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Ranjan G, Scaria V, Sivasubbu S. Syntenic lncRNA locus exhibits DNA regulatory functions with sequence evolution. Gene 2025; 933:148988. [PMID: 39378975 DOI: 10.1016/j.gene.2024.148988] [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: 04/17/2024] [Revised: 07/12/2024] [Accepted: 10/04/2024] [Indexed: 10/10/2024]
Abstract
Syntenic long non-coding RNAs (lncRNAs) often show limited sequence conservation across species, prompting concern in the field. This study delves into functional signatures of syntenic lncRNAs between humans and zebrafish. Syntenic lncRNAs are highly expressed in zebrafish, with ∼90 % located near protein-coding genes, either in sense or antisense orientation. During early zebrafish development and in human embryonic stem cells (H1-hESC), syntenic lncRNA loci are enriched with cis-regulatory repressor signatures, influencing the expression of development-associated genes. In later zebrafish developmental stages and specific human cell lines, these syntenic lncRNA loci function as enhancers or transcription start sites (TSS) for protein-coding genes. Analysis of transposable elements (TEs) in syntenic lncRNA sequences revealed intriguing patterns: human lncRNAs are enriched in simple repeat elements, while their zebrafish counterparts show enrichment in LTR elements. This sequence evolution likely arises from post-rearrangement mutations that enhance DNA elements or cis-regulatory functions. It may also contribute to vertebrate innovation by creating novel transcription factor binding sites within the locus. This study highlights the conserved functionality of syntenic lncRNA loci through DNA elements, emphasizing their conserved roles across species despite sequence divergence.
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Affiliation(s)
- Gyan Ranjan
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Vishwanath Cancer Care Foundation, Mumbai, India.; Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Vishwanath Cancer Care Foundation, Mumbai, India.; Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
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2
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Tierney JAS, Świrski MI, Tjeldnes H, Kiran AM, Carancini G, Kiniry SJ, Michel AM, Kufel J, Valen E, Baranov PV. RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization. Nucleic Acids Res 2025; 53:D268-D274. [PMID: 39540432 PMCID: PMC11701704 DOI: 10.1093/nar/gkae1020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 10/11/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024] Open
Abstract
Ribosome profiling (Ribo-Seq) has revolutionised our understanding of translation, but the increasing complexity and volume of Ribo-Seq data present challenges for its reuse. Here, we formally introduce RiboSeq.Org, an integrated suite of resources designed to facilitate Ribo-Seq data analysis and visualisation within a web browser. RiboSeq.Org comprises several interconnected tools: GWIPS-viz for genome-wide visualisation, Trips-Viz for transcriptome-centric analysis, RiboGalaxy for data processing and the newly developed RiboSeq data portal (RDP) for centralised dataset identification and access. The RDP currently hosts preprocessed datasets corresponding to 14840 sequence libraries (samples) from 969 studies across 96 species, in various file formats along with standardised metadata. RiboSeq.Org addresses key challenges in Ribo-Seq data reuse through standardised sample preprocessing, semi-automated metadata curation and programmatic information access via a REST API and command-line utilities. RiboSeq.Org enhances the accessibility and utility of public Ribo-Seq data, enabling researchers to gain new insights into translational regulation and protein synthesis across diverse organisms and conditions. By providing these integrated, user-friendly resources, RiboSeq.Org aims to lower the barrier to reproducible research in the field of translatomics and promote more efficient utilisation of the wealth of available Ribo-Seq data.
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Affiliation(s)
- Jack A S Tierney
- School of Biochemistry and Cell Biology, University College Cork, Western Rd, Cork, T12 CY82, Ireland
- SFI CRT in Genomics Data Science, University of Galway, University Rd, Galway, H91 TK33, Ireland
| | - Michał I Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, ul. Pawińskiego 5A, Warsaw, 02-106, Poland
| | - Håkon Tjeldnes
- School of Biochemistry and Cell Biology, University College Cork, Western Rd, Cork, T12 CY82, Ireland
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlensgate Bergen, 55N-5008, Norway
| | - Anmol M Kiran
- School of Biochemistry and Cell Biology, University College Cork, Western Rd, Cork, T12 CY82, Ireland
| | - Gionmattia Carancini
- School of Biochemistry and Cell Biology, University College Cork, Western Rd, Cork, T12 CY82, Ireland
- SFI CRT in Genomics Data Science, University of Galway, University Rd, Galway, H91 TK33, Ireland
| | - Stephen J Kiniry
- EIRNA Bio, Food Science and Technology Building, 1 College Rd, Cork, T12 Y337, Ireland
| | - Audrey M Michel
- EIRNA Bio, Food Science and Technology Building, 1 College Rd, Cork, T12 Y337, Ireland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, ul. Pawińskiego 5A, Warsaw, 02-106, Poland
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlensgate Bergen, 55N-5008, Norway
- Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0731 Oslo, Norway
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Western Rd, Cork, T12 CY82, Ireland
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Li M, Zhang Z, Geng Q, Lu Y, Miao S, Zhang X, Song W, Li K. A testis-specific long non-coding RNA, 1700052I22Rik, regulates spermatid chromatin condensation in mice. Int J Biochem Cell Biol 2024; 179:106725. [PMID: 39667612 DOI: 10.1016/j.biocel.2024.106725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 11/24/2024] [Accepted: 12/09/2024] [Indexed: 12/14/2024]
Abstract
Long non-coding RNAs (lncRNAs), serving as diverse functional regulators, are abundantly expressed in the testis. However, many testis-specific or preferentially expressed lncRNAs remain uncharacterized. Here, we report a testis-specific lncRNA, 1700052I22Rik, which exhibits a dynamic expression pattern during spermatogenesis. Our findings demonstrate that knockout of 1700052I22Rik in mice leads to reduced sperm counts and subfertility in males, as well as defective spermatid chromatin condensation. We further elucidate the underlying mechanism by which 1700052I22Rik modulates the translation of protamine 1 (PRM1) through interaction with Y-box binding protein 2 (YBX2). Collectively, our results uncover a crucial role for the testis-specific lncRNA 1700052I22Rik in regulating spermatid chromatin condensation in mice, providing novel insights into the functions of lncRNAs in spermatogenesis and potential targets for the diagnosis and treatment of male infertility.
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Affiliation(s)
- Mengzhen Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Zexuan Zhang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Qi Geng
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yan Lu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Shiying Miao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Xingguang Zhang
- Department of Health Statistics, Public Health College, Inner Mongolia Medical University, Hohhot, Inner Mongolia 010000, China.
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.
| | - Kai Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.
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4
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Montano C, Flores-Arenas C, Carpenter S. LncRNAs, nuclear architecture and the immune response. Nucleus 2024; 15:2350182. [PMID: 38738760 PMCID: PMC11093052 DOI: 10.1080/19491034.2024.2350182] [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: 02/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.
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Affiliation(s)
- Christy Montano
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Flores-Arenas
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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Lécuyer E, Sauvageau M, Kothe U, Unrau PJ, Damha MJ, Perreault J, Abou Elela S, Bayfield MA, Claycomb JM, Scott MS. Canada's contributions to RNA research: past, present, and future perspectives. Biochem Cell Biol 2024; 102:472-491. [PMID: 39320985 DOI: 10.1139/bcb-2024-0176] [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] [Indexed: 09/27/2024] Open
Abstract
The field of RNA research has provided profound insights into the basic mechanisms modulating the function and adaption of biological systems. RNA has also been at the center stage in the development of transformative biotechnological and medical applications, perhaps most notably was the advent of mRNA vaccines that were critical in helping humanity through the Covid-19 pandemic. Unbeknownst to many, Canada boasts a diverse community of RNA scientists, spanning multiple disciplines and locations, whose cutting-edge research has established a rich track record of contributions across various aspects of RNA science over many decades. Through this position paper, we seek to highlight key contributions made by Canadian investigators to the RNA field, via both thematic and historical viewpoints. We also discuss initiatives underway to organize and enhance the impact of the Canadian RNA research community, particularly focusing on the creation of the not-for-profit organization RNA Canada ARN. Considering the strategic importance of RNA research in biology and medicine, and its considerable potential to help address major challenges facing humanity, sustained support of this sector will be critical to help Canadian scientists play key roles in the ongoing RNA revolution and the many benefits this could bring about to Canada.
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Affiliation(s)
- Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Martin Sauvageau
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Masad J Damha
- Department of Chemistry, McGill University, Montréal, QC, Canada
| | - Jonathan Perreault
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada
| | - Sherif Abou Elela
- Département de Microbiologie et Infectiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michelle S Scott
- Département de Biochimie et de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, QC, Canada
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Shi X, Liu S, Zou Y, Wu H, Ma J, Lin J, Zhang X. LncRNA Taurine Up-Regulated 1 Knockout Provides Neuroprotection in Ischemic Stroke Rats by Inhibiting Nuclear-Cytoplasmic Shuttling of HuR. Biomedicines 2024; 12:2520. [PMID: 39595085 PMCID: PMC11592331 DOI: 10.3390/biomedicines12112520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 10/28/2024] [Accepted: 10/29/2024] [Indexed: 11/28/2024] Open
Abstract
Background: Long non-coding RNA taurine-upregulated gene 1 (TUG1) is involved in various cellular processes, but its role in cerebral ischemia-reperfusion injury remains unclear. This study investigated TUG1's role in regulating the nucleocytoplasmic shuttling of human antigen R (HuR), a key apoptosis regulator under ischemic conditions. Methods: CRISPR-Cas9 technology was used to generate TUG1 knockout Sprague Dawley rats to assess TUG1's impact on ischemic injury. The infarct area and neuronal apoptosis were evaluated using TUNEL, hematoxylin and eosin (HE), and TTC staining, while behavioral functions were assessed. Immunofluorescence staining with confocal microscopy was employed to examine TUG1-mediated HuR translocation and expression changes in the apoptosis-related proteins COX-2 and Bax. Results: TUG1 knockout rats showed significantly reduced cerebral infarct areas, decreased neuronal apoptosis, and improved neurological functions compared to controls. Immunofluorescence staining revealed that HuR translocation from the nucleus to the cytoplasm was inhibited, leading to decreased COX-2 and Bax expression levels. Conclusions: TUG1 knockout reduces ischemic damage and neuronal apoptosis by inhibiting HuR nucleocytoplasmic shuttling, making TUG1 a potential therapeutic target for ischemic stroke.
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Affiliation(s)
- Xiaocheng Shi
- Department of Neurological Rehabilitation, Zhongnan Hospital of Wuhan University, Wuhan 430071, China;
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; (Y.Z.); (H.W.); (J.M.)
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China;
| | - Sha Liu
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China;
- Department of General Practice, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yichun Zou
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; (Y.Z.); (H.W.); (J.M.)
| | - Hengping Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; (Y.Z.); (H.W.); (J.M.)
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China;
| | - Jinyang Ma
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; (Y.Z.); (H.W.); (J.M.)
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China;
| | - Junbin Lin
- Department of Neurological Rehabilitation, Zhongnan Hospital of Wuhan University, Wuhan 430071, China;
| | - Xin Zhang
- Department of Neurological Rehabilitation, Zhongnan Hospital of Wuhan University, Wuhan 430071, China;
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Ranjan G, Sehgal P, Scaria V, Sivasubbu S. SCAR-6 elncRNA locus epigenetically regulates PROZ and modulates coagulation and vascular function. EMBO Rep 2024; 25:4950-4978. [PMID: 39358551 PMCID: PMC11549340 DOI: 10.1038/s44319-024-00272-w] [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: 05/04/2024] [Revised: 09/03/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
In this study, we characterize a novel lncRNA-producing gene locus that we name Syntenic Cardiovascular Conserved Region-Associated lncRNA-6 (scar-6) and functionally validate its role in coagulation and cardiovascular function. A 12-bp deletion of the scar-6 locus in zebrafish (scar-6gib007Δ12/Δ12) results in cranial hemorrhage and vascular permeability. Overexpression, knockdown and rescue with the scar-6 lncRNA modulates hemostasis in zebrafish. Molecular investigation reveals that the scar-6 lncRNA acts as an enhancer lncRNA (elncRNA), and controls the expression of prozb, an inhibitor of factor Xa, through an enhancer element in the scar-6 locus. The scar-6 locus suppresses loop formation between prozb and scar-6 sequences, which might be facilitated by the methylation of CpG islands via the prdm14-PRC2 complex whose binding to the locus might be stabilized by the scar-6 elncRNA transcript. Binding of prdm14 to the scar-6 locus is impaired in scar-6gib007Δ12/Δ12 zebrafish. Finally, activation of the PAR2 receptor in scar-6gib007Δ12/Δ12 zebrafish triggers NF-κB-mediated endothelial cell activation, leading to vascular dysfunction and hemorrhage. We present evidence that the scar-6 locus plays a role in regulating the expression of the coagulation cascade gene prozb and maintains vascular homeostasis.
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Affiliation(s)
- Gyan Ranjan
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110024, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Paras Sehgal
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110024, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110024, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Vishwanath Cancer Care Foundation, Mumbai, India.
- Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110024, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Vishwanath Cancer Care Foundation, Mumbai, India.
- Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
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8
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Darwish AM, Almehiza AA, Khattab AEN, Sharaf HA, Naglah AM, Bhat MA, Zen AA, Kalmouch A. Using Selenium-enriched Mutated Probiotics as Enhancer for Fertility Parameters in Mice. Biol Trace Elem Res 2024; 202:5118-5125. [PMID: 38321304 DOI: 10.1007/s12011-024-04067-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024]
Abstract
Increasing fertility rates have become one of the factors that concern all people in the world. Therefore, the study aims to use two mutated strains of probiotics enriched with selenium (PSe40/60/1 and BSe50/20/1) to improve fertility. Thirty Swiss albino male mice were divided into three groups; control, LP + S was given Lactobacillus plantarum PSe40/60/1 plus selenium, and BL + S was given Bifidobacterium longum BSe50/20/1 plus selenium. Free testosterone, LH, and FSH were measured in serum by biochemical analysis. Testicular tissues were examined by histopathological analysis. The count and motility of sperm, and sperm abnormalities were determined by microscopic examination. The method of qRT-PCR was used to detect gene expression of Tspyl1, Hsd3b6, and Star genes. The biochemical results showed that serum content of free testosterone (FT) hormone had significantly increase in the BL + S and LP + S groups compared with control. Levels of LH and FSH hormones were the highest in the BL + S group. The treated groups showed all developmental stages of spermatogenesis, including spermatogenesis, spermatocytes, and seminiferous tubule spermatids, as well as intact Sertoli cells and Leydig cells without changes. When compared to the control group, sperm count and motility increased in the BL + S group, while sperm abnormalities decreased. The expression of Tspyl1 gene in testicular tissues decreased in the LP + S and BL + S groups, while the expression of Star and Hsd3b6 genes was higher in the BL + S group and lower in the LP + S group compared with the control group. Therefore, Bifidobacterium longum BSe50/20/1 enriched with selenium could be useful in enhancing male fertility.
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Affiliation(s)
- Ahmed Mohamed Darwish
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, Giza, Egypt
| | - Abdulrahman A Almehiza
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. BOX 2457, 11451, Riyadh, Saudi Arabia
| | - Abd El-Nasser Khattab
- Genetics and Cytology Department, Biotechnology Research Institute, National Research Centre, Dokki, Giza, Egypt.
| | - Hafiza A Sharaf
- Pathology Department, National Research Centre, Dokki, Giza, Egypt
| | - Ahmed M Naglah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. BOX 2457, 11451, Riyadh, Saudi Arabia
| | - Mashooq A Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. BOX 2457, 11451, Riyadh, Saudi Arabia
| | - Amer Alhaj Zen
- Chemistry & Forensics Department, Clifton Camus, Nottingham Trent University, Nottingham, Ng118NS, UK
| | - Atef Kalmouch
- Peptide Chemistry Department, Chemical Industries Institute, National Research Centre, Dokki, Giza, Egypt
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Fang X, Lu X, Ma Y, Sun N, Jiao Y, Meng H, Song M, Jin H, Yao G, Song N, Wu Z, Wen S, Guo H, Xiong H, Song W. Possible involvement of a MEG3-miR-21-SPRY1-NF-κB feedback loop in spermatogenic cells proliferation, autophagy, and apoptosis. iScience 2024; 27:110904. [PMID: 39398251 PMCID: PMC11467676 DOI: 10.1016/j.isci.2024.110904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/20/2024] [Accepted: 09/05/2024] [Indexed: 10/15/2024] Open
Abstract
Non-obstructive azoospermia (NOA) is the most incurable form of male infertility with a complex etiology. Long non-cording RNAs (lncRNAs) were associated with regulating spermatogenesis. Herein, differentially expressed lncRNAs between NOA and control male were screened by RNA-seq analysis. MEG3 was upregulated in NOA tissues and inhibited cell proliferation and promoted cell autophagy and apoptosis in vitro. Through RNA immunoprecipitation (RIP), biotin pull-down assays, and dual-luciferase reporter assays, MEG3 was proved to act as a competing endogenous RNA of microRNA (miR)-21 and thus influenced the SPRY1/ERK/mTOR signaling pathway. Additionally, bioinformatic prediction and chip assay revealed that MEG3 was possibly regulated by nuclear factor κB (NF-κB) and SPRY1/NF-κB/MEG3 formed a feedback loop. Seminiferous tubule microinjection further investigated the effects of MEG3 on testes in vivo. These findings demonstrated that MEG3-miR-21-SPRY1-NF-κB probably acted as a feedback loop leading to azoospermia. Our study might provide a target and theoretical basis for diagnosing and treating NOA.
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Affiliation(s)
- Xingyu Fang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xiaotong Lu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yujie Ma
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ning Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yunyun Jiao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Hui Meng
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Mengjiao Song
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Haixia Jin
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Guidong Yao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ning Song
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhaoting Wu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Shuang Wen
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Haoran Guo
- School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Haosen Xiong
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Wenyan Song
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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Li Z, Li X, Lin J, Wang Y, Cao H, Zhou J. Reevaluation by the CRISPR/Cas9 knockout approach revealed that multiple pluripotency-associated lncRNAs are dispensable for pluripotency maintenance while Snora73a/b is essential for pluripotency exit. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2198-2212. [PMID: 38995489 DOI: 10.1007/s11427-023-2594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 03/15/2024] [Indexed: 07/13/2024]
Abstract
Many long noncoding RNAs (lncRNAs) have been identified through siRNA-based screening as essential regulators of embryonic stem cell (ESC) pluripotency. However, the biological and molecular functions of most lncRNAs remain unclear. Here, we employed CRISPR/Cas9-mediated knockout technology to explore the functions of 8 lncRNAs previously reported to promote pluripotency in mouse ESCs. Unexpectedly, all of these lncRNAs were dispensable for pluripotency maintenance and proliferation in mouse ESCs when disrupted individually or in combination. Single-cell transcriptomic analysis also showed that the knockout of these lncRNAs has a minimal impact on pluripotency gene expression and cell identity. We further showed that several small hairpin RNAs (shRNAs) previously used to knock down lncRNAs caused the downregulation of pluripotency genes in the corresponding lncRNA-knockout ESCs, indicating that off-target effects likely responsible for the pluripotency defects caused by these shRNAs. Interestingly, linc1343-knockout and linc1343-knockdown ESCs failed to form cystic structures and exhibited high expression of pluripotency genes during embryoid body (EB) differentiation. By reintroducing RNA products generated from the linc1343 locus, we found that two snoRNAs, Snora73a and Snora73b, but not lncRNAs, could rescue pluripotency silencing defects during EB differentiation of linc1343 knockout ESCs. Our results suggest that the 8 previously annotated pluripotency-regulating lncRNAs have no overt functions in conventional ESC culture; however, we identified snoRNA products derived from an annotated lncRNA locus as essential regulators for silencing pluripotency genes.
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Affiliation(s)
- Zhen Li
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Xuefei Li
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, China
| | - Huiqing Cao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China.
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.
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Zhan M, Xu H, Yu G, Chen Q, Yang R, Chen Y, Ge J, Wang Z, Yang R, Xu B. Androgen receptor deficiency-induced TUG1 in suppressing ferroptosis to promote benign prostatic hyperplasia through the miR-188-3p/GPX4 signal pathway. Redox Biol 2024; 75:103298. [PMID: 39121689 PMCID: PMC11364272 DOI: 10.1016/j.redox.2024.103298] [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: 04/12/2024] [Revised: 07/14/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Benign prostatic hyperplasia (BPH), characterized by the non-malignant enlargement of the prostate, exhibits a pronounced association with inflammation resulting from androgen receptor (AR) deficiency. Ferroptosis, a cell death mechanism triggered by iron-dependent lipid peroxidation and closely linked to inflammation, has yet to be fully understood in the context of BPH. Using RNA sequencing, we observed a significant elevation of taurine-upregulated gene 1 (TUG1) long noncoding RNA (lncRNA) in BPH tissues compared to normal prostate tissue. High levels of TUG1 exhibited a discernible correlation with both prostate volume and the extent of inflammatory infiltration in BPH patients. The suppression of TUG1 not only led to a reduction in prostate size but also ameliorated AR-deficiency-induced prostatic hyperplasia. Mechanistically, a decrease in AR in prostate luminal cells prompted macrophage aggregation and the release of IL-1β, subsequently fostering the transcription of TUG1 via MYC. Induced TUG1, through competitive binding with miR-188-3p, facilitated the expression of GPX4, thereby diminishing intracellular ROS levels and impeding ferroptosis in prostate luminal cells. Notably, the ferroptosis inducer JKE-1674 alleviated inflammation-induced prostatic hyperplasia in vivo. Together, these findings suggest that AR deficiency crucially inhibits ferroptosis, promoting BPH via the TUG1/miR-188-3p/GPX4 signaling axis, and making ferroptosis induction a promising therapeutic strategy for BPH patients with AR deficiency.
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Affiliation(s)
- Ming Zhan
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; Department of Systems Biology, Beckman Research Institute, City of Hope, Monrovia, CA, 91016, USA
| | - Huan Xu
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Guopeng Yu
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Qi Chen
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Ruifeng Yang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Yanbo Chen
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Jianchao Ge
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Zhong Wang
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; Department of Urology, Shanghai Pudong New Area Gongli Hospital, Shanghai, 200135, China.
| | - Ruimeng Yang
- Department of Pathology, City of Hope, Duarte, CA, 91010, USA; Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
| | - Bin Xu
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
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12
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Xi Q, Yang G, He X, Zhuang H, Li L, Lin B, Wang L, Wang X, Fang C, Chen Q, Yang Y, Yu Z, Zhang H, Cai W, Li Y, Shen H, Liu L, Zhang R. M 6A-mediated upregulation of lncRNA TUG1 in liver cancer cells regulates the antitumor response of CD8 + T cells and phagocytosis of macrophages. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400695. [PMID: 38981064 PMCID: PMC11425850 DOI: 10.1002/advs.202400695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Tumor immune evasion relies on the crosstalk between tumor cells and adaptive/innate immune cells. Immune checkpoints play critical roles in the crosstalk, and immune checkpoint inhibitors have achieved promising clinical effects. The long non-coding RNA taurine-upregulated gene 1 (TUG1) is upregulated in hepatocellular carcinoma (HCC). However, how TUG1 is upregulated and the effects on tumor immune evasion are incompletely understood. Here, METTL3-mediated m6A modification led to TUG1 upregulation is demonstrated. Knockdown of TUG1 inhibited tumor growth and metastasis, increased the infiltration of CD8+ T cells and M1-like macrophages in tumors, promoted the activation of CD8+ T cells through PD-L1, and improved the phagocytosis of macrophages through CD47. Mechanistically, TUG1 regulated PD-L1 and CD47 expressions by acting as a sponge of miR-141 and miR-340, respectively. Meanwhile, TUG1 interacted with YBX1 to facilitate the upregulation of PD-L1 and CD47 transcriptionally, which ultimately regulated tumor immune evasion. Clinically, TUG1 positively correlated with PD-L1 and CD47 in HCC tissues. Moreover, the combination of Tug1-siRNA therapy with a Pdl1 antibody effectively suppressed tumor growth. Therefore, the mechanism of TUG1 in regulating tumor immune evasion is revealed and can inform existing strategies targeting TUG1 for enhancing HCC immune therapy and drug development.
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Affiliation(s)
- Qing Xi
- Department of Gastroenterology and HepatologyThe First Affiliated Hospital of Guangdong Pharmaceutical UniversityGuangzhou510080China
- School of Biomedical Sciences and EngineeringSouth China University of TechnologyGuangzhou511442China
| | - Guangze Yang
- Laboratory of Immunology and InflammationDepartment of ImmunologyKey Laboratory of Immune Microenvironment and Diseases of Educational Ministry of ChinaTianjin Medical UniversityTianjin300070China
| | - Xue He
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Hao Zhuang
- Department of Hepatobiliopancreatic SurgeryThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou450008China
| | - Li Li
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Bing Lin
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Lingling Wang
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Xianyang Wang
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Chunqiang Fang
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Qiurui Chen
- Department of BioscienceSchool of Life Sciences and BiopharmaceuticsGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Yongjie Yang
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Zhaoan Yu
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Hao Zhang
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Wenqian Cai
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Yan Li
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Han Shen
- Department of BioscienceSchool of Life Sciences and BiopharmaceuticsGuangdong Pharmaceutical UniversityGuangzhou51006China
| | - Li Liu
- Department of RadiologyThe University of Texas Southwestern Medical Center5323 Harry Hines Blvd.DallasTX75390USA
| | - Rongxin Zhang
- Laboratory of Immunology and InflammationDepartment of BiotechnologySchool of Life Sciences and BiopharmaceuticsGuangdong Provincial Key Laboratory of Advanced Drug DeliveryGuangdong Provincial Engineering Center of Topical Precise Drug Delivery SystemGuangdong Pharmaceutical UniversityGuangzhou51006China
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Wang GN, Yang M, Wu B, Huo Y, Xu W. The long non-coding RNA mir155hg promotes NLRP3-inflammasome activation and oxidative stress response in acute lung injury by targeting miR-450b-5p to regulate HIF-1α. Free Radic Biol Med 2024; 222:638-649. [PMID: 39019096 DOI: 10.1016/j.freeradbiomed.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/19/2024]
Abstract
BACKGROUND Acute lung injury (ALI) can cause multiple organ dysfunction and a high mortality rate. Inflammatory responses, oxidative stress, and immune damage contribute to their pathogenic mechanisms. We studied the role of the newly discovered lncRNA, Lncmir155hg, in ALI. METHODS The levels of Lncmir155hg and miR-450b-5p from mice with ALI were detected via polymerase chain reaction analysis (qRT-PCR) and Fluorescence in situ hybridization (FISH). Pathological changes of lung were detected by HE (hematoxylin and eosin) staining, and HIF-1α, NOD-like receptor 3 (NLRP3) and caspase-1 protein changes were detected by immunohistochemistry. MLE-12 cells proliferation was detected by Cell-Counting Kit 8 analysis, and reactive oxygen species (ROS) was detected via flow cytometry. NLRP3, apoptosis-associated speck-like protein (ASC), and caspase-1 were measured via western blotting, and enzyme-linked immunosorbent assays detected the expression of Inflammatory factors. Lncmir155hg, miR-450b-5p, miR-450b-5p, and HIF-1α targets were predicted using LncTar and miRWalk and confirmed in dual-luciferase reporter assays. RESULTS In mice with ALI and MLE-12 cells induced by lipopolysaccharide (LPS), Lncmir155hg was high-expressed and miR-450b-5p was low-expressed. sh-Lncmir155hg reduced the damage of lung tissue, the production of inflammatory cytokines and oxidative stress reaction induced by LPS,miR-450b-5p reverses the effect of Lncmir155hg in mice. sh-Lncmir155hg decreased the protein levels of HIF-1α, NLRP3 and caspase-1 in LPS-induced lung tissues. sh-Lncmir155hg + miR-450b-5p inhibitor transfection reversed the effect of sh-Lncmir155hg on the expression of HIF-1α, NLRP3 and caspase-1. Lncmir155hg knockdown induced proliferation and inhibited NLRP3-inflammasome activation and oxidative stress in MLE-12 cells of ALI. miR-450b-5p was identified to have binding with Lncmir155hg, and inhibition of miR-450b-5p eliminated the effect of si-Lncmir155hg in MLE-12 cells of ALI. More importantly, miR-450b-5p was directly combined with HIF-1α, miR-450b-5p mimic promoted proliferation and inhibited activation of inflammasome associated proteins and reaction of oxidative stress, and HIF-1α overexpression abolished these effects. CONCLUSION Lncmir155hg aggravated ALI via the miR-450b-5p/HIF-1α axis.
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Affiliation(s)
- Gui Na Wang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Miao Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Bo Wu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yan Huo
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wei Xu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
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14
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Xu C, Cao JF, Pei Y, Kim Y, Moon H, Fan CQ, Liao MC, Wang XY, Yao F, Zhang YJ, Zhang SH, Zhang J, Li JZ, Kim JS, Ma L, Xie ZJ. Injectable hydrogel harnessing foreskin mesenchymal stem cell-derived extracellular vesicles for treatment of chronic diabetic skin wounds. J Control Release 2024; 370:339-353. [PMID: 38685383 DOI: 10.1016/j.jconrel.2024.04.049] [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: 11/14/2023] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Chronic skin wounds are a serious complication of diabetes with a high incidence rate, which can lead to disability or even death. Previous studies have shown that mesenchymal stem cells derived extracellular vesicles (EVs) have beneficial effects on wound healing. However, the human foreskin mesenchymal stem cell (FSMSCs)-derived extracellular vesicle (FM-EV) has not yet been isolated and characterized. Furthermore, the limited supply and short lifespan of EVs also hinder their practical use. In this study, we developed an injectable dual-physical cross-linking hydrogel (PSiW) with self-healing, adhesive, and antibacterial properties, using polyvinylpyrrolidone and silicotungstic acid to load FM-EV. The EVs were evenly distributed in the hydrogel and continuously released. In vivo and vitro tests demonstrated that the synergistic effect of EVs and hydrogel could significantly promote the repair of diabetic wounds by regulating macrophage polarization, promoting angiogenesis, and improving the microenvironment. Overall, the obtained EVs-loaded hydrogels developed in this work exhibited promising applicability for the repair of chronic skin wounds in diabetes patients.
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Affiliation(s)
- Chang Xu
- Institute of Pediatrics, Shenzhen Children's Hospital, Clinical Medical College of Southern University of Science and Technology, Shenzhen 518038, China
| | - Jin-Feng Cao
- Beijing Key Laboratory of Wood Science and Engineering, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Wood Material Science and Application (Beijing Forestry University), Ministry of Education, Beijing 100083, China
| | - Yue Pei
- Institute of Pediatrics, Shenzhen Children's Hospital, Clinical Medical College of Southern University of Science and Technology, Shenzhen 518038, China
| | - Yujin Kim
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Huiyeon Moon
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Chui-Qin Fan
- Institute of Pediatrics, Shenzhen Children's Hospital, Clinical Medical College of Southern University of Science and Technology, Shenzhen 518038, China
| | - Mao-Chuan Liao
- Institute of Pediatrics, Shenzhen Children's Hospital, Clinical Medical College of Southern University of Science and Technology, Shenzhen 518038, China
| | - Xing-Yu Wang
- Department of Emergency, ChangYang Tujia Autonomous County People's Hospital, Yichang 443000, China
| | - Fei Yao
- Eye Center of Xiangya Hospital, Central South University, Changsha 410000, China
| | - Yu-Jun Zhang
- Institute of Pediatrics, Shenzhen Children's Hospital, Clinical Medical College of Southern University of Science and Technology, Shenzhen 518038, China
| | - Shao-Hui Zhang
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jian Zhang
- Institute of Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jian-Zhang Li
- Beijing Key Laboratory of Wood Science and Engineering, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Wood Material Science and Application (Beijing Forestry University), Ministry of Education, Beijing 100083, China.
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Lian Ma
- Institute of Pediatrics, Shenzhen Children's Hospital, Clinical Medical College of Southern University of Science and Technology, Shenzhen 518038, China; Department of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen 518038, China; Department of Pediatrics, The Third Affifiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China.
| | - Zhong-Jian Xie
- Institute of Pediatrics, Shenzhen Children's Hospital, Clinical Medical College of Southern University of Science and Technology, Shenzhen 518038, China; Shenzhen International Institute for Biomedical Research, Shenzhen 518116, Guangdong, China.
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15
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Piégu B, Lefort G, Douet C, Milhes M, Jacques A, Lareyre JJ, Monget P, Fouchécourt S. A first complete catalog of highly expressed genes in eight chicken tissues reveals uncharacterized gene families specific for the chicken testis. Physiol Genomics 2024; 56:445-456. [PMID: 38497118 DOI: 10.1152/physiolgenomics.00151.2023] [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: 12/22/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024] Open
Abstract
Based on next-generation sequencing, we established a repertoire of differentially overexpressed genes (DoEGs) in eight adult chicken tissues: the testis, brain, lung, liver, kidney, muscle, heart, and intestine. With 4,499 DoEGs, the testis had the highest number and proportion of DoEGs compared with the seven somatic tissues. The testis DoEG set included the highest proportion of long noncoding RNAs (lncRNAs; 1,851, representing 32% of the lncRNA genes in the whole genome) and the highest proportion of protein-coding genes (2,648, representing 14.7% of the protein-coding genes in the whole genome). The main significantly enriched Gene Ontology terms related to the protein-coding genes were "reproductive process," "tubulin binding," and "microtubule cytoskeleton." Using real-time quantitative reverse transcription-polymerase chain reaction, we confirmed the overexpression of genes that encode proteins already described in chicken sperm [such as calcium binding tyrosine phosphorylation regulated (CABYR), spermatogenesis associated 18 (SPATA18), and CDK5 regulatory subunit associated protein (CDK5RAP2)] but whose testis origin had not been previously confirmed. Moreover, we demonstrated the overexpression of vertebrate orthologs of testis genes not yet described in the adult chicken testis [such as NIMA related kinase 2 (NEK2), adenylate kinase 7 (AK7), and CCNE2]. Using clustering according to primary sequence homology, we found that 1,737 of the 2,648 (67%) testis protein-coding genes were unique genes. This proportion was significantly higher than the somatic tissues except muscle. We clustered the other 911 testis protein-coding genes into 495 families, from which 47 had all paralogs overexpressed in the testis. Among these 47 testis-specific families, eight contained uncharacterized duplicated paralogs without orthologs in other metazoans except birds: these families are thus specific for chickens/birds.NEW & NOTEWORTHY Comparative next-generation sequencing analysis of eight chicken tissues showed that the testis has highest proportion of long noncoding RNA and protein-coding genes of the whole genome. We identified new genes in the chicken testis, including orthologs of known mammalian testicular genes. We also identified 47 gene families in which all the members were overexpressed, if not exclusive, in the testis. Eight families, organized in duplication clusters, were unknown, without orthologs in metazoans except birds, and are thus specific for chickens/birds.
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Affiliation(s)
- Benoît Piégu
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Gaëlle Lefort
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Cécile Douet
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Marine Milhes
- US 1426, GeT-PlaGe, Genotoul, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castanet-Tolosan, France
| | - Aurore Jacques
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Jean-Jacques Lareyre
- UR1037 LPGP, Fish Physiology and Genomics, Campus de Beaulieu, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Rennes, France
| | - Philippe Monget
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
| | - Sophie Fouchécourt
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, Université de Tours, PRC, Nouzilly, France
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Lin X, Lu Y, Zhang C, Cui Q, Tang YD, Ji X, Cui C. LncRNADisease v3.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Res 2024; 52:D1365-D1369. [PMID: 37819033 PMCID: PMC10767967 DOI: 10.1093/nar/gkad828] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
Systematic integration of lncRNA-disease associations is of great importance for further understanding their underlying molecular mechanisms and exploring lncRNA-based biomarkers and therapeutics. The database of long non-coding RNA-associated diseases (LncRNADisease) is designed for the above purpose. Here, an updated version (LncRNADisease v3.0) has curated comprehensive lncRNA (including circRNA) and disease associations from the burgeoning literatures. LncRNADisease v3.0 exhibits an over 2-fold increase in experimentally supported associations, with a total of 25440 entries, compared to the last version. Besides, each lncRNA-disease pair is assigned a confidence score based on experimental evidence. Moreover, all associations between lncRNAs/circRNAs and diseases are classified into general associations and causal associations, representing whether lncRNAs or circRNAs can directly lead to the development or progression of corresponding diseases, with 15721 and 9719 entries, respectively. In a case study, we used the data of LncRNADisease v3.0 to calculate the phenotypic similarity between human and mouse lncRNAs. This database will continue to serve as a valuable resource for potential clinical applications related to lncRNAs and circRNAs. LncRNADisease v3.0 is freely available at http://www.rnanut.net/lncrnadisease.
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Affiliation(s)
- Xiao Lin
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China
| | - Yingyu Lu
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China
| | - Chenhao Zhang
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China
| | - Qinghua Cui
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China
- School of Sports Medicine, Wuhan Institute of Physical Education, No.461 Luoyu Rd. Wuchang District, WuHan 430079, Hubei Province, China
| | - Yi-Da Tang
- Department of Cardiology and Institute of Vascular Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Third Hospital, 49 Huayuanbei Road, Beijing 100191, China
| | - Xiangwen Ji
- Department of Cardiology and Institute of Vascular Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Third Hospital, 49 Huayuanbei Road, Beijing 100191, China
| | - Chunmei Cui
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China
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Haybar H, Sadati NS, Purrahman D, Mahmoudian-Sani MR, Saki N. lncRNA TUG1 as potential novel biomarker for prognosis of cardiovascular diseases. Epigenomics 2023; 15:1273-1290. [PMID: 38088089 DOI: 10.2217/epi-2023-0242] [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] [Indexed: 01/05/2024] Open
Abstract
Globally, cardiovascular diseases (CVDs) are among the leading causes of death. In light of the high prevalence and mortality of CVDs, it is imperative to understand the molecules involved in CVD pathogenesis and the signaling pathways that they initiate. This may facilitate the development of more precise and expedient diagnostic techniques, the identification of more effective prognostic molecules and the identification of potential therapeutic targets. Numerous studies have examined the role of lncRNAs, such as TUG1, in CVD pathogenesis in recent years. According to this review article, TUG1 can be considered a biomarker for predicting the prognosis of CVD.
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Affiliation(s)
- Habib Haybar
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Narjes Sadat Sadati
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Daryush Purrahman
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Reza Mahmoudian-Sani
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Hu Q, Xia X, Lian Z, Tian H, Li Z. Regulatory mechanism of LncRNAs in gonadal differentiation of hermaphroditic fish, Monopterus albus. Biol Sex Differ 2023; 14:74. [PMID: 37880697 PMCID: PMC10598917 DOI: 10.1186/s13293-023-00559-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Monopterus albus is a hermaphroditic fish with sex reversal from ovaries to testes via the ovotestes in the process of gonadal development, but the molecular mechanism of the sex reversal was unknown. METHODS We produced transcriptomes containing mRNAs and lncRNAs in the crucial stages of the gonad, including the ovary, ovotestis and testis. The expression of the crucial lncRNAs and their target genes was detected using qRT‒PCR and in situ hybridization. The methylation level and activity of the lncRNA promoter were analysed by applying bisulfite sequencing PCR and dual-luciferase reporter assays, respectively. RESULTS This effort revealed that gonadal development was a dynamic expression change. Regulatory networks of lncRNAs and their target genes were constructed through integrated analysis of lncRNA and mRNA data. The expression and DNA methylation of the lncRNAs MSTRG.38036 and MSTRG.12998 and their target genes Psmβ8 and Ptk2β were detected in developing gonads and sex reversal gonads. The results showed that lncRNAs and their target genes exhibited consistent expression profiles and that the DNA methylation levels were negatively regulated lncRNA expression. Furthermore, we found that Ptk2β probably regulates cyp19a1 expression via the Ptk2β/EGFR/STAT3 pathway to reprogram sex differentiation. CONCLUSIONS This study provides novel insight from lncRNA to explore the potential molecular mechanism by which DNA methylation regulates lncRNA expression to facilitate target gene transcription to reprogram sex differentiation in M. albus, which will also enrich the sex differentiation mechanism of teleosts.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China.
| | - Xueping Xia
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China
| | - Zitong Lian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China.
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19
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Trewin AJ, Weeks KL, Wadley GD, Lamon S. Regulation of mitochondrial calcium uniporter expression and calcium-dependent cell signaling by lncRNA Tug1 in cardiomyocytes. Am J Physiol Cell Physiol 2023; 325:C1097-C1105. [PMID: 37721002 DOI: 10.1152/ajpcell.00339.2023] [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: 07/26/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Cardiomyocyte calcium homeostasis is a tightly regulated process. The mitochondrial calcium uniporter (MCU) complex can buffer elevated cytosolic Ca2+ levels and consists of pore-forming proteins including MCU, and various regulatory proteins such as mitochondrial calcium uptake proteins 1 and 2 (MICU1/2). The stoichiometry of these proteins influences the sensitivity to Ca2+ and the activity of the complex. However, the factors that regulate their gene expression remain incompletely understood. Long noncoding RNAs (lncRNAs) regulate gene expression through various mechanisms, and we recently found that the lncRNA Tug1 increased the expression of Mcu and associated genes. To further explore this, we performed antisense LNA knockdown of Tug1 (Tug1 KD) in H9c2 rat cardiomyocytes. Tug1 KD increased MCU protein expression, yet pyruvate dehydrogenase dephosphorylation, which is indicative of mitochondrial Ca2+ uptake, was not enhanced. However, RNA-seq revealed that Tug1 KD increased Mcu along with differential expression of >1,000 genes including many related to Ca2+ regulation pathways in the heart. To understand the effect of this on Ca2+ signaling, we measured phosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaMKII) and its downstream target cAMP Response Element-Binding protein (CREB), a transcription factor known to drive Mcu gene expression. In response to a Ca2+ stimulus, the increase in CaMKII and CREB phosphorylation was attenuated by Tug1 KD. Inhibition of CaMKII, but not CREB, partially prevented the Tug1 KD-mediated increase in Mcu. Together, these data suggest that Tug1 modulates MCU expression via a mechanism involving CaMKII and regulates cardiomyocyte Ca2+ signaling, which could have important implications for cardiac function.NEW & NOTEWORTHY Calcium is essential for signaling, excitation contraction, and energy homeostasis in the heart. Despite this, molecular regulators of these processes are not completely understood. We report that knockdown of lncRNA Tug1 alters the calcium handling transcriptome and increases mitochondrial calcium uniporter expression via a mechanism involving CaMKII. As overexpression of MCU is known to be protective against pathological cardiac remodeling, targeting Tug1 may be a potential strategy for treating cardiovascular disease.
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Affiliation(s)
- Adam J Trewin
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University, Geelong, Victoria, Australia
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kate L Weeks
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Glenn D Wadley
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University, Geelong, Victoria, Australia
| | - Séverine Lamon
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University, Geelong, Victoria, Australia
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20
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Hashemi Karoii D, Azizi H. Functions and mechanism of noncoding RNA in regulation and differentiation of male mammalian reproduction. Cell Biochem Funct 2023; 41:767-778. [PMID: 37583312 DOI: 10.1002/cbf.3838] [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: 05/16/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/17/2023]
Abstract
Noncoding RNAs (ncRNAs) are active regulators of a wide range of biological and physiological processes, including the majority of mammalian reproductive events. Knowledge of the biological activities of ncRNAs in the context of mammalian reproduction will allow for a more comprehensive and comparative understanding of male sterility and fertility. In this review, we describe recent advances in ncRNA-mediated control of mammalian reproduction and emphasize the importance of ncRNAs in several aspects of mammalian reproduction, such as germ cell biogenesis and reproductive organ activity. Furthermore, we focus on gene expression regulatory feedback loops including hormones and ncRNA expression to better understand germ cell commitment and reproductive organ function. Finally, this study shows the role of ncRNAs in male reproductive failure and provides suggestions for further research.
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Affiliation(s)
- Danial Hashemi Karoii
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Hossein Azizi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
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21
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Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. The status of the human gene catalogue. Nature 2023; 622:41-47. [PMID: 37794265 PMCID: PMC10575709 DOI: 10.1038/s41586-023-06490-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/27/2023] [Indexed: 10/06/2023]
Abstract
Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.
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Affiliation(s)
- Paulo Amaral
- INSPER Institute of Education and Research, Sao Paulo, Brazil
| | | | - Francisco M De La Vega
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Tempus Labs, Chicago, IL, USA
| | | | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas Gingeras
- Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jennifer L Harrow
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Royston, UK
| | - Artemis G Hatzigeorgiou
- Department of Computer Science and Biomedical Informatics, Universithy of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens, Greece
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Christine A Wells
- Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Yandell
- Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Human Technopole, Milan, Italy.
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
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22
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Hu K, Wang C, Xu Y, Li F, Han X, Song C, Liang M. Interaction of lncRNA Gm2044 and EEF2 promotes estradiol synthesis in ovarian follicular granulosa cells. J Ovarian Res 2023; 16:171. [PMID: 37612724 PMCID: PMC10464411 DOI: 10.1186/s13048-023-01232-z] [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: 08/29/2022] [Accepted: 07/07/2023] [Indexed: 08/25/2023] Open
Abstract
The functions and molecular mechanisms of long noncoding RNA (lncRNA) in reproduction have been widely studied at present. However, lncRNA regulating hormone synthesis in ovarian follicular granulosa cells has not been sufficiently studied. Our previous research demonstrated that lncRNA Gm2044 could promote estradiol synthesis in follicular granulosa cells. In this study, we identified 21 binding proteins of lncRNA Gm2044 in ovarian follicles using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS). RNA immunoprecipitation (RNA IP) and reverse transcription PCR (RT-PCR) confirmed that lncRNA Gm2044 can interact with eukaryotic translation elongation factor 2 (EEF2) protein. Furthermore, we constructed lncRNA Gm2044 knockout mice using the CRISPR/Cas9 method. Although the follicular development and fertility of female lncRNA Gm2044 knockout mice were not affected, the serum estradiol concentration in female lncRNA Gm2044 knockout mice significantly decreased. Western blotting and ELISA revealed that lncRNA Gm2044 may promote the binding of EEF2 to Nr5a1 mRNA and then enhance the Nr5a1 mRNA translation, and the upregulated NR5A1 protein can strengthen estradiol synthesis. To determine the potential signaling pathway of lncRNA Gm2044 regulating estradiol synthesis, transcriptome sequencing was performed for ovaries of adult lncRNA Gm2044 knockout mice, which identified 565 significant up-regulated genes and 303 significant down-regulated genes, which were then analyzed with Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and validated by molecular experiments. Understanding how lncRNA Gm2044/EEF2 protein regulates estradiol synthesis will help treat estrogen-related reproductive diseases.
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Affiliation(s)
- Ke Hu
- School of Life Science, Bengbu Medical College, Bengbu, China
| | - Chen Wang
- School of Life Science, Bengbu Medical College, Bengbu, China
| | - Yifan Xu
- School of Life Science, Bengbu Medical College, Bengbu, China
| | - Fan Li
- School of Laboratory Medicine, Bengbu Medical College, Bengbu, China
| | - Xuefeng Han
- School of Life Science, Bengbu Medical College, Bengbu, China
| | - Chuanwang Song
- School of Laboratory Medicine, Bengbu Medical College, Bengbu, China.
| | - Meng Liang
- School of Life Science, Bengbu Medical College, Bengbu, China.
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23
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Li Y, Zhai H, Tong L, Wang C, Xie Z, Zheng K. LncRNA Functional Screening in Organismal Development. Noncoding RNA 2023; 9:36. [PMID: 37489456 PMCID: PMC10366883 DOI: 10.3390/ncrna9040036] [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: 05/10/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023] Open
Abstract
Controversy continues over the functional prevalence of long non-coding RNAs (lncRNAs) despite their being widely investigated in all kinds of cells and organisms. In animals, lncRNAs have aroused general interest from exponentially increasing transcriptomic repertoires reporting their highly tissue-specific and developmentally dynamic expression, and more importantly, from growing experimental evidence supporting their functionality in facilitating organogenesis and individual fitness. In mammalian testes, while a great multitude of lncRNA species are identified, only a minority of them have been shown to be useful, and even fewer have been demonstrated as true requirements for male fertility using knockout models to date. This noticeable gap is attributed to the virtual existence of a large number of junk lncRNAs, the lack of an ideal germline culture system, difficulty in loss-of-function interrogation, and limited screening strategies. Facing these challenges, in this review, we discuss lncRNA functionality in organismal development and especially in mouse testis, with a focus on lncRNAs with functional screening.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Huicong Zhai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Lingxiu Tong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Cuicui Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhiming Xie
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
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24
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 711] [Impact Index Per Article: 355.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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25
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Lismer A, Kimmins S. Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development. Nat Commun 2023; 14:2142. [PMID: 37059740 PMCID: PMC10104880 DOI: 10.1038/s41467-023-37820-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Although more studies are demonstrating that a father's environment can influence child health and disease, the molecular mechanisms underlying non-genetic inheritance remain unclear. It was previously thought that sperm exclusively contributed its genome to the egg. More recently, association studies have shown that various environmental exposures including poor diet, toxicants, and stress, perturbed epigenetic marks in sperm at important reproductive and developmental loci that were associated with offspring phenotypes. The molecular and cellular routes that underlie how epigenetic marks are transmitted at fertilization, to resist epigenetic reprogramming in the embryo, and drive phenotypic changes are only now beginning to be unraveled. Here, we provide an overview of the state of the field of intergenerational paternal epigenetic inheritance in mammals and present new insights into the relationship between embryo development and the three pillars of epigenetic inheritance: chromatin, DNA methylation, and non-coding RNAs. We evaluate compelling evidence of sperm-mediated transmission and retention of paternal epigenetic marks in the embryo. Using landmark examples, we discuss how sperm-inherited regions may escape reprogramming to impact development via mechanisms that implicate transcription factors, chromatin organization, and transposable elements. Finally, we link paternally transmitted epigenetic marks to functional changes in the pre- and post-implantation embryo. Understanding how sperm-inherited epigenetic factors influence embryo development will permit a greater understanding related to the developmental origins of health and disease.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal Hospital Research Centre, Montreal, QC, H2X 0A9, Canada.
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26
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Yan C, Meng Y, Yang J, Chen J, Jiang W. Translational landscape in human early neural fate determination. Development 2023; 150:297188. [PMID: 36846898 DOI: 10.1242/dev.201177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 02/19/2023] [Indexed: 03/01/2023]
Abstract
Gene expression regulation in eukaryotes is a multi-level process, including transcription, mRNA translation and protein turnover. Many studies have reported sophisticated transcriptional regulation during neural development, but the global translational dynamics are still ambiguous. Here, we differentiate human embryonic stem cells (ESCs) into neural progenitor cells (NPCs) with high efficiency and perform ribosome sequencing and RNA sequencing on both ESCs and NPCs. Data analysis reveals that translational controls engage in many crucial pathways and contribute significantly to regulation of neural fate determination. Furthermore, we show that the sequence characteristics of the untranslated region (UTR) might regulate translation efficiency. Specifically, genes with short 5'UTR and intense Kozak sequence are associated with high translation efficiency in human ESCs, whereas genes with long 3'UTR are related to high translation efficiency in NPCs. In addition, we have identified four biasedly used codons (GAC, GAT, AGA and AGG) and dozens of short open reading frames during neural progenitor differentiation. Thus, our study reveals the translational landscape during early human neural differentiation and provides insights into the regulation of cell fate determination at the translational level.
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Affiliation(s)
- Chenchao Yan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yajing Meng
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jie Yang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jian Chen
- Chinese Institute for Brain Research (Beijing), Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Human Genetics Resource Preservation Center of Wuhan University, Wuhan 430071, China
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27
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Li Y, Wang L, Tian J, Zu Y, Wang F, Yang Y, Ma S, Cao J, Huang Q, Ha C. The role of Connexin26 regulated by MiR-2114-3p in the pathogenesis of ovarian cancer. Biochem Biophys Res Commun 2023; 640:105-116. [PMID: 36565612 DOI: 10.1016/j.bbrc.2022.11.082] [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: 11/14/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES The purpose of our research was to determine the expression of Cx26 and miR-2114-3p, and their effects on proliferation, migration, and invasion in ovarian cancer and their mechanisms. MATERIALS AND METHODS Transcriptome sequencing was performed and differentially expressed Cx26 was screened. The mRNA and protein levels of Cx26 in EOC and normal ovarian tissues were verified. The relationship between Cx26 levels and prognostics was analyzed. Cx26 Lentiviral vectors were constructed to detect its effect on ovarian cancer. WB verified that PI3K/AKT pathway was the possible signal pathway regulated by Cx26. The interaction between miR-2114-3p and Cx26 was detected by double luciferase reporter assay and qrt-PCR. CCK8, clone formation, transwell, and flow cytometry assays were conducted in cells transfected miR-2114-3p plasmids. The vivo experiment investigated the effects of Cx26 on subcutaneous tumor growth, PI3K expression, proliferation proteins Ki67 and PCNA. RESULTS Cx26 was up-regulated in EOC tissue and cell lines, and was associated with poor prognosis of ovarian cancer, while miR-2114-3p was down-regulated in EOC cell lines. Cx26 was a direct target of miR-2114-3p. Cx26 overexpression and miR-2114-3p inhibition promoted the growth, motility, invasiveness, and S phase arrest of EOC cells. Additionally, Cx26 could activated PI3K pathway whatever in vivo and in vitro. CONCLUSIONS Dysregulation of Cx26 is critical in EOC patients. Manipulation of this mechanism may influence the survival of EOC patients. MiR-2114-3p regulates the tumor-promoting activity of Cx26 in EOC. By inhibiting the PI3K pathway or knocking down Cx26 effectively inhibits tumor growth in EOC cells and Nude mouse model.
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Affiliation(s)
- Yongmei Li
- General Hospital of Ningxia Medical University, Department of Gynecology, Yinchuan, China; Ningxia Medical University, Clinical Medical College, Yinchuan, China
| | - Libin Wang
- General Hospital of Ningxia Medical University, Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, China
| | - Jinhai Tian
- Ningxia Medical University, Clinical Medical College, Yinchuan, China; General Hospital of Ningxia Medical University, Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, China
| | - Yizheng Zu
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Fang Wang
- People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Yu'e Yang
- Ningxia Medical University, Clinical Medical College, Yinchuan, China
| | - Shaohan Ma
- Ningxia Medical University, Clinical Medical College, Yinchuan, China
| | - Jia Cao
- General Hospital of Ningxia Medical University, Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, China
| | - Qi Huang
- General Hospital of Ningxia Medical University, Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, China
| | - Chunfang Ha
- General Hospital of Ningxia Medical University, Department of Gynecology, Yinchuan, China; Ningxia Medical University, Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Yinchuan, China.
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Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW. Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types. Cell Rep 2022; 41:111893. [PMID: 36577377 DOI: 10.1016/j.celrep.2022.111893] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/30/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Within the scope of the FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem cells (iPSCs) and systematically characterize their roles in self-renewal and pluripotency. We find 36 lncRNAs (18%) exhibiting cell growth inhibition. From the knockdown of 123 lncRNAs with transcriptome profiling, 36 lncRNAs (29.3%) show molecular phenotypes. Integrating the molecular phenotypes with chromatin-interaction assays further reveals cis- and trans-interacting partners as potential primary targets. Additionally, cell-type enrichment analysis identifies lncRNAs associated with pluripotency, while the knockdown of LINC02595, CATG00000090305.1, and RP11-148B6.2 modulates colony formation of iPSCs. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit a consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights that molecular phenotyping is more comprehensive in revealing affected pathways.
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Affiliation(s)
- Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Anika V Prabhu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Callum Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yan Jun Lan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, QC, Canada
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | | | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masaki Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Wing Hin Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Xufeng Shu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Human Technopole, via Rita Levi Montalcini 1, Milan, Italy
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore.
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Shi X, Wei W, Zou Y, Dong L, Wu H, Jiang J, Li X, Chen J. LncRNA Taurine Up-Regulated 1 plays a proapoptotic role by regulating nuclear-cytoplasmic shuttle of HuR under the condition of neuronal ischemia. Neuroreport 2022; 33:799-811. [PMID: 36367790 PMCID: PMC9648984 DOI: 10.1097/wnr.0000000000001848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022]
Abstract
The study aimed to identify TUG1 as an essential regulator of apoptosis in HT22 (mouse hippocampal neuronal cells) by direct interaction with the RNA-binding protein HuR. In order to study the role of TUG1 in the context of ischemia, we used mouse hippocampal neuronal cells treated with oxyglucose deprivation to establish an in-vitro ischemia model. A bioinformatic analysis and formaldehyde RNA immunoprecipitation (fRIP) were used to investigate the biological functions. A Western blot assay and reverse transcription polymerase chain reaction were used to explore the expression of the molecules involved. A cell proliferation and cytotoxicity assay was performed to detect neuronal apoptosis. TUG1 exhibits a localization-specific expression pattern in HT22 cells under OGD treatment. The bioinformatics analysis showed a strong correlation between the TUG1 and HuR as predicted, and this interaction was subsequently confirmed by fRIP-qPCR. We found that HuR was translocated from the nucleus to the cytoplasm after ischemia treatment and subsequently targeted and stabilized COX-2 mRNA, which led to elevated COX-2 mRNA levels and apoptosis of the HT22 cells. Furthermore, nuclear-specific disruption of TUG1 prevented the translocation of HuR to the cytoplasm and decreased COX-2 mRNA expression, resulting in increased cell viability and partially reversed apoptosis. In conclusion, it was demonstrated that TUG1 accelerates the process of apoptosis by promoting the transfer of HuR to the cytoplasm and stabilizing COX-2 mRNA. These results provide useful information concerning a therapeutic target for ischemic stroke.
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Affiliation(s)
- Xiaocheng Shi
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University
| | - Yichun Zou
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lixin Dong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University
| | - Hengping Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University
| | - Jiazhi Jiang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
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30
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Zheng X, Xiang M. Mitochondrion-located peptides and their pleiotropic physiological functions. FEBS J 2022; 289:6919-6935. [PMID: 35599630 DOI: 10.1111/febs.16532] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 01/13/2023]
Abstract
With the development of advanced technologies, many small open reading frames (sORFs) have been found to be translated into micropeptides. Interestingly, a considerable proportion of micropeptides are located in mitochondria, which are designated here as mitochondrion-located peptides (MLPs). These MLPs often contain a transmembrane domain and show a high degree of conservation across species. They usually act as co-factors of large proteins and play regulatory roles in mitochondria such as electron transport in the respiratory chain, reactive oxygen species (ROS) production, metabolic homeostasis, and so on. Deficiency of MLPs disturbs diverse physiological processes including immunity, differentiation, and metabolism both in vivo and in vitro. These findings reveal crucial functions for MLPs and provide fresh insights into diverse mitochondrion-associated biological processes and diseases.
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Affiliation(s)
- Xintong Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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31
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Tzur YB. lncRNAs in fertility: redefining the gene expression paradigm? Trends Genet 2022; 38:1170-1179. [PMID: 35728988 DOI: 10.1016/j.tig.2022.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/02/2022] [Accepted: 05/26/2022] [Indexed: 01/24/2023]
Abstract
Comparative transcriptome approaches assume that highly or dynamically expressed genes are important. This has led to the identification of many genes critical for cellular activity and organism development. However, while testes express the highest levels of long noncoding RNAs (lncRNAs), there is scarcely any evidence for lncRNAs with significant roles in fertility. This was explained by changes in chromatin structure during spermatogenesis that lead to 'promiscuous transcription' with no functional roles for the transcripts. Recent discoveries offer novel and surprising alternatives. Here, I review the current knowledge regarding the involvement of lncRNAs in fertility, why I find gametogenesis different from other developmental processes, offer models to explain why the experimental evidence did not meet theoretical predictions, and suggest possible approaches to test the models.
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Affiliation(s)
- Yonatan B Tzur
- Department of Genetics, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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32
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Gimbel AT, Koziarek S, Theodorou K, Schulz JF, Stanicek L, Kremer V, Ali T, Günther S, Kumar S, Jo H, Hübner N, Maegdefessel L, Dimmeler S, van Heesch S, Boon RA. Aging-regulated TUG1 is dispensable for endothelial cell function. PLoS One 2022; 17:e0265160. [PMID: 36173935 PMCID: PMC9522302 DOI: 10.1371/journal.pone.0265160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022] Open
Abstract
The evolutionary conserved Taurine Upregulated Gene 1 (TUG1) is a ubiquitously expressed gene that is one of the highest expressed genes in human and rodent endothelial cells (ECs). We here show that TUG1 expression decreases significantly in aging mouse carotid artery ECs and human ECs in vitro, indicating a potential role in the aging endothelial vasculature system. We therefore investigated if, and how, TUG1 might function in aging ECs, but despite extensive phenotyping found no alterations in basal EC proliferation, apoptosis, barrier function, migration, mitochondrial function, or monocyte adhesion upon TUG1 silencing in vitro. TUG1 knockdown did slightly and significantly decrease cumulative sprout length upon vascular endothelial growth factor A stimulation in human umbilical vein endothelial cells (HUVECs), though TUG1-silenced HUVECs displayed no transcriptome-wide mRNA expression changes explaining this effect. Further, ectopic expression of the highly conserved and recently discovered 153 amino acid protein translated from certain TUG1 transcript isoforms did not alter angiogenic sprouting in vitro. Our data show that, despite a high expression and strong evolutionary conservation of both the TUG1 locus and the protein sequence it encodes, TUG1 does not seem to play a major role in basic endothelial cell function.
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Affiliation(s)
- Anna Theresa Gimbel
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
| | - Susanne Koziarek
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
| | - Kosta Theodorou
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Laura Stanicek
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, Amsterdam, Netherlands
| | - Veerle Kremer
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, Amsterdam, Netherlands
| | - Tamer Ali
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
| | - Stefan Günther
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
- Max Planck Institute for Heart and Lung Research, Bioinformatics and Deep Sequencing Platform, Bad Nauheim, Germany
| | - Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
- Division of Cardiology, Emory University, Atlanta, Georgia, United States of America
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
- Division of Cardiology, Emory University, Atlanta, Georgia, United States of America
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
| | - Lars Maegdefessel
- Department of Vascular and Endovascular Surgery, Technical University Munich, Munich, Germany
- German Center for Cardiovascular Research DZHK, Partner Site Munich, Munich, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Stefanie Dimmeler
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
| | | | - Reinier A. Boon
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, Amsterdam, Netherlands
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Farzaneh M, Ghasemian M, Ghaedrahmati F, Poodineh J, Najafi S, Masoodi T, Kurniawan D, Uddin S, Azizidoost S. Functional roles of lncRNA-TUG1 in hepatocellular carcinoma. Life Sci 2022; 308:120974. [PMID: 36126725 DOI: 10.1016/j.lfs.2022.120974] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022]
Abstract
Hepatocellular carcinoma (HCC) or hepatoma is malignant cancer that starts from the main liver cells. Although various classical methods have been used for patients with HCC, various molecular mechanisms involved in HCC progression should be invested. Previous studies demonstrated that abnormal expression of long non-coding RNAs (lncRNAs) presented important roles in the pathogenesis of HCC cells. LncRNA TUG1 was found to mediate HCC cell growth, EMT, and metastasis. Therefore, targeting TUG1 and its downstream genes may be a suitable approach for patients with HCC. In this review, we summarized the potential roles of TUG1 in HCC.
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Affiliation(s)
- Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Majid Ghasemian
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jafar Poodineh
- Department of Clinical Biochemistry, School of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tariq Masoodi
- Cancer Research Department, Sidra Medicine, Doha 26999, Qatar
| | - Dedy Kurniawan
- Laboratory Animal and Stem Cells, PT Bio Farma (Persero), Bandung 40161, West Java, Indonesia
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar.
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Bechara ST, Kabbani LES, Maurer-Alcalá XX, Nowacki M. Identification of novel, functional, long noncoding RNAs involved in programmed, large-scale genome rearrangements. RNA (NEW YORK, N.Y.) 2022; 28:1110-1127. [PMID: 35680167 PMCID: PMC9297840 DOI: 10.1261/rna.079134.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Noncoding RNAs (ncRNAs) make up to ∼98% percent of the transcriptome of a given organism. In recent years, one relatively new class of ncRNAs, long noncoding RNAs (lncRNAs), were shown to be more than mere by-products of gene expression and regulation. The unicellular eukaryote Paramecium tetraurelia is a member of the ciliate phylum, an extremely heterogeneous group of organisms found in most bodies of water across the globe. A hallmark of ciliate genetics is nuclear dimorphism and programmed elimination of transposons and transposon-derived DNA elements, the latter of which is essential for the maintenance of the somatic genome. Paramecium and ciliates in general harbor a plethora of different ncRNA species, some of which drive the process of large-scale genome rearrangements, including DNA elimination, during sexual development. Here, we identify and validate the first known functional lncRNAs in ciliates to date. Using deep-sequencing and subsequent bioinformatic processing and experimental validation, we show that Paramecium expresses at least 15 lncRNAs. These candidates were predicted by a highly conservative pipeline, and informatic analyses hint at differential expression during development. Depletion of two lncRNAs, lnc1 and lnc15, resulted in clear phenotypes, decreased survival, morphological impairment, and a global effect on DNA elimination.
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Affiliation(s)
- Sebastian T Bechara
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Lyna E S Kabbani
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Xyrus X Maurer-Alcalá
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
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35
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Trewin AJ, Silver J, Dillon HT, Della Gatta PA, Parker L, Hiam DS, Lee YP, Richardson M, Wadley GD, Lamon S. Long non-coding RNA Tug1 modulates mitochondrial and myogenic responses to exercise in skeletal muscle. BMC Biol 2022; 20:164. [PMID: 35850762 PMCID: PMC9295458 DOI: 10.1186/s12915-022-01366-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Mitochondria have an essential role in regulating metabolism and integrate environmental and physiological signals to affect processes such as cellular bioenergetics and response to stress. In the metabolically active skeletal muscle, mitochondrial biogenesis is one important component contributing to a broad set of mitochondrial adaptations occurring in response to signals, which converge on the biogenesis transcriptional regulator peroxisome proliferator-activated receptor coactivator 1-alpha (PGC-1α), and is central to the beneficial effects of exercise in skeletal muscle. We investigated the role of long non-coding RNA (lncRNA) taurine-upregulated gene 1 (TUG1), which interacts with PGC-1α in regulating transcriptional responses to exercise in skeletal muscle. RESULTS In human skeletal muscle, TUG1 gene expression was upregulated post-exercise and was also positively correlated with the increase in PGC-1α gene expression (PPARGC1A). Tug1 knockdown (KD) in differentiating mouse myotubes led to decreased Ppargc1a gene expression, impaired mitochondrial respiration and morphology, and enhanced myosin heavy chain slow isoform protein expression. In response to a Ca2+-mediated stimulus, Tug1 KD prevented an increase in Ppargc1a expression. RNA sequencing revealed that Tug1 KD impacted mitochondrial Ca2+ transport genes and several downstream PGC-1α targets. Finally, Tug1 KD modulated the expression of ~300 genes that were upregulated in response to an in vitro model of exercise in myotubes, including genes involved in regulating myogenesis. CONCLUSIONS We found that TUG1 is upregulated in human skeletal muscle after a single session of exercise, and mechanistically, Tug1 regulates transcriptional networks associated with mitochondrial calcium handling, muscle differentiation and myogenesis. These data demonstrate that lncRNA Tug1 exerts regulation over fundamental aspects of skeletal muscle biology and response to exercise stimuli.
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Affiliation(s)
- Adam J Trewin
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia.
| | - Jessica Silver
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Hayley T Dillon
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
- Human Integrated Physiology and Sports Cardiology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Paul A Della Gatta
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Lewan Parker
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Danielle S Hiam
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Yin Peng Lee
- Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, Victoria, Australia
| | - Mark Richardson
- Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, Victoria, Australia
| | - Glenn D Wadley
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Séverine Lamon
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia.
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Overexpression of lncRNA-Gm2044 in spermatogonia impairs spermatogenesis in partial seminiferous tubules. Poult Sci 2022; 101:101930. [PMID: 35691049 PMCID: PMC9192819 DOI: 10.1016/j.psj.2022.101930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been demonstrated to regulate reproduction in mammals. Our previous study revealed that the expression level of lncRNA-Gm2044 was obviously elevated in nonobstructive azoospermia with spermatogonial arrest. Here, a transgenic mouse model of lncRNA-Gm2044 in spermatogonia using the Stra8 promoter was constructed to explore the roles of upregulated lncRNA-Gm2044 in male fertility. Testicular morphology and fertility weren't affected in transgenic mice expressing lncRNA-Gm2044. However, overexpression of lncRNA-Gm2044 in spermatogonia partially impaired spermatogenesis in the transgenic mice. Then, transcriptome sequencing was executed to find the potential signaling pathway repressing spermatogenesis in germ cells of lncRNA-Gm2044 transgenic mice. Through quantitative analysis of differentially expressed genes, 442 upregulated mRNAs and 147 downregulated mRNAs were displayed in male germ cells of Gm2044-transgenic mice (Gm2044-Tg) compared with non-transgenic mice (Non-Tg). Using gene ontology (GO) analysis, differentially expressed genes were shown to play vital roles in RNA_metabolic_process, Central_element, Enzyme_binding, and Intracellular_bridge. Using Kyoto encyclopedia of genes and genomes (KEGG) analysis, differentially expressed genes were shown to participate in RNA_transport, Cell_cycle, Renin-angiotensin_system, and Chemokine_signaling_pathway. Gene Set Enrichment Analysis (GSEA) revealed that Acrosome_assembly and Sperm_plasma_membrane were involved in the overexpression of lncRNA-Gm2044 blocking spermatogenesis. Furthermore, some of the most differentially expressed mRNAs were verified by RT-qPCR. In addition, we determined that the lncRNA-Gm2044 has no ability to translate into peptides by the bioinformatics method and molecular experiment. Thus, lncRNA-Gm2044 is a novel molecular target for the diagnosis and treatment of male infertility.
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Pavlaki I, Shapiro M, Pisignano G, Jones SME, Telenius J, Muñoz-Descalzo S, Williams RJ, Hughes JR, Vance KW. Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells. PLoS Genet 2022; 18:e1010230. [PMID: 35709096 PMCID: PMC9202886 DOI: 10.1371/journal.pgen.1010230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 11/19/2022] Open
Abstract
Central nervous system-expressed long non-coding RNAs (lncRNAs) are often located in the genome close to protein coding genes involved in transcriptional control. Such lncRNA-protein coding gene pairs are frequently temporally and spatially co-expressed in the nervous system and are predicted to act together to regulate neuronal development and function. Although some of these lncRNAs also bind and modulate the activity of the encoded transcription factors, the regulatory mechanisms controlling co-expression of neighbouring lncRNA-protein coding genes remain unclear. Here, we used high resolution NG Capture-C to map the cis-regulatory interaction landscape of the key neuro-developmental Paupar-Pax6 lncRNA-mRNA locus. The results define chromatin architecture changes associated with high Paupar-Pax6 expression in neurons and identify both promoter selective as well as shared cis-regulatory-promoter interactions involved in regulating Paupar-Pax6 co-expression. We discovered that the TCF7L2 transcription factor, a regulator of chromatin architecture and major effector of the Wnt signalling pathway, binds to a subset of these candidate cis-regulatory elements to coordinate Paupar and Pax6 co-expression. We describe distinct roles for Paupar in Pax6 expression control and show that the Paupar DNA locus contains a TCF7L2 bound transcriptional silencer whilst the Paupar transcript can act as an activator of Pax6. Our work provides important insights into the chromatin interactions, signalling pathways and transcription factors controlling co-expression of adjacent lncRNAs and protein coding genes in the brain.
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Affiliation(s)
- Ioanna Pavlaki
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Michael Shapiro
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Giuseppina Pisignano
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - Jelena Telenius
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia Muñoz-Descalzo
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Universidad Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Robert J. Williams
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Keith W. Vance
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- * E-mail:
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Chen M, Wang F, Fan L, Wang H, Gu S. Long Noncoding RNA TUG1 Aggravates Cerebral Ischemia/Reperfusion Injury by Acting as a ceRNA for miR-3072-3p to Target St8sia2. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9381203. [PMID: 35498127 PMCID: PMC9042630 DOI: 10.1155/2022/9381203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 03/07/2022] [Indexed: 12/20/2022]
Abstract
Long noncoding RNA taurine-upregulated gene 1 (TUG1) is considered to be involved in postischemic cerebral inflammation, whereas polysialic acid (polySia, PSA), the product of St8sia2, constitutes polysialylated neural adhesion cell molecule (PSA-NCAM) in both mice and humans and that cerebral PSA-NCAM level is elevated in neuronal progenitor cells in response to transient focal ischemia. Herein, we aim to identify novel miRNAs that bridge the functions of St8sia2 and TUG1 in ischemia-associated injuries. In both in vivo (C57BL/6J mouse ischemia/reperfusion, I/R model) and in vitro (mouse neuroblastoma N2A cell oxygen glucose deprivation/reoxygenation, OGD model) settings, we observed upregulated TUG1 and St8sia2 after the induction of ischemic injury, accompanied by reduced miR-3072-3p expression. We performed siRNA-induced TUG1 knockdown combined with the induction of ischemic injury; the results showed that inhibiting TUG1 expression led to the reduced infarct area and improved neurological deficit. Through bioinformatics analysis, miR-3072-3p was found to target both St8sia2 and TUG1, which was subsequently verified by the luciferase reporter system and RNA binding protein immunoprecipitation assay. Also, the addition of miR-3072-3p mimic/inhibitor resulted in reduced/elevated St8sia2 expression at the protein level. Further studies revealed that in both in vivo and in vitro settings, TUG1 bound competitively to miR-3072-3p to regulate St8sia2 expression and promote apoptosis. In summary, targeting the TUG1/miR-3072-3p/St8sia2 regulatory cascade, a novel cascade we identified in cerebral ischemia injury, may render feasible therapeutic possibilities for overcoming cerebral ischemic insults.
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Affiliation(s)
- Miao Chen
- Department of Emergency, The First Affiliated Hospital of Hainan Medical University, No. 31, Longhua Road, Longhua District, Haikou City, Hainan Province 570102, China
| | - Feng Wang
- Neurology Department, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, China
| | - Limin Fan
- The Institute for Biomedical Engineering and Nano Science, Tongji University School of Medicine, No. 1239, Siping Road, Shanghai 200092, China
| | - Hairong Wang
- Department of Emergency, Xinhua Hospital Affiliated to Shanghai Jiaotong University, School of Medicine, No. 1665, Kongjiang Road, Shanghai 20092, China
| | - Shuo Gu
- Department of Pediatric Neurosurgery, The First Affiliated Hospital of Hainan Medical University, No. 31, Longhua Road, Longhua District, Haikou City, Hainan Province 570102, China
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Robinson EK, Worthington A, Poscablo D, Shapleigh B, Salih MM, Halasz H, Seninge L, Mosqueira B, Smaliy V, Forsberg EC, Carpenter S. lincRNA-Cox2 Functions to Regulate Inflammation in Alveolar Macrophages during Acute Lung Injury. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1886-1900. [PMID: 35365562 PMCID: PMC9038212 DOI: 10.4049/jimmunol.2100743] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/05/2022] [Indexed: 12/15/2022]
Abstract
Our respiratory system is vital to protect us from the surrounding nonsterile environment; therefore, it is critical for a state of homeostasis to be maintained through a balance of inflammatory cues. Recent studies have shown that actively transcribed noncoding regions of the genome are emerging as key regulators of biological processes, including inflammation. lincRNA-Cox2 is one such example of an inflammatory inducible long intergenic noncoding RNA functioning to fine-tune immune gene expression. Using bulk and single-cell RNA sequencing, in addition to FACS, we find that lincRNA-Cox2 is most highly expressed in the lung and is most upregulated after LPS-induced lung injury (acute lung injury [ALI]) within alveolar macrophages, where it functions to regulate inflammation. We previously reported that lincRNA-Cox2 functions to regulate its neighboring protein Ptgs2 in cis, and in this study, we use genetic mouse models to confirm its role in regulating gene expression more broadly in trans during ALI. Il6, Ccl3, and Ccl5 are dysregulated in the lincRNA-Cox2-deficient mice and can be rescued to wild type levels by crossing the deficient mice with our newly generated lincRNA-Cox2 transgenic mice, confirming that this gene functions in trans. Many genes are specifically regulated by lincRNA-Cox2 within alveolar macrophages originating from the bone marrow because the phenotype can be reversed by transplantation of wild type bone marrow into the lincRNA-Cox2-deficient mice. In conclusion, we show that lincRNA-Cox2 is a trans-acting long noncoding RNA that functions to regulate immune responses and maintain homeostasis within the lung at baseline and on LPS-induced ALI.
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Affiliation(s)
- Elektra Kantzari Robinson
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Atesh Worthington
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA; and
| | - Donna Poscablo
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA; and
| | - Barbara Shapleigh
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Mays Mohammed Salih
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Haley Halasz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Lucas Seninge
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Benny Mosqueira
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Valeriya Smaliy
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - E Camilla Forsberg
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA; and
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA;
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From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. Nat Rev Genet 2022; 23:229-243. [PMID: 34837040 DOI: 10.1038/s41576-021-00427-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide sequencing has led to the discovery of thousands of long non-coding RNA (lncRNA) loci in the human genome, but evidence of functional significance has remained controversial for many lncRNAs. Genetically engineered model organisms are considered the gold standard for linking genotype to phenotype. Recent advances in CRISPR-Cas genome editing have led to a rapid increase in the use of mouse models to more readily survey lncRNAs for functional significance. Here, we review strategies to investigate the physiological relevance of lncRNA loci by highlighting studies that have used genetic mouse models to reveal key in vivo roles for lncRNAs, from fertility to brain development. We illustrate how an investigative approach, starting with whole-gene deletion followed by transcription termination and/or transgene rescue strategies, can provide definitive evidence for the in vivo function of mammalian lncRNAs.
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41
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Wang S, Qian Z, Ge X, Li C, Xue M, Liang K, Ma R, Ouyang L, Zheng L, Jing J, Cao S, Zhang Y, Yang Y, Chen Y, Ma J, Yao B. LncRNA Tug1 maintains blood-testis barrier integrity by modulating Ccl2 expression in high-fat diet mice. Cell Mol Life Sci 2022; 79:114. [PMID: 35103851 PMCID: PMC11073184 DOI: 10.1007/s00018-022-04142-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 01/02/2023]
Abstract
Sertoli cells are essential for spermatogenesis in the testicular seminiferous tubules by forming blood-testis barrier (BTB) and creating a unique microenvironment for spermatogenesis. Many lncRNAs have been reported to participate in spermatogenesis. However, the role of long noncoding RNAs (lncRNAs) in Sertoli cells has rarely been examined. Herein, we found that a high-fat diet (HFD) decreased sperm quality, impaired BTB integrity and resulted in accumulation of saturated fatty acids (SFAs), especially palmitic acid (PA), in mouse testes. PA decreased the expression of tight junction (TJ)-related proteins, increased permeability and decreased transepithelial electrical resistance (TER) in primary Sertoli cells and TM4 cells. Moreover, lncRNA Tug1 was found to be involved in PA-induced BTB disruption by RNA-seq. Tug1 depletion distinctly impaired the TJs of Sertoli cells and overexpression of Tug1 alleviated the disruption of BTB integrity induced by PA. Moreover, Ccl2 was found to be a downstream target of Tug1, and decreased TJ-related protein levels and TER and increased FITC-dextran permeability in vitro. Furthermore, the addition of Ccl2 damaged BTB integrity after overexpression of Tug1 in the presence of PA. Mechanistically, we found that Tug1 could directly bind to EZH2 and regulate H3K27me3 occupancy in the Ccl2 promoter region by RNA immunoprecipitation and chromatin immunoprecipitation assays. Our study revealed an important role of Tug1 in the BTB integrity of Sertoli cells and provided a new view of the role of lncRNAs in male infertility.
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Affiliation(s)
- Shuxian Wang
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Zhang Qian
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Xie Ge
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Chuwei Li
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Mengqi Xue
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Kuan Liang
- Center of Reproductive Medicine, Nanjing Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210002, Jiangsu, China
| | - Rujun Ma
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Lei Ouyang
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Lu Zheng
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Jun Jing
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Siyuan Cao
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Yu Zhang
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Yang Yang
- Basic Medical Laboratory, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Yabing Chen
- Immunology and Reproduction Biology Laboratory and State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, 210093, China
| | - Jinzhao Ma
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China.
| | - Bing Yao
- Center of Reproductive Medicine, Nanjing Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, 210002, Jiangsu, China.
- Center of Reproductive Medicine, Nanjing Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210002, Jiangsu, China.
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Xue M, Xia F, Wang Y, Zhu L, Li Y, Jia D, Gao Y, Shi U, Zhang C, He Y, Liu C, Yuan D, Yuan C. The Role of LncRNA TUG1 in Obesity-Related Diseases. Mini Rev Med Chem 2022; 22:1305-1313. [PMID: 35040400 DOI: 10.2174/1389557522666220117120228] [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: 09/03/2021] [Revised: 10/16/2021] [Accepted: 11/16/2021] [Indexed: 11/22/2022]
Abstract
With the continuous improvement of living standards, obesity has become an inevitable hotspot in our daily life. It remains a chronic and recurrent disease with serious adverse consequences. Over the past few years, several articles suggested that long non-coding RNA taurine increased gene 1(lncRNA TUG1), a useful RNA, was suggested to show a relationship to obesity-related disease occurrence and development. Exosome is an emerging research field, which contains substances that are actively involved in regulating the molecular mechanisms of disease. This review summarizes the current relevant TUG1 in different molecular pathways of diseases related to obesity, relationship between exosomes and TUG1 or diseases related to obesity. The aim is to explore TUG1 as a novel target for obesity, which can deepen the knowledge regarding epigenetic regulation pathway. Besides, it is likely to be a potential future targeting diseases related to obesity site treatment and diagnosis.
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Affiliation(s)
- Mengzhen Xue
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Fangqi Xia
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Yaqi Wang
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Leiqi Zhu
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Yuanyang Li
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Dengke Jia
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Yan Gao
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Ue Shi
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Changcheng Zhang
- College of Medical Science, China Three Gorges University, Yichang 443002, China
- Third-Grade Pharmacological Laboratory on Chinese Medicine Approved by State Administration of Traditional Chinese Medicine, Medical College of China Three Gorges, Yichang. Hubei 443002. China
| | - Yumin He
- College of Medical Science, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Chaoqi Liu
- College of Medical Science, China Three Gorges University, Yichang 443002, China
- Third-Grade Pharmacological Laboratory on Chinese Medicine Approved by State Administration of Traditional Chinese Medicine, Medical College of China Three Gorges, Yichang. Hubei 443002. China
| | - Ding Yuan
- College of Medical Science, China Three Gorges University, Yichang 443002, China;
- Third-Grade Pharmacological Laboratory on Chinese Medicine Approved by State Administration of Traditional Chinese Medicine, Medical College of China Three Gorges, Yichang. Hubei 443002. China
| | - Chengfu Yuan
- College of Medical Science, China Three Gorges University, Yichang 443002, China;
- Third-Grade Pharmacological Laboratory on Chinese Medicine Approved by State Administration of Traditional Chinese Medicine, Medical College of China Three Gorges, Yichang. Hubei 443002. China
- Hubei Key Laboratory of Tumour Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
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Mou X, Liew SW, Kwok CK. Identification and targeting of G-quadruplex structures in MALAT1 long non-coding RNA. Nucleic Acids Res 2022; 50:397-410. [PMID: 34904666 PMCID: PMC8754639 DOI: 10.1093/nar/gkab1208] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/07/2021] [Accepted: 11/24/2021] [Indexed: 12/11/2022] Open
Abstract
RNA G-quadruplexes (rG4s) have functional roles in many cellular processes in diverse organisms. While a number of rG4 examples have been reported in coding messenger RNAs (mRNA), so far only limited works have studied rG4s in non-coding RNAs (ncRNAs), especially in long non-coding RNAs (lncRNAs) that are of emerging interest and significance in biology. Herein, we report that MALAT1 lncRNA contains conserved rG4 motifs, forming thermostable rG4 structures with parallel topology. We also show that rG4s in MALAT1 lncRNA can interact with NONO protein with high specificity and affinity in vitro and in nuclear cell lysate, and we provide cellular data to support that NONO protein recognizes MALAT1 lncRNA via rG4 motifs. Notably, we demonstrate that rG4s in MALAT1 lncRNA can be targeted by the rG4-specific small molecule, peptide, and L-aptamer, leading to the dissociation of MALAT1 rG4-NONO protein interaction. Altogether, this study uncovers new and important rG4s in MALAT1 lncRNAs, reveals their specific interactions with NONO protein, offers multiple strategies for targeting MALAT1 and its RNA-protein complex via its rG4 structure and illustrates the prevalence and significance of rG4s in ncRNAs.
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Affiliation(s)
- Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City
University of Hong Kong, Kowloon Tong, Hong Kong
SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City
University of Hong Kong, Kowloon Tong, Hong Kong
SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City
University of Hong Kong, Kowloon Tong, Hong Kong
SAR, China
- Shenzhen Research Institute of City University of Hong Kong,
Shenzhen, China
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Wu H, Zhang X, Yang J, Feng T, Chen Y, Feng R, Wang H, Qian Y. OUP accepted manuscript. Hum Reprod 2022; 37:1229-1243. [PMID: 35526154 PMCID: PMC9156853 DOI: 10.1093/humrep/deac089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/02/2022] [Indexed: 11/13/2022] Open
Abstract
STUDY QUESTION Are taurine and its transporter TAUT associated with spermiogenesis and early embryo development? SUMMARY ANSWER Morphologically abnormal spermatozoa increased after local functional interference by intratesticular injection, and taurine depletion significantly reduced the normal embryo numbers in vivo and blastocyst formation rate in vitro. WHAT IS KNOWN ALREADY Taurine is one of the most abundant amino acids in the male reproductive system and it has been demonstrated that taurine can efficiently improve spermatogenic function in rat models of testicular injury. However, limited information is known about the role of taurine and its transporter TAUT in spermatogenesis and early embryo development. STUDY DESIGN, SIZE, DURATION Clinical characteristics from 110 couples who have experienced recurrent pregnancy loss (RPL) were collected from December 2014 to March 2018. According to whether a fetal heartbeat was seen in the previous pregnancy under ultrasonic monitoring, patients with RPL were divided into two groups: an RPL without heartbeat (pregnancy with no fetal heartbeat, ROH) group, and an RPL with heartbeat (one or more pregnancies with fetal heartbeat, RWH) group. Semen samples (21 ROH and 20 RWH) were finally used for metabolomic analysis. Furthermore, semen samples were obtained from 30 patients with teratozoospermia (normal sperm morphology <4%) seeking evaluation for infertility and 25 age-matched control subjects with normal semen quality for western blotting. Animal experiments were performed in CD-1/ICR mice. PARTICIPANTS/MATERIALS, SETTING, METHODS Metabolomics was performed to determine the metabolic changes between the ROH and RWH groups. Sperm proteins from patients with teratozoospermia and healthy controls were extracted for detecting TAUT expression using western blot analysis. Immunofluorescence was used to characterize the localization of TAUT in the testis and ejaculated spermatozoa. Functional analysis in mice was performed by intratesticular injection of siRNAs or antagonist (β-alanine) and 5% β-alanine was provided in drinking water to 3-week-old male mice for 5 weeks with the aim of depleting taurine. Murine epididymal spermatozoa were stained with hematoxylin and eosin for morphological assessment. IVF and mating tests were performed in mice for assessing fertility. MAIN RESULTS AND THE ROLE OF CHANCE Metabolomic analysis demonstrated that the taurine content was lower in spermatozoa but higher in seminal plasma from the ROH than the RWH group. TAUT expression was lower in spermatozoa from patients with teratozoospermia than controls. Immunofluorescence showed that TAUT was localized to the manchette in mouse elongated spermatids functional analysis showed that morphologically abnormal spermatozoa increased after interference, and this defect increased after supplementation with 5% β-alanine but was improved by 5% taurine supplementation. Supplementation with 5% β-alanine significantly reduced the normal embryo number in the mouse uterus as well as blastocyst formation rate in vitro. LARGE SCALE DATA N/A LIMITATIONS, REASONS FOR CAUTION The sample size was low and larger cohorts are needed to confirm the positive effect of taurine on human sperm quality. A comprehensive safety examination should be performed to evaluate whether taurine is a possible treatment for teratozoospermia. Furthermore, the specific molecular mechanism of TAUT involvement in spermiogenesis remains to be clarified. WIDER IMPLICATIONS OF THE FINDINGS The study provides new insights into the role of taurine and its transporter TAUT in male reproduction and embryo development. The results also indicate that TAUT is a promising molecular candidate for the assessment of sperm quality, which may contribute to the diagnosis and treatment for teratozoospermia. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by grants from the National Natural Science Foundation of China (no. 81774075, 31900605, 81971451), Jiangsu Science and Technology Program Grant (BK20190654) and Maternal and child health scientific research of Jiangsu Province (F202121). The authors declare no competing financial interests.
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Affiliation(s)
| | | | - Jihong Yang
- Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ting Feng
- Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Chen
- Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ruizhi Feng
- State Key Laboratory of Reproductive Medicine, Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Hui Wang
- Correspondence address. Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, 121 Jiangjiayuan Road, Nanjing 210011, China. Tel: +86-025-58771027; E-mail: (Y.Q.); Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China. Tel: +86-025-86869380; E-mail: (H.W.)
| | - Yun Qian
- Correspondence address. Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, 121 Jiangjiayuan Road, Nanjing 210011, China. Tel: +86-025-58771027; E-mail: (Y.Q.); Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, China. Tel: +86-025-86869380; E-mail: (H.W.)
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Liu C, Qu J, Wu M, Huang X, Li L. Cypermethrin triggers YY1-mediated testosterone biosynthesis suppression. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112792. [PMID: 34544022 DOI: 10.1016/j.ecoenv.2021.112792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Cypermethrin (CYP), an extensively-used broad-spectrum pyrethroid pesticide, is regarded as a potential environmental endocrine disruptor with the anti-androgenic characteristic. To explore underlying roles of non-coding RNAs and the Jak/Stat pathway in CYP-mediated testosterone biosynthesis suppression, SD rats and Leydig cells were employed in this work. Results displayed that β-CYP decreased plasma testosterone levels and led to abnormal alterations of testicular histomorphology and ultrastructures. LncRNA XIST and miR-142-5p were co-localized in the cytoplasm of Leydig cells, but the expression of XIST was inhibited by β-CYP while that of miR-142-5p was induced. Then overexpressed miR-142-5p dampened the Jak1/Stat1 pathway by directly targeting Jak1. Transcription factors NFκB and YY1 impeded by β-CYP were positively regulated by the Jak1/Stat1 pathway. Bidirectional Co-IP and ChIP assays demonstrated that NFκB interacted with and modulated YY1 by directly binding to the promoter region of YY1. ChIP, qPCR, and YY1 knockdown/overexpression assays indicated that YY1 acted as a transcriptional activator to directly modulate steroidogenic StAR and 3β-HSD in Leydig cells. Taken together, miR-142-5p sponged by lncRNA XIST directly targets the Jak1/Stat1 pathway, which regulates steroidogenic StAR and 3β-HSD via NFκB and YY1, and ultimately dampens testosterone production in Leydig cells.
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Affiliation(s)
- Changjiang Liu
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, 420 Baohuan Road, Chongqing 400020, China; Medical Research Institute, Southwest University, Chongqing 400715, China.
| | - Jiayuan Qu
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, 420 Baohuan Road, Chongqing 400020, China
| | - Mingzhu Wu
- Medical Research Institute, Southwest University, Chongqing 400715, China
| | - Xu Huang
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, 420 Baohuan Road, Chongqing 400020, China
| | - Lianbing Li
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, 420 Baohuan Road, Chongqing 400020, China
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Long non-coding RNAs: novel regulators of cellular physiology and function. Pflugers Arch 2021; 474:191-204. [PMID: 34791525 PMCID: PMC8766390 DOI: 10.1007/s00424-021-02641-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/19/2022]
Abstract
Long non-coding RNAs were once considered as “junk” RNA produced by aberrant DNA transcription. They are now understood to play central roles in diverse cellular processes from proliferation and migration to differentiation, senescence and DNA damage control. LncRNAs are classed as transcripts longer than 200 nucleotides that do not encode a peptide. They are relevant to many physiological and pathophysiological processes through their control of fundamental molecular functions. This review summarises the recent progress in lncRNA research and highlights the far-reaching physiological relevance of lncRNAs. The main areas of lncRNA research encompassing their characterisation, classification and mechanisms of action will be discussed. In particular, the regulation of gene expression and chromatin landscape through lncRNA control of proteins, DNA and other RNAs will be introduced. This will be exemplified with a selected number of lncRNAs that have been described in numerous physiological contexts and that should be largely representative of the tens-of-thousands of mammalian lncRNAs. To some extent, these lncRNAs have inspired the current thinking on the central dogmas of epigenetics, RNA and DNA mechanisms.
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Bonilauri B, Holetz FB, Dallagiovanna B. Long Non-Coding RNAs Associated with Ribosomes in Human Adipose-Derived Stem Cells: From RNAs to Microproteins. Biomolecules 2021; 11:1673. [PMID: 34827671 PMCID: PMC8615451 DOI: 10.3390/biom11111673] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
Ribosome profiling reveals the translational dynamics of mRNAs by capturing a ribosomal footprint snapshot. Growing evidence shows that several long non-coding RNAs (lncRNAs) contain small open reading frames (smORFs) that are translated into functional peptides. The difficulty in identifying bona-fide translated smORFs is a constant challenge in experimental and bioinformatics fields due to their unconventional characteristics. This motivated us to isolate human adipose-derived stem cells (hASC) from adipose tissue and perform a ribosome profiling followed by bioinformatics analysis of transcriptome, translatome, and ribosome-protected fragments of lncRNAs. Here, we demonstrated that 222 lncRNAs were associated with the translational machinery in hASC, including the already demonstrated lncRNAs coding microproteins. The ribosomal occupancy of some transcripts was consistent with the translation of smORFs. In conclusion, we were able to identify a subset of 15 lncRNAs containing 35 smORFs that likely encode functional microproteins, including four previously demonstrated smORF-derived microproteins, suggesting a possible dual role of these lncRNAs in hASC self-renewal.
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Affiliation(s)
- Bernardo Bonilauri
- Laboratory of Basic Biology of Stem Cells (LABCET), Carlos Chagas Institute-Fiocruz-Paraná, Curitiba 81350-010, Brazil;
| | - Fabiola Barbieri Holetz
- Laboratory of Gene Expression Regulation (LABREG), Carlos Chagas Institute-Fiocruz-Paraná, Curitiba 81350-010, Brazil;
| | - Bruno Dallagiovanna
- Laboratory of Basic Biology of Stem Cells (LABCET), Carlos Chagas Institute-Fiocruz-Paraná, Curitiba 81350-010, Brazil;
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Han G, Hong SH, Lee SJ, Hong SP, Cho C. Transcriptome Analysis of Testicular Aging in Mice. Cells 2021; 10:2895. [PMID: 34831115 PMCID: PMC8616291 DOI: 10.3390/cells10112895] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 02/07/2023] Open
Abstract
Male reproductive aging, or andropause, is associated with gradual age-related changes in testicular properties, sperm production, and erectile function. The testis, which is the primary male reproductive organ, produces sperm and androgens. To understand the transcriptional changes underlying male reproductive aging, we performed transcriptome analysis of aging testes in mice. A total of 31,386 mRNAs and 9387 long non-coding RNAs (lncRNAs) were identified in the mouse testes of diverse age groups (3, 6, 12, and 18 months old) by total RNA sequencing. Of them, 1571 mRNAs and 715 lncRNAs exhibited changes in their levels during testicular aging. Most of these aging-related transcripts exhibited slight and continuous expression changes during aging, whereas some (9.6%) showed larger expression changes. The aging-related transcripts could be classified into diverse expression patterns, in which the transcripts changed mainly at 3-6 months or at 12-18 months. Our subsequent in silico analysis provided insight into the potential features of testicular aging-related mRNAs and lncRNAs. We identified testis-specific aging-related transcripts (121 mRNAs and 25 lncRNAs) by comparison with a known testis-specific transcript profile, and then predicted the potential reproduction-related functions of the mRNAs. By selecting transcripts that are altered only between 3 and 18 months, we identified 46 mRNAs and 34 lncRNAs that are stringently related to the terminal stage of male reproductive aging. Some of these mRNAs were related to hormonal regulation. Finally, our in silico analysis of the 34 aging-related lncRNAs revealed that they co-localized with 19 testis-expressed protein-coding genes, 13 of which are considered to show testis-specific or -predominant expression. These nearby genes could be potential targets of cis-regulation by the aging-related lncRNAs. Collectively, our results identify a number of testicular aging-related mRNAs and lncRNAs in mice and provide a basis for the future investigation of these transcripts in the context of aging-associated testicular dysfunction.
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Affiliation(s)
| | | | | | | | - Chunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (G.H.); (S.-H.H.); (S.-J.L.); (S.-P.H.)
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Winkler L, Dimitrova N. A mechanistic view of long noncoding RNAs in cancer. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1699. [PMID: 34668345 PMCID: PMC9016092 DOI: 10.1002/wrna.1699] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important modulators of a wide range of biological processes in normal and disease states. In particular, lncRNAs have garnered significant interest as novel players in the molecular pathology of cancer, spurring efforts to define the functions, and elucidate the mechanisms through which cancer‐associated lncRNAs operate. In this review, we discuss the prevalent mechanisms employed by lncRNAs, with a critical assessment of the methodologies used to determine each molecular function. We survey the abilities of cancer‐associated lncRNAs to enact diverse trans functions throughout the nucleus and in the cytoplasm and examine the local roles of cis‐acting lncRNAs in modulating the expression of neighboring genes. In linking lncRNA functions and mechanisms to their roles in cancer biology, we contend that a detailed molecular understanding of lncRNA functionality is key to elucidating their contributions to tumorigenesis and to unlocking their therapeutic potential. This article is categorized under:
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Lauren Winkler
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
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Burgos M, Hurtado A, Jiménez R, Barrionuevo FJ. Non-Coding RNAs: lncRNAs, miRNAs, and piRNAs in Sexual Development. Sex Dev 2021; 15:335-350. [PMID: 34614501 DOI: 10.1159/000519237] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are a group of RNAs that do not encode functional proteins, including long non-coding RNAs (lncRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), and short interfering RNAs (siRNAs). In the last 2 decades an effort has been made to uncover the role of ncRNAs during development and disease, and nowadays it is clear that these molecules have a regulatory function in many of the developmental and physiological processes where they have been studied. In this review, we provide an overview of the role of ncRNAs during gonad determination and development, focusing mainly on mammals, although we also provide information from other species, in particular when there is not much information on the function of particular types of ncRNAs during mammalian sexual development.
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Affiliation(s)
- Miguel Burgos
- Departamento de Genética e Instituto de Biotecnología, Lab. 127, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Alicia Hurtado
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Rafael Jiménez
- Departamento de Genética e Instituto de Biotecnología, Lab. 127, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Francisco J Barrionuevo
- Departamento de Genética e Instituto de Biotecnología, Lab. 127, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
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