, Parasitología, Química Clínica e InmunologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Steve Quirós
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Man‐Sai Acón
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
| | - Christian Marín‐Müller
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Miguel Ibáñez‐Hernández
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
| | - Rodrigo A. Mora‐Rodríguez
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
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6
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Nuclear microRNAs release paused Pol II via the DDX21-CDK9 complex. Cell Rep 2022; 39:110673. [PMID: 35417682 DOI: 10.1016/j.celrep.2022.110673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/26/2021] [Accepted: 03/22/2022] [Indexed: 11/22/2022] Open
Abstract
RNA activation (RNAa) is an uncharacterized mechanism of transcriptional activation mediated by small RNAs, such as microRNAs (miRNAs). A critical issue in RNAa research is that it is difficult to distinguish between changes in gene expression caused indirectly by post-transcriptional regulation and direct induction of gene expression by RNAa. Therefore, in this study, we seek to identify a key factor involved in RNAa, using the induction of ZMYND10 by miR-34a as a system to evaluate RNAa. We identify the positive transcription elongation factors CDK9 and DDX21, which form a complex with nuclear AGO and TNRC6A, as important transcriptional activators of RNAa. In addition, we find that inhibition of DDX21 suppresses RNAa by miR-34a and other miRNAs without inhibiting post-transcriptional regulation. Our findings reveal a strong connection between RNAa and release of paused Pol II, facilitating RNAa research by making it possible to separately analyze post-transcriptional regulation and RNAa.
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7
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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8
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Abstract
Cerebral ischemic injury may lead to a series of serious brain diseases, death or different degrees of disability. Hypoxia-inducible factor-1α (HIF-1α) is an oxygen-sensitive transcription factor, which mediates the adaptive metabolic response to hypoxia and serves a key role in cerebral ischemia. HIF-1α is the main molecule that responds to hypoxia. HIF-1α serves an important role in the development of cerebral ischemia by participating in numerous processes, including metabolism, proliferation and angiogenesis. The present review focuses on the endogenous protective mechanism of cerebral ischemia and elaborates on the role of HIF-1α in cerebral ischemia. In addition, it focuses on cerebral ischemia interventions that act on the HIF-1α target, including biological factors, non-coding RNA, hypoxic-ischemic preconditioning and drugs, and expands upon the measures to strengthen the endogenous compensatory response to support HIF-1α as a therapeutic target, thus providing novel suggestions for the treatment of cerebral ischemia.
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Affiliation(s)
- Peiliang Dong
- Institute of Traditional Chinese Medicine, Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang 150040, P.R. China
| | - Qingna Li
- College of Pharmacy, Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang 150040, P.R. China
| | - Hua Han
- College of Pharmacy, Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang 150040, P.R. China
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9
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Chu Y, Yokota S, Liu J, Kilikevicius A, Johnson KC, Corey DR. Argonaute binding within human nuclear RNA and its impact on alternative splicing. RNA (NEW YORK, N.Y.) 2021; 27:991-1003. [PMID: 34108230 PMCID: PMC8370746 DOI: 10.1261/rna.078707.121] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/04/2021] [Indexed: 05/03/2023]
Abstract
Mammalian RNA interference (RNAi) is often linked to the regulation of gene expression in the cytoplasm. Synthetic RNAs, however, can also act through the RNAi pathway to regulate transcription and splicing. While nuclear regulation by synthetic RNAs can be robust, a critical unanswered question is whether endogenous functions for nuclear RNAi exist in mammalian cells. Using enhanced crosslinking immunoprecipitation (eCLIP) in combination with RNA sequencing (RNA-seq) and multiple AGO knockout cell lines, we mapped AGO2 protein binding sites within nuclear RNA. The strongest AGO2 binding sites were mapped to micro RNAs (miRNAs). The most abundant miRNAs were distributed similarly between the cytoplasm and nucleus, providing no evidence for mechanisms that facilitate localization of miRNAs in one compartment versus the other. Beyond miRNAs, most statistically significant AGO2 binding was within introns. Splicing changes were confirmed by RT-PCR and recapitulated by synthetic miRNA mimics complementary to the sites of AGO2 binding. These data support the hypothesis that miRNAs can control gene splicing. While nuclear RNAi proteins have the potential to be natural regulatory mechanisms, careful study will be necessary to identify critical RNA drivers of normal physiology and disease.
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Affiliation(s)
- Yongjun Chu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Shinnichi Yokota
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Jing Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Audrius Kilikevicius
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
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10
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Phosphorylation of Ago2 is required for its role in DNA double-strand break repair. J Genet Genomics 2021; 48:333-340. [PMID: 34039517 DOI: 10.1016/j.jgg.2021.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/09/2021] [Accepted: 03/13/2021] [Indexed: 11/21/2022]
Abstract
Repair of DNA double-strand break (DSB) is critical for the maintenance of genome integrity. A class of DSB-induced small RNAs (diRNAs) has been shown to play an important role in DSB repair. In humans, diRNAs are associated with Ago2 and guide the recruitment of Rad51 to DSB sites to facilitate repair by homologous recombination (HR). Ago2 activity has been reported to be regulated by phosphorylation under normal and hypoxic conditions. However, the role of Ago2 phosphorylation in DNA damage repair is unexplored. Here, we show that S672, S828, T830, and S831 of human Ago2 are phosphorylated in response to ionizing radiation (IR). S672A mutation of Ago2 leads to significant reduction in Rad51 foci formation and HR efficiency. We further show that defective association of Ago2 S672A variant with DSB sites, instead of defects in diRNA and Rad51 binding, may account for decreased Rad51 foci formation and HR efficiency. Our study reveals a novel regulatory mechanism for the function of Ago2 in DNA repair.
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11
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Ghanbarian H, Aghamiri S, Eftekhary M, Wagner N, Wagner KD. Small Activating RNAs: Towards the Development of New Therapeutic Agents and Clinical Treatments. Cells 2021; 10:cells10030591. [PMID: 33800164 PMCID: PMC8001863 DOI: 10.3390/cells10030591] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
Small double-strand RNA (dsRNA) molecules can activate endogenous genes via an RNA-based promoter targeting mechanism. RNA activation (RNAa) is an evolutionarily conserved mechanism present in diverse eukaryotic organisms ranging from nematodes to humans. Small activating RNAs (saRNAs) involved in RNAa have been successfully used to activate gene expression in cultured cells, and thereby this emergent technique might allow us to develop various biotechnological applications, without the need to synthesize hazardous construct systems harboring exogenous DNA sequences. Accordingly, this thematic issue aims to provide insights into how RNAa cellular machinery can be harnessed to activate gene expression leading to a more effective clinical treatment of various diseases.
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MESH Headings
- Animals
- Brain/cytology
- Brain/growth & development
- Brain/metabolism
- Genetic Therapy/methods
- Humans
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Muscle Development/genetics
- Muscular Atrophy, Spinal/genetics
- Muscular Atrophy, Spinal/metabolism
- Muscular Atrophy, Spinal/pathology
- Muscular Atrophy, Spinal/therapy
- Myocardium/cytology
- Myocardium/metabolism
- Myocytes, Cardiac/cytology
- Myocytes, Cardiac/metabolism
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Neoplasms/therapy
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Neurogenesis/genetics
- Neurons/cytology
- Neurons/metabolism
- Promoter Regions, Genetic
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Double-Stranded/therapeutic use
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA, Small Untranslated/therapeutic use
- Survival of Motor Neuron 1 Protein/genetics
- Survival of Motor Neuron 1 Protein/metabolism
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Affiliation(s)
- Hossein Ghanbarian
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran 19857-17443, Iran;
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran;
| | - Shahin Aghamiri
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran;
| | - Mohamad Eftekhary
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran;
| | - Nicole Wagner
- Université Côte d’Azur, CNRS, INSERM, iBV, 06107 Nice, France
- Correspondence: (N.W.); (K.-D.W.); Tel.: +33-493-3776-65 (K.-D.W.)
| | - Kay-Dietrich Wagner
- Université Côte d’Azur, CNRS, INSERM, iBV, 06107 Nice, France
- Correspondence: (N.W.); (K.-D.W.); Tel.: +33-493-3776-65 (K.-D.W.)
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12
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Catellani C, Ravegnini G, Sartori C, Angelini S, Street ME. GH and IGF System: The Regulatory Role of miRNAs and lncRNAs in Cancer. Front Endocrinol (Lausanne) 2021; 12:701246. [PMID: 34484116 PMCID: PMC8415755 DOI: 10.3389/fendo.2021.701246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Growth hormone (GH) and the insulin-like growth factor (IGF) system are involved in many biological processes and have growth-promoting actions regulating cell proliferation, differentiation, apoptosis and angiogenesis. A recent chapter in epigenetics is represented by microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) which regulate gene expression. Dysregulated miRNAs and lncRNAs have been associated with several diseases including cancer. Herein we report the most recent findings concerning miRNAs and lncRNAs regulating GH and the IGF system in the context of pituitary adenomas, osteosarcoma and colorectal cancer, shedding light on new possible therapeutic targets. Pituitary adenomas are increasingly common intracranial tumors and somatotroph adenomas determine supra-physiological GH secretion and cause acromegaly. Osteosarcoma is the most frequent bone tumor in children and adolescents and was reported in adults who were treated with GH in childhood. Colorectal cancer is the third cancer in the world and has a higher prevalence in acromegalic patients.
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Affiliation(s)
- Cecilia Catellani
- Department of Mother and Child, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
- PhD Program in Clinical and Experimental Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Gloria Ravegnini
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, Italy
| | - Chiara Sartori
- Department of Mother and Child, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Sabrina Angelini
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, Italy
| | - Maria E. Street
- Department of Mother and Child, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
- *Correspondence: Maria E. Street,
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13
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Zhang S, Zhang W, Li Y, Ren L, Deng H, Yin X, Gao X, Pan S, Niu Y. Cotransplantation of human umbilical cord mesenchymal stem cells and endothelial cells for angiogenesis and pulp regeneration in vivo. Life Sci 2020; 255:117763. [PMID: 32389831 DOI: 10.1016/j.lfs.2020.117763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023]
Abstract
AIMS To explored the potential of human umbilical cord mesenchymal stem cells (hUCMSCs) as seed cells for dental pulp regeneration and the possibility of cotransplantation hUCMSCs and endothelial cells (ECs) for angiogenesis and pulp regeneration in vivo. MATERIALS AND METHODS hUCMSCs and human umbilical vein endothelial cells (HUVECs) were cocultured for matrigel angiogenesis assay in vitro and Matrigel plug assay in vivo. Next, we used the transwell coculture system to coculture hUCMSCs and HUVECs in vitro for RNA- sequencing (RNA-seq). Last, encapsulated hUCMSCs and HUVECs in scaffolds were injected into the root segments, and transplanted into immunodeficient mice for dental pulp regeneration. KEY FINDINGS In vitro Matrigel angiogenesis assay and in vivo Matrigel plug assay indicated that cocultured hUCMSCs and HUVECs promote vascular formation of HUVECs, especially in 1:5 (hUCMSCs:HUVECs) coculture group. The RNA-seq result indicated that cocultured HUVECs exhibited high Hif-1 signaling pathway activity. We performed the cell transfection assay to knock down HIF1A-AS2 in HUVECs and then coculture with hUCMSCs, and the expression of VEGFA, HIF1A and PECAM1 were reduced. In pulp regeneration assay, Cotransplantation of hUCMSCs and HUVECs (1,5) group showed pulp-like tissue regeneration. SIGNIFICANCE Cocultured hUCMSCs and HUVECs can promote vascular formation of HUVECs, and the optimal coculture ration is 1:5 (hUCMSCs:HUVECs). hUCMSCs promote angiogenesis of HUVECs through the long noncoding RNA HIF1A-AS2-activation of the Hif-1 signaling pathway. Cotransplantation of hUCMSCs and HUVECs can regenerate dental pulp-like tissue in vivo.
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Affiliation(s)
- Shuang Zhang
- The First Affiliated Hospital of Harbin Medical University, No. 23 Youzheng Street, Nangang District, Harbin 150001, China; Department of Endodontics, School of Stomatology, Harbin Medical University, No. 143 Yiman Street, Nangang District, Harbin 150001, China
| | - Weiwei Zhang
- The First Affiliated Hospital of Harbin Medical University, No. 23 Youzheng Street, Nangang District, Harbin 150001, China; Department of Endodontics, School of Stomatology, Harbin Medical University, No. 143 Yiman Street, Nangang District, Harbin 150001, China
| | - Yanping Li
- The First Affiliated Hospital of Harbin Medical University, No. 23 Youzheng Street, Nangang District, Harbin 150001, China; Department of Endodontics, School of Stomatology, Harbin Medical University, No. 143 Yiman Street, Nangang District, Harbin 150001, China
| | - Liping Ren
- Department of Prosthodontics, The First Affiliated Hospital of Harbin Medical University, No. 143 Yiman Street, Nangang District, Harbin 150001, China
| | - Haotian Deng
- The First Affiliated Hospital of Harbin Medical University, No. 23 Youzheng Street, Nangang District, Harbin 150001, China; Department of Endodontics, School of Stomatology, Harbin Medical University, No. 143 Yiman Street, Nangang District, Harbin 150001, China
| | - Xiaowei Yin
- The First Affiliated Hospital of Harbin Medical University, No. 23 Youzheng Street, Nangang District, Harbin 150001, China; Department of Endodontics, School of Stomatology, Harbin Medical University, No. 143 Yiman Street, Nangang District, Harbin 150001, China
| | - Xu Gao
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin 150081, China
| | - Shuang Pan
- The First Affiliated Hospital of Harbin Medical University, No. 23 Youzheng Street, Nangang District, Harbin 150001, China; Department of Endodontics, School of Stomatology, Harbin Medical University, No. 143 Yiman Street, Nangang District, Harbin 150001, China.
| | - Yumei Niu
- The First Affiliated Hospital of Harbin Medical University, No. 23 Youzheng Street, Nangang District, Harbin 150001, China; Department of Endodontics, School of Stomatology, Harbin Medical University, No. 143 Yiman Street, Nangang District, Harbin 150001, China.
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14
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Asa'ad F, Monje A, Larsson L. Role of epigenetics in alveolar bone resorption and regeneration around periodontal and peri‐implant tissues. Eur J Oral Sci 2019; 127:477-493. [DOI: 10.1111/eos.12657] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Farah Asa'ad
- Institute of Odontology The Sahlgrenska Academy University of Gothenburg Göteborg Sweden
| | - Alberto Monje
- Department of Oral Surgery and Stomatology ZMK School of Dentistry Bern Switzerland
- Department of Periodontology Universitat Internacional de Catalunya Barcelona Spain
| | - Lena Larsson
- Department of Periodontology Institute of Odontology University of Gothenburg Göteborg Sweden
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15
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Melia T, Waxman DJ. Sex-Biased lncRNAs Inversely Correlate With Sex-Opposite Gene Coexpression Networks in Diversity Outbred Mouse Liver. Endocrinology 2019; 160:989-1007. [PMID: 30840070 PMCID: PMC6449536 DOI: 10.1210/en.2018-00949] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/27/2019] [Indexed: 01/05/2023]
Abstract
Sex differences in liver gene expression are determined by pituitary growth hormone secretion patterns, which regulate sex-dependent liver transcription factors and establish sex-specific chromatin states. Hypophysectomy (hypox) identifies two major classes of liver sex-biased genes, defined by their sex-dependent positive or negative responses to pituitary hormone ablation. However, the mechanisms that underlie each hypox-response class are unknown. We sought to discover candidate, regulatory, long noncoding RNAs (lncRNAs) controlling responsiveness to hypox. We characterized gene structures and expression patterns for 15,558 mouse liver-expressed lncRNAs, including many sex-specific lncRNAs regulated during postnatal development or subject to circadian regulation. Using the high natural allelic variance of Diversity Outbred (DO) mice, we discovered tightly coexpressed clusters of sex-specific protein-coding genes (gene modules) in male and female DO liver. Remarkably, many gene modules were strongly enriched for sex-specific genes within a single hypox-response class, indicating that the genetic heterogeneity of DO mice encompasses responsiveness to hypox. Moreover, several distant gene modules were enriched for gene subsets of the same hypox-response class, highlighting the complex regulation of hypox-responsiveness. Finally, we identified eight sex-specific lncRNAs with strong negative regulatory potential, as indicated by their strong negative correlation of expression across DO mouse livers with that of protein-coding gene modules enriched for genes of the opposite sex bias and inverse hypox-response class. These findings reveal an important role for genetic factors in regulating responsiveness to hypox, and present testable hypotheses for the roles of sex-biased liver lncRNAs in controlling the sex-bias of liver gene expression.
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Affiliation(s)
- Tisha Melia
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts
- Correspondence: David J. Waxman, PhD, Department of Biology, Boston University, 5 Cummington Mall, Boston, Massachusetts 02215. E-mail:
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16
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Sun T, Wang K, Liu C, Wang Y, Wang J, Li P. Identification of Extrachromosomal Linear microDNAs Interacted with microRNAs in the Cell Nuclei. Cells 2019; 8:cells8020111. [PMID: 30717295 PMCID: PMC6406244 DOI: 10.3390/cells8020111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/17/2019] [Accepted: 01/31/2019] [Indexed: 01/20/2023] Open
Abstract
Extrachromosomal DNA exists in two forms: Covalently closed circular and linear. While diverse types of circular extrachromosomal DNA have been identified with validated in vivo functions, little is known about linear extrachromosomal DNA. In this study, we identified small, single-stranded linear extrachromosomal DNAs (SSLmicroDNAs) in the nuclei of mouse hearts, mouse brains, HEK293, and HeLa cells. We used a pull-down system based on the single-stranded DNA binding protein RecAf. We found that SSLmicroDNAs aligned predominantly to intergenic and intragenic regions of the genome, owned a variety of single nucleotide polymorphism sites, and strongly associated with H3K27Ac marks. The regions were tens to hundreds of nucleotides long, periodically separated by AT, TT, or AA dinucleotides. It has been demonstrated that SSLmicroDNAs in the nuclei of normal cells target microRNAs, which regulate biological processes. In summary, our present work identified a new form of extrachromosomal DNAs, which function inside nuclei and interact with microRNAs. This finding provides a possible research field into the function of extrachromosomal DNA.
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Affiliation(s)
- Teng Sun
- Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan 030001, China.
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China.
| | - Kun Wang
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
| | - Cuiyun Liu
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
| | - Yin Wang
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
| | - Jianxun Wang
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao, China.
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17
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Barman P, Reddy D, Bhaumik SR. Mechanisms of Antisense Transcription Initiation with Implications in Gene Expression, Genomic Integrity and Disease Pathogenesis. Noncoding RNA 2019; 5:ncrna5010011. [PMID: 30669611 PMCID: PMC6468509 DOI: 10.3390/ncrna5010011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/01/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Non-coding antisense transcripts arise from the strand opposite the sense strand. Over 70% of the human genome generates non-coding antisense transcripts while less than 2% of the genome codes for proteins. Antisense transcripts and/or the act of antisense transcription regulate gene expression and genome integrity by interfering with sense transcription and modulating histone modifications or DNA methylation. Hence, they have significant pathological and physiological relevance. Indeed, antisense transcripts were found to be associated with various diseases including cancer, diabetes, cardiac and neurodegenerative disorders, and, thus, have promising potentials for prognostic and diagnostic markers and therapeutic development. However, it is not clearly understood how antisense transcription is initiated and epigenetically regulated. Such knowledge would provide new insights into the regulation of antisense transcription, and hence disease pathogenesis with therapeutic development. The recent studies on antisense transcription initiation and its epigenetic regulation, which are limited, are discussed here. Furthermore, we concisely describe how antisense transcription/transcripts regulate gene expression and genome integrity with implications in disease pathogenesis and therapeutic development.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| | - Divya Reddy
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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18
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Yoon S, Rossi JJ. Therapeutic Potential of Small Activating RNAs (saRNAs) in Human Cancers. Curr Pharm Biotechnol 2018; 19:604-610. [PMID: 29804529 PMCID: PMC6204660 DOI: 10.2174/1389201019666180528084059] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/09/2018] [Accepted: 05/23/2018] [Indexed: 01/24/2023]
Abstract
Background: RNA is increasingly recognized as a powerful molecule that can be used to control gene expression. Sophisticated, well-engineered RNA-based regulators are being developed as oligotherapeutics. Methods: In particular, small activating RNAs (saRNAs) are promising therapeutic options for targeting human diseases. Numerous saRNAs targeting multiple cancers have been developed in preclinical models. One saRNA targeting C/EBPα is currently undergoing clinical trials in liver cancer. Results and Conclusion: In this review, we describe the current working model of the intracellular mechanism of saRNA, discuss the recent progress of saRNA therapeutics in preclinical and clinical trials, and current advances in targeted delivery using aptamers in detail.
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Affiliation(s)
- Sorah Yoon
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, United States
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, United States.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, California, United States
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19
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Muñoz M, García-Casco JM, Caraballo C, Fernández-Barroso MÁ, Sánchez-Esquiliche F, Gómez F, Rodríguez MDC, Silió L. Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs. Front Genet 2018; 9:608. [PMID: 30564273 PMCID: PMC6288315 DOI: 10.3389/fgene.2018.00608] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/19/2018] [Indexed: 12/20/2022] Open
Abstract
One of the most important determinants of meat quality is the intramuscular fat (IMF) content. The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the present study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for their IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq allowed identifying ∼10,000 of the 25,878 annotated genes in the analyzed samples. In addition to this, 42.46% of the identified transcripts corresponded to newly predicted isoforms. Differential expression analyses revealed a total of 221 DE annotated genes and 116 DE new isoforms. Functional analyses identified an enrichment of overexpressed genes involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC, and ADIPOQ) in animals with a higher content of IMF and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB, and SEMA4D) in the animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. Co-expression networks analyses revealed six long non-coding RNAs (lncRNAs) (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, and ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1, and CIDEC. Analyses of the regulatory impact factors (RIFs) revealed 301 transcriptionally regulatory factors involved in expression differences, with five of them involved in adipogenesis (ARID5B, CREB1, VDR, ATF6, and SP1) and other three taking part of myogenesis and development of skeletal muscle (ATF3, KLF11, and MYF6). The results obtained provide relevant insights about the genetic mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors for further identification of polymorphisms susceptible of being incorporated in a selection program.
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Affiliation(s)
- María Muñoz
- Centro I+D en Cerdo Ibérico INIA-Zafra, Zafra, Spain.,Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Juan María García-Casco
- Centro I+D en Cerdo Ibérico INIA-Zafra, Zafra, Spain.,Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Carmen Caraballo
- Centro I+D en Cerdo Ibérico INIA-Zafra, Zafra, Spain.,Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Miguel Ángel Fernández-Barroso
- Centro I+D en Cerdo Ibérico INIA-Zafra, Zafra, Spain.,Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | | | | | - María Del Carmen Rodríguez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Luis Silió
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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20
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Beal A, Rodriguez-Casariego J, Rivera-Casas C, Suarez-Ulloa V, Eirin-Lopez JM. Environmental Epigenomics and Its Applications in Marine Organisms. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_28] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Goyal A, Fiškin E, Gutschner T, Polycarpou-Schwarz M, Groß M, Neugebauer J, Gandhi M, Caudron-Herger M, Benes V, Diederichs S. A cautionary tale of sense-antisense gene pairs: independent regulation despite inverse correlation of expression. Nucleic Acids Res 2017; 45:12496-12508. [PMID: 29059299 PMCID: PMC5716207 DOI: 10.1093/nar/gkx952] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 10/05/2017] [Indexed: 01/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been proven to play important roles in diverse cellular processes including the DNA damage response. Nearly 40% of annotated lncRNAs are transcribed in antisense direction to other genes and have often been implicated in their regulation via transcript- or transcription-dependent mechanisms. However, it remains unclear whether inverse correlation of gene expression would generally point toward a regulatory interaction between the genes. Here, we profiled lncRNA and mRNA expression in lung and liver cancer cells after exposure to DNA damage. Our analysis revealed two pairs of mRNA-lncRNA sense-antisense transcripts being inversely expressed upon DNA damage. The lncRNA NOP14-AS1 was strongly upregulated upon DNA damage, while the mRNA for NOP14 was downregulated, both in a p53-dependent manner. For another pair, the lncRNA LIPE-AS1 was downregulated, while its antisense mRNA CEACAM1 was upregulated. To test whether as expected the antisense genes would regulate each other resulting in this highly significant inverse correlation, we employed antisense oligonucleotides and RNAi to study transcript-dependent effects as well as dCas9-based transcriptional modulation by CRISPRi/CRISPRa for transcription-dependent effects. Surprisingly, despite the strong stimulus-dependent inverse correlation, our data indicate that neither transcript- nor transcription-dependent mechanisms explain the inverse regulation of NOP14-AS1:NOP14 or LIPE-AS1:CEACAM1 expression. Hence, sense-antisense pairs whose expression is strongly—positively or negatively—correlated can be nonetheless regulated independently. This highlights the requirement of individual experimental studies for each antisense pair and prohibits drawing conclusions on regulatory mechanisms from expression correlations.
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Affiliation(s)
- Ashish Goyal
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Evgenij Fiškin
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Tony Gutschner
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Maria Polycarpou-Schwarz
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Matthias Groß
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Julia Neugebauer
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Minakshi Gandhi
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Maiwen Caudron-Herger
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany.,Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany.,Faculty of Medicine, University of Freiburg, 79085 Freiburg, Germany.,German Cancer Consortium (DKTK), 79104 Freiburg, Germany
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22
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Li L, Wang M, Mei Z, Cao W, Yang Y, Wang Y, Wen A. lncRNAs HIF1A-AS2 facilitates the up-regulation of HIF-1α by sponging to miR-153-3p, whereby promoting angiogenesis in HUVECs in hypoxia. Biomed Pharmacother 2017; 96:165-172. [DOI: 10.1016/j.biopha.2017.09.113] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/12/2017] [Accepted: 09/23/2017] [Indexed: 12/15/2022] Open
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23
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Avivi S, Mor A, Dotan I, Tzadok S, Kanter I, Kinor N, Canaani D, Shav-Tal Y. Visualizing nuclear RNAi activity in single living human cells. Proc Natl Acad Sci U S A 2017; 114:E8837-E8846. [PMID: 29073029 PMCID: PMC5651755 DOI: 10.1073/pnas.1707440114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Nuclear RNA interference (RNAi) is mediated by the canonical RNAi machinery and can lead to transcriptional silencing, transcriptional activation, or modulation of alternative splicing patterns. These effects transpire through changes in histone and DNA modifications via RNAi-mediated recruitment of chromatin-modifying enzymes. To prove that nuclear RNAi occurs and modulates transcription in human cells, we used live-cell imaging to detect and track nuclear RNAi transcriptional repression in single living human cells. While employing reporter genes constructed with inducible promoters and cognate-inducible short hairpin RNA (shRNA) targeted against the reporter coding region, we have characterized the dynamics of the nuclear RNAi process in living human cells. We show that the silencing effect is mediated through the nascent mRNA, followed by activity of histone methylating enzymes, but not through DNA methylation.
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Affiliation(s)
- Shira Avivi
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Amir Mor
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Iris Dotan
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Sivan Tzadok
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Kanter
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Noa Kinor
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Canaani
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
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Abstract
Several recent studies in a number of model systems including zebrafish, Arabidopsis, and mouse have revealed phenotypic differences between knockouts (i.e., mutants) and knockdowns (e.g., antisense-treated animals). These differences have been attributed to a number of reasons including off-target effects of the antisense reagents. An alternative explanation was recently proposed based on a zebrafish study reporting that genetic compensation was observed in egfl7 mutant but not knockdown animals. Dosage compensation was first reported in Drosophila in 1932, and genetic compensation in response to a gene knockout was first reported in yeast in 1969. Since then, genetic compensation has been documented many times in a number of model organisms; however, our understanding of the underlying molecular mechanisms remains limited. In this review, we revisit studies reporting genetic compensation in higher eukaryotes and outline possible molecular mechanisms, which may include both transcriptional and posttranscriptional processes.
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Affiliation(s)
- Mohamed A. El-Brolosy
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- * E-mail:
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25
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Li LC. Small RNA-Guided Transcriptional Gene Activation (RNAa) in Mammalian Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [DOI: 10.1007/978-981-10-4310-9_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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26
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Microfluidics Engineering: Recent Trends, Valorization, and Applications. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2017. [DOI: 10.1007/s13369-017-2662-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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27
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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28
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Small RNA-directed epigenetic programming of embryonic stem cell cardiac differentiation. Sci Rep 2017; 7:41799. [PMID: 28165496 PMCID: PMC5292948 DOI: 10.1038/srep41799] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/30/2016] [Indexed: 02/06/2023] Open
Abstract
Microinjection of small noncoding RNAs in one-cell embryos was reported in several instances to result in transcriptional activation of target genes. To determine the molecular mechanisms involved and to explore whether such epigenetic regulations could play a role in early development, we used a cell culture system as close as possible to the embryonic state. We report efficient cardiac differentiation of embryonic stem (ES) cells induced by small non-coding RNAs with sequences of Cdk9, a key player in cardiomyocyte differentiation. Transfer of oligoribonucleotides representing parts of the Cdk9 mRNA into ES and mouse embryo fibroblast cultures resulted in upregulation of transcription. Dependency on Argonaute proteins and endogenous antisense transcripts indicated that the inducer oligoribonucleotides were processed by the RNAi machinery. Upregulation of Cdk9 expression resulted in increased efficiency of cardiac differentiation suggesting a potential tool for stem cell-based regenerative medicine.
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29
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Wan Q, Guan X, Yang N, Wu H, Pan M, Liu B, Fang L, Yang S, Hu Y, Ye W, Zhang H, Ma P, Chen J, Wang Q, Mei G, Cai C, Yang D, Wang J, Guo W, Zhang W, Chen X, Zhang T. Small interfering RNAs from bidirectional transcripts of GhMML3_A12 regulate cotton fiber development. THE NEW PHYTOLOGIST 2016; 210:1298-310. [PMID: 26832840 DOI: 10.1111/nph.13860] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/09/2015] [Indexed: 05/18/2023]
Abstract
Natural antisense transcripts (NATs) are commonly observed in eukaryotic genomes, but only a limited number of such genes have been identified as being involved in gene regulation in plants. In this research, we investigated the function of small RNA derived from a NAT in fiber cell development. Using a map-based cloning strategy for the first time in tetraploid cotton, we cloned a naked seed mutant gene (N1 ) encoding a MYBMIXTA-like transcription factor 3 (MML3)/GhMYB25-like in chromosome A12, GhMML3_A12, that is associated with fuzz fiber development. The extremely low expression of GhMML3_A12 in N1 is associated with NAT production, driven by its 3' antisense promoter, as indicated by the promoter-driven histochemical staining assay. In addition, small RNA deep sequencing analysis suggested that the bidirectional transcriptions of GhMML3_A12 form double-stranded RNAs and generate 21-22 nt small RNAs. Therefore, in a fiber-specific manner, small RNA derived from the GhMML3_A12 locus can mediate GhMML3_A12 mRNA self-cleavage and result in the production of naked seeds followed by lint fiber inhibition in N1 plants. The present research reports the first observation of gene-mediated NATs and siRNA directly controlling fiber development in cotton.
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Affiliation(s)
- Qun Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xueying Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nannan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huaitong Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengqiao Pan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingliang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lei Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shouping Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peiyong Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiedan Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gaofu Mei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Caiping Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Donglei Yang
- National Laboratory of Plant Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiawei Wang
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenhua Zhang
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
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30
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Portnoy V, Lin SHS, Li KH, Burlingame A, Hu ZH, Li H, Li LC. saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res 2016; 26:320-35. [PMID: 26902284 PMCID: PMC4783471 DOI: 10.1038/cr.2016.22] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/22/2015] [Accepted: 01/12/2016] [Indexed: 12/21/2022] Open
Abstract
Small activating RNAs (saRNAs) targeting specific promoter regions are able to stimulate gene expression at the transcriptional level, a phenomenon known as RNA activation (RNAa). It is known that RNAa depends on Ago2 and is associated with epigenetic changes at the target promoters. However, the precise molecular mechanism of RNAa remains elusive. Using human CDKN1A (p21) as a model gene, we characterized the molecular nature of RNAa. We show that saRNAs guide Ago2 to and associate with target promoters. saRNA-loaded Ago2 facilitates the assembly of an RNA-induced transcriptional activation (RITA) complex, which, in addition to saRNA-Ago2 complex, includes RHA and CTR9, the latter being a component of the PAF1 complex. RITA interacts with RNA polymerase II to stimulate transcription initiation and productive elongation, accompanied by monoubiquitination of histone 2B. Our results establish the existence of a cellular RNA-guided genome-targeting and transcriptional activation mechanism and provide important new mechanistic insights into the RNAa process.
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Affiliation(s)
- Victoria Portnoy
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Szu Hua Sharon Lin
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Zheng-Hui Hu
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Long-Cheng Li
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA.,Laboratory of Molecular Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
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31
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Kalantari R, Chiang CM, Corey DR. Regulation of mammalian transcription and splicing by Nuclear RNAi. Nucleic Acids Res 2016; 44:524-37. [PMID: 26612865 PMCID: PMC4737150 DOI: 10.1093/nar/gkv1305] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) is well known as a mechanism for controlling mammalian mRNA translation in the cytoplasm, but what would be the consequences if it also functions in cell nuclei? Although RNAi has also been found in nuclei of plants, yeast, and other organisms, there has been relatively little progress towards understanding the potential involvement of mammalian RNAi factors in nuclear processes including transcription and splicing. This review summarizes evidence for mammalian RNAi factors in cell nuclei and mechanisms that might contribute to the control of gene expression. When RNAi factors bind small RNAs, they form ribonucleoprotein complexes that can be selective for target sequences within different classes of nuclear RNA substrates. The versatility of nuclear RNAi may supply a previously underappreciated layer of regulation to transcription, splicing, and other nuclear processes.
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Affiliation(s)
- Roya Kalantari
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Cheng-Ming Chiang
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-8807, USA
| | - David R Corey
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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32
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The Ins and Outs of miRNA-Mediated Gene Silencing during Neuronal Synaptic Plasticity. Noncoding RNA 2016; 2:ncrna2010001. [PMID: 29657259 PMCID: PMC5831896 DOI: 10.3390/ncrna2010001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 12/18/2022] Open
Abstract
Neuronal connections through specialized junctions, known as synapses, create circuits that underlie brain function. Synaptic plasticity, i.e., structural and functional changes to synapses, occurs in response to neuronal activity and is a critical regulator of various nervous system functions, including long-term memory formation. The discovery of mRNAs, miRNAs, ncRNAs, ribosomes, translational repressors, and other RNA binding proteins in dendritic spines allows individual synapses to alter their synaptic strength rapidly through regulation of local protein synthesis in response to different physiological stimuli. In this review, we discuss our understanding of a number of miRNAs, ncRNAs, and RNA binding proteins that are emerging as important regulators of synaptic plasticity, which play a critical role in memory, learning, and diseases that arise when neuronal circuits are impaired.
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33
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Matsui M, Li L, Janowski BA, Corey DR. Reduced Expression of Argonaute 1, Argonaute 2, and TRBP Changes Levels and Intracellular Distribution of RNAi Factors. Sci Rep 2015; 5:12855. [PMID: 26242502 PMCID: PMC4525381 DOI: 10.1038/srep12855] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/06/2015] [Indexed: 11/25/2022] Open
Abstract
Until recently, Argonaute 2 (AGO2) and other RNA factors were believed to be restricted to the cytoplasm of mammalian somatic cells. It is now becoming appreciated that RNAi factors can also be found in cell nuclei, but much remains to be learned about their transport, molecular recognition, and function. We find that siRNA-mediated reduction of AGO1 or AGO2 increases the proportion of AGO1 or AGO2 in cell nuclei. Inhibition of AGO1 expression led to increased AGO2 levels, while knockdown of AGO2 led to increased levels of AGO1. Blocking AGO1, AGO2, or TRBP expression changed expression levels and nuclear distribution of RNAi factors Dicer, TNRC6A (GW182), and TRBP. These data reveal the expression of RNAi proteins is mutually dependent and that perturbation can affect subcellular distribution of those factors inside cells.
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Affiliation(s)
- Masayuki Matsui
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Liande Li
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - Bethany A Janowski
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
| | - David R Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9041
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34
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Bobbin ML, Burnett JC, Rossi JJ. RNA interference approaches for treatment of HIV-1 infection. Genome Med 2015; 7:50. [PMID: 26019725 PMCID: PMC4445287 DOI: 10.1186/s13073-015-0174-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/13/2015] [Indexed: 01/05/2023] Open
Abstract
HIV/AIDS is a chronic and debilitating disease that cannot be cured with current antiretroviral drugs. While combinatorial antiretroviral therapy (cART) can potently suppress HIV-1 replication and delay the onset of AIDS, viral mutagenesis often leads to viral escape from multiple drugs. In addition to the pharmacological agents that comprise cART drug cocktails, new biological therapeutics are reaching the clinic. These include gene-based therapies that utilize RNA interference (RNAi) to silence the expression of viral or host mRNA targets that are required for HIV-1 infection and/or replication. RNAi allows sequence-specific design to compensate for viral mutants and natural variants, thereby drastically expanding the number of therapeutic targets beyond the capabilities of cART. Recent advances in clinical and preclinical studies have demonstrated the promise of RNAi therapeutics, reinforcing the concept that RNAi-based agents might offer a safe, effective, and more durable approach for the treatment of HIV/AIDS. Nevertheless, there are challenges that must be overcome in order for RNAi therapeutics to reach their clinical potential. These include the refinement of strategies for delivery and to reduce the risk of mutational escape. In this review, we provide an overview of RNAi-based therapies for HIV-1, examine a variety of combinatorial RNAi strategies, and discuss approaches for ex vivo delivery and in vivo delivery.
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Affiliation(s)
- Maggie L Bobbin
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA
| | - John C Burnett
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA ; Department of Molecular and Cell Biology, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 9101 USA
| | - John J Rossi
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA ; Department of Molecular and Cell Biology, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 9101 USA
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35
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Sun T, Ye H, Wu CL, Lee GSM, Kantoff PW. Emerging players in prostate cancer: long non-coding RNAs. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2014; 2:294-299. [PMID: 25606575 PMCID: PMC4297325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/09/2014] [Indexed: 06/04/2023]
Abstract
Recent observations of novel long non-coding RNAs (lncRNAs) have considerably altered our understanding of cell biology. The role of lncRNAs as tumor suppressors or oncogenes has been extensively studied. Over-expression of oncogenic lncRNAs promotes tumor-cell proliferation and metastasis through chromatin looping and distal engagement with the androgen receptor, anti-sense gene regulation, alternative splicing, and impeding DNA repair. Prostate cancer is the most common type of cancer and frequent cause of cancer-related mortality in men worldwide. Unraveling the molecular and biological processes that contribute to prostate cancer development and progression is a challenging task. In prostate cancer, aberrant expression of lncRNAs has been associated with disease progression. In this review, we highlight the emerging impact of lncRNAs in prostate cancer research, with a particular focus on the mechanisms and functions of lncRNAs. Increased research on lncRNAs will lead to a greater understanding of prostate cancercinogenesis and progression and may lead to novel clinical applications. LncRNAs have great potential to become new biomarkers for detection, prognostication and prediction in prostate cancer.
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Affiliation(s)
- Tong Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical SchoolUSA
| | - Huihui Ye
- Department of Pathology, Beth-Israel Deaconess Medical Center, Harvard Medical SchoolUSA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical SchoolUSA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical SchoolUSA
| | - Philip W Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical SchoolUSA
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36
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Larsson L, Castilho RM, Giannobile WV. Epigenetics and its role in periodontal diseases: a state-of-the-art review. J Periodontol 2014; 86:556-68. [PMID: 25415244 DOI: 10.1902/jop.2014.140559] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The immune response to oral bacteria and the subsequent activation of inflammatory signaling is not only dependent on genetic factors. The importance of so-called epigenetic mechanisms presents additional regulatory pathways of genes involved in maintaining chronic inflammation, including gingivitis and periodontitis. The term epigenetics relates to changes in gene expression that are not encoded in the DNA sequence itself and include chemical alterations of DNA and its associated proteins. These changes lead to remodeling of the chromatin and subsequent activation or inactivation of a gene. Epigenetic mechanisms have been found to contribute to disease, including cancer and autoimmune or inflammatory diseases. In this state-of-the art review, the authors provide the latest findings on the involvement of epigenetic modifications in the development of periodontal disease and present emerging therapeutic strategies aimed at epigenetic targets (epidrugs) associated with the disruption of tissue homeostasis and the development of periodontitis.
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Affiliation(s)
- Lena Larsson
- Currently, Department of Periodontology, Institute of Odontology, University of Gothenburg, Sweden; previously, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI
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