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Hu X, Yin G, Zhang Y, Zhu L, Huang H, Lv K. Recent advances in the functional explorations of nuclear microRNAs. Front Immunol 2023; 14:1097491. [PMID: 36911728 PMCID: PMC9992549 DOI: 10.3389/fimmu.2023.1097491] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Approximately 22 nucleotide-long non-coding small RNAs (ncRNAs) play crucial roles in physiological and pathological activities, including microRNAs (miRNAs). Long ncRNAs often stay in the cytoplasm, modulating post-transcriptional gene expression. Briefly, miRNA binds with the target mRNA and builds a miRNA-induced silencing complex to silence the transcripts or prevent their translation. Interestingly, data from recent animal and plant studies suggested that mature miRNAs are present in the nucleus, where they regulate transcriptionally whether genes are activated or silenced. This significantly broadens the functional range of miRNAs. Here, we reviewed and summarized studies on the functions of nuclear miRNAs to better understand the modulatory networks associated with nuclear miRNAs.
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Affiliation(s)
- Xiaozhu Hu
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Guoquan Yin
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Yuan Zhang
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Liangyu Zhu
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Haoyu Huang
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Kun Lv
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
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Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Rep 2021; 31:107795. [PMID: 32579922 DOI: 10.1016/j.celrep.2020.107795] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/01/2020] [Accepted: 05/29/2020] [Indexed: 11/25/2022] Open
Abstract
Sex differences manifest in many diseases and may drive sex-specific therapeutic responses. To understand the molecular basis of sex differences, we evaluated sex-biased gene regulation by constructing sample-specific gene regulatory networks in 29 human healthy tissues using 8,279 whole-genome expression profiles from the Genotype-Tissue Expression (GTEx) project. We find sex-biased regulatory network structures in each tissue. Even though most transcription factors (TFs) are not differentially expressed between males and females, many have sex-biased regulatory targeting patterns. In each tissue, genes that are differentially targeted by TFs between the sexes are enriched for tissue-related functions and diseases. In brain tissue, for example, genes associated with Parkinson's disease and Alzheimer's disease are targeted by different sets of TFs in each sex. Our systems-based analysis identifies a repertoire of TFs that play important roles in sex-specific architecture of gene regulatory networks, and it underlines sex-specific regulatory processes in both health and disease.
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Affiliation(s)
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Marieke L Kuijjer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., San Francisco, CA, USA
| | - Abhijeet R Sonawane
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Maud Fagny
- Genetique Quantitative et Evolution-Le Moulon, Universite Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - John Platig
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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RNA and Oxidative Stress in Alzheimer's Disease: Focus on microRNAs. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:2638130. [PMID: 33312335 PMCID: PMC7721489 DOI: 10.1155/2020/2638130] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 01/31/2023]
Abstract
Oxidative stress (OS) is one of the major pathomechanisms of Alzheimer's disease (AD), which is closely associated with other key events in neurodegeneration such as mitochondrial dysfunction, inflammation, metal dysregulation, and protein misfolding. Oxidized RNAs are identified in brains of AD patients at the prodromal stage. Indeed, oxidized mRNA, rRNA, and tRNA lead to retarded or aberrant protein synthesis. OS interferes with not only these translational machineries but also regulatory mechanisms of noncoding RNAs, especially microRNAs (miRNAs). MiRNAs can be oxidized, which causes misrecognizing target mRNAs. Moreover, OS affects the expression of multiple miRNAs, and conversely, miRNAs regulate many genes involved in the OS response. Intriguingly, several miRNAs embedded in upstream regulators or downstream targets of OS are involved also in neurodegenerative pathways in AD. Specifically, seven upregulated miRNAs (miR-125b, miR-146a, miR-200c, miR-26b, miR-30e, miR-34a, miR-34c) and three downregulated miRNAs (miR-107, miR-210, miR-485), all of which are associated with OS, are found in vulnerable brain regions of AD at the prodromal stage. Growing evidence suggests that altered miRNAs may serve as targets for developing diagnostic or therapeutic tools for early-stage AD. Focusing on a neuroprotective transcriptional repressor, REST, and the concept of hormesis that are relevant to the OS response may provide clues to help us understand the role of the miRNA system in cellular and organismal adaptive mechanisms to OS.
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Chetta M, Di Pietro L, Bukvic N, Lattanzi W. Rising Roles of Small Noncoding RNAs in Cotranscriptional Regulation: In Silico Study of miRNA and piRNA Regulatory Network in Humans. Genes (Basel) 2020; 11:genes11050482. [PMID: 32365489 PMCID: PMC7290514 DOI: 10.3390/genes11050482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/09/2020] [Accepted: 04/27/2020] [Indexed: 01/10/2023] Open
Abstract
Gene expression regulation is achieved through an intricate network of molecular interactions, in which trans-acting transcription factors (TFs) and small noncoding RNAs (sncRNAs), including microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), play a key role. Recent observations allowed postulating an interplay between TFs and sncRNAs, in that they may possibly share DNA-binding sites. The aim of this study was to analyze the complete subset of miRNA and piRNA sequences stored in the main databases in order to identify the occurrence of conserved motifs and subsequently predict a possible innovative interplay with TFs at a transcriptional level. To this aim, we adopted an original in silico workflow to search motifs and predict interactions within genome-scale regulatory networks. Our results allowed categorizing miRNA and piRNA motifs, with corresponding TFs sharing complementary DNA-binding motifs. The biological interpretation of the gene ontologies of the TFs permitted observing a selective enrichment in developmental pathways, allowing the distribution of miRNA motifs along a topological and chronological frame. In addition, piRNA motifs were categorized for the first time and revealed specific functional implications in somatic tissues. These data might pose experimental hypotheses to be tested in biological models, towards clarifying novel in gene regulatory routes.
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Affiliation(s)
- Massimiliano Chetta
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy
- Correspondence: (M.C.); (L.D.P.); Tel.: +39-333187551 (M.C.); +39-0630154464 (L.D.P.)
| | - Lorena Di Pietro
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Biologia Applicata, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Correspondence: (M.C.); (L.D.P.); Tel.: +39-333187551 (M.C.); +39-0630154464 (L.D.P.)
| | - Nenad Bukvic
- UOC Lab. di Genetica Medica, Azienda Ospedaliero Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Wanda Lattanzi
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Biologia Applicata, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
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