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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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2
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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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3
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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] [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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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 2024:10.1007/s12011-024-04067-x. [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] [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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5
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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: 0] [Impact Index Per Article: 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: 0] [Impact Index Per Article: 0] [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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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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9
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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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10
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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: 8] [Impact Index Per Article: 8.0] [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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11
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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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12
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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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13
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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: 323] [Impact Index Per Article: 323.0] [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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14
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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: 16] [Impact Index Per Article: 16.0] [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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15
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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: 2.0] [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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16
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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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17
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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: 0] [Impact Index Per Article: 0] [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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18
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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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19
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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: 3.5] [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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20
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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: 0.5] [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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21
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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: 1.0] [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
- * E-mail:
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22
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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: 13] [Impact Index Per Article: 6.5] [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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23
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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: 0.5] [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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24
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [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. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01366-4.
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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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25
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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: 1.5] [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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26
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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: 2.0] [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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27
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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: 1.5] [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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28
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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: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [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: 41] [Impact Index Per Article: 20.5] [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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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: 9] [Impact Index Per Article: 4.5] [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: 2.0] [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: 6.5] [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: 0] [Impact Index Per Article: 0] [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: 4] [Impact Index Per Article: 1.3] [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: 10.0] [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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Long Non-Coding RNAs Associated with Ribosomes in Human Adipose-Derived Stem Cells: From RNAs to Microproteins. Biomolecules 2021; 11:biom11111673. [PMID: 34827671 PMCID: PMC8615451 DOI: 10.3390/biom11111673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [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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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: 5] [Impact Index Per Article: 1.7] [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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38
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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: 15] [Impact Index Per Article: 5.0] [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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39
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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: 7] [Impact Index Per Article: 2.3] [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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40
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DiStefano JK, Gerhard GS. Long Noncoding RNAs and Human Liver Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:1-21. [PMID: 34416820 DOI: 10.1146/annurev-pathol-042320-115255] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome, exhibit a diverse range of biological functions, and exert effects through a variety of mechanisms. The sheer number of lncRNAs in the human genome has raised important questions about their potential biological significance and roles in human health and disease. Technological and computational advances have enabled functional annotation of a large number of lncRNAs. Though the number of publications related to lncRNAs has escalated in recent years, relatively few have focused on those involved in hepatic physiology and pathology. We provide an overview of evolving lncRNA classification systems and characteristics and highlight important advances in our understanding of the contribution of lncRNAs to liver disease, with a focus on nonalcoholic steatohepatitis, hepatocellular carcinoma, and cholestatic liver disease. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Johanna K DiStefano
- Diabetes and Fibrotic Disease Research Unit, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA;
| | - Glenn S Gerhard
- Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA;
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41
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Andjus S, Morillon A, Wery M. From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory. Noncoding RNA 2021; 7:ncrna7030044. [PMID: 34449682 PMCID: PMC8395947 DOI: 10.3390/ncrna7030044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022] Open
Abstract
The Nonsense-Mediated mRNA Decay (NMD) has been classically viewed as a translation-dependent RNA surveillance pathway degrading aberrant mRNAs containing premature stop codons. However, it is now clear that mRNA quality control represents only one face of the multiple functions of NMD. Indeed, NMD also regulates the physiological expression of normal mRNAs, and more surprisingly, of long non-coding (lnc)RNAs. Here, we review the different mechanisms of NMD activation in yeast and mammals, and we discuss the molecular bases of the NMD sensitivity of lncRNAs, considering the functional roles of NMD and of translation in the metabolism of these transcripts. In this regard, we describe several examples of functional micropeptides produced from lncRNAs. We propose that translation and NMD provide potent means to regulate the expression of lncRNAs, which might be critical for the cell to respond to environmental changes.
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Affiliation(s)
- Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France;
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France
- Correspondence: (A.M.); (M.W.)
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France
- Correspondence: (A.M.); (M.W.)
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42
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Dumbović G, Braunschweig U, Langner HK, Smallegan M, Biayna J, Hass EP, Jastrzebska K, Blencowe B, Cech TR, Caruthers MH, Rinn JL. Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention. Nat Commun 2021; 12:3308. [PMID: 34083519 PMCID: PMC8175569 DOI: 10.1038/s41467-021-23221-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 04/07/2021] [Indexed: 12/27/2022] Open
Abstract
The spatial partitioning of the transcriptome in the cell is an important form of gene-expression regulation. Here, we address how intron retention influences the spatio-temporal dynamics of transcripts from two clinically relevant genes: TERT (Telomerase Reverse Transcriptase) pre-mRNA and TUG1 (Taurine-Upregulated Gene 1) lncRNA. Single molecule RNA FISH reveals that nuclear TERT transcripts uniformly and robustly retain specific introns. Our data suggest that the splicing of TERT retained introns occurs during mitosis. In contrast, TUG1 has a bimodal distribution of fully spliced cytoplasmic and intron-retained nuclear transcripts. We further test the functionality of intron-retention events using RNA-targeting thiomorpholino antisense oligonucleotides to block intron excision. We show that intron retention is the driving force for the nuclear compartmentalization of these RNAs. For both RNAs, altering this splicing-driven subcellular distribution has significant effects on cell viability. Together, these findings show that stable retention of specific introns can orchestrate spatial compartmentalization of these RNAs within the cell. This process reveals that modulating RNA localization via targeted intron retention can be utilized for RNA-based therapies.
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Affiliation(s)
- Gabrijela Dumbović
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | | | - Heera K Langner
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Michael Smallegan
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Josep Biayna
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
| | - Evan P Hass
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Katarzyna Jastrzebska
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | | | - Thomas R Cech
- 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
| | - Marvin H Caruthers
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - 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.
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43
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Li L, Sun L, Danesh FR. The multifaceted contributions of long noncoding RNAs on mitochondrial dysfunction in diabetic nephropathy. DIABETIC NEPHROPATHY : DN 2021; 1:5-8. [PMID: 34690415 PMCID: PMC8536200 DOI: 10.2478/dine-2021-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Li Li
- Section of Nephrology, Division of Internal Medicine, The University of Texas at MD Anderson Cancer Center, Houston, TX, USA
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Lin Sun
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Farhad R. Danesh
- Section of Nephrology, Division of Internal Medicine, The University of Texas at MD Anderson Cancer Center, Houston, TX, USA
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX, USA
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44
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Hong SH, Han G, Lee SJ, Cocquet J, Cho C. Testicular germ cell-specific lncRNA, Teshl, is required for complete expression of Y chromosome genes and a normal offspring sex ratio. SCIENCE ADVANCES 2021; 7:7/24/eabg5177. [PMID: 34108217 PMCID: PMC8189594 DOI: 10.1126/sciadv.abg5177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/23/2021] [Indexed: 05/09/2023]
Abstract
Heat shock factor 2 (HSF2) regulates the transcription of the male-specific region of the mouse Y chromosome long arm (MSYq) multicopy genes only in testes, but the molecular mechanism underlying this tissue specificity remains largely unknown. Here, we report that the testicular germ cell-specific long noncoding RNA (lncRNA), NR_038002, displays a characteristic spatiotemporal expression pattern in the nuclei of round and elongating spermatids. NR_038002-knockout male mice produced sperm with abnormal head morphology and exhibited reduced fertility accompanied by a female-biased sex ratio in offspring. Molecular analyses revealed that NR_038002 interacts with HSF2 and thereby activates expression of the MSYq genes. We designate NR_038002 as testicular germ cell-specific HSF2-interacting lncRNA (Teshl). Together, our study is the first to demonstrate that the testis specificity of HSF2 activity is regulated by the lncRNA Teshl and establishes a Teshl-HSF2-MSYq molecular axis for normal Y-bearing sperm qualities and consequent balanced offspring sex ratio.
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Affiliation(s)
- Seong Hyeon Hong
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Gwidong Han
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Seung Jae Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Julie Cocquet
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, F-75014 Paris, France
| | - Chunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
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45
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Jantrapirom S, Koonrungsesomboon N, Yoshida H, M Candeias M, Pruksakorn D, Lo Piccolo L. Long noncoding RNA-dependent methylation of nonhistone proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1661. [PMID: 33913612 DOI: 10.1002/wrna.1661] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/18/2021] [Accepted: 04/04/2021] [Indexed: 12/15/2022]
Abstract
In the last decade, an intriguing new paradigm of regulation has emerged in which some transcripts longer than 200 nucleotides and no coding potential, long noncoding RNA (lncRNAs), exhibit the capability to control posttranslational modifications of nonhistone proteins in both invertebrates and vertebrates. The extent of such a regulation is still largely unknown. We performed a systematic review to identify and evaluate the potential impact of lncRNA-dependent methylation of nonhistone proteins. Collectively, these lncRNAs primarily act as scaffolds upon which methyltransferases (MTases) and targets are brought in proximity. In this manner, the N-MTase activity of EZH2, protein arginine-MTase 1/4/5, and SMYD2 is exploited to modulate the stability or the compartmentalization of several nonhistone proteins with roles in cell signaling, gene expression, and RNA processing. Moreover, these lncRNAs can indirectly affect the methylation of nonhistone proteins by transcriptional or posttranscriptional regulation of MTases. Strikingly, the lncRNAs/MTases/nonhistone proteins networking seem to be relevant to carcinogenesis and neurological disorders. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Salinee Jantrapirom
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Drosophila Center for Human Diseases and Drug Discovery (DHD), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nut Koonrungsesomboon
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Musculoskeletal Science and Translational Research Center (MSTR), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hideki Yoshida
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - Marco M Candeias
- MaRCU-Molecular and RNA Cancer Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Human Genetics, National Health Institute Dr Ricardo Jorge, Lisbon, Portugal
| | - Dumnoensun Pruksakorn
- Musculoskeletal Science and Translational Research Center (MSTR), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Omics Center for Health Science, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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46
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Huan Z, Mei Z, Na H, Xinxin M, Yaping W, Ling L, Lei W, Kejin Z, Yanan L. lncRNA MIR155HG Alleviates Depression-Like Behaviors in Mice by Regulating the miR-155/BDNF Axis. Neurochem Res 2021; 46:935-944. [PMID: 33511575 DOI: 10.1007/s11064-021-03234-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/27/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022]
Abstract
Depression is one of most common psychiatric disorders, and the detailed molecular mechanism remains to be fully elucidated. Brain-derived neurotrophic factor (BDNF) is a critical neurotrophic factor that is decreased and closely involved in the development of depression. Noncoding RNAs are central regulators of cellular activities that modulate target genes. However, the roles of long noncoding RNA (lncRNA) MIR155HG and miRNA-155 (miR-155) in the pathophysiology of depression are unclear. In the present study, we aimed to explore the effects of lncRNA MIR155HG and miR-155 on the development of depression and uncover the underlying molecular mechanism. Real-time quantitative polymerase chain reaction was used to examine the expression of MIR155HG and miR-155. Western blotting was applied to measure the expression of BDNF. A luciferase reporter assay was utilized to determine the regulatory relationship between MIR155HG and miR-155. Our current work found that lncRNA MIR155HG and BDNF levels decreased while miR-155 levels increased in the hippocampal region of CUMS (chronic unpredictable mild stress) mice, a well-accepted mouse model of depression. Moreover, MIR155HG rescued while miR-155 exacerbated the depression-like behaviors of CUMS mice. Through bioinformatics analysis and luciferase reporter assays, we found that MIR155HG directly bound to and negatively modulated the expression of miR-155. Moreover, increased miR-155 was found to repress the expression of BDNF, a critical neurotrophic factor that has been reported to alleviate the depression-like behaviors of CUMS mice. Our present study revealed that lncRNA MIR155HG protected CUMS mice by regulating the miR-155/BDNF axis. Our study aimed to understand the pathophysiology of depression and provided potential therapeutic targets to diagnose and treat depression.
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Affiliation(s)
- Zhang Huan
- Department of Psychology and Psychiatry, The Second Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xian, 710004, China
| | - Zhu Mei
- Department of Psychology and Psychiatry, The Second Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xian, 710004, China
| | - Huang Na
- Core Research Laboratory, The Second Affiliated Hospital, College of Medicine, Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Ma Xinxin
- Department of Psychology and Psychiatry, The Second Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xian, 710004, China
| | - Wang Yaping
- Department of Psychology and Psychiatry, The Second Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xian, 710004, China
| | - Liu Ling
- Department of Psychology and Psychiatry, The Second Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xian, 710004, China
| | - Wang Lei
- Department of Psychology and Psychiatry, The Second Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xian, 710004, China
| | - Zhang Kejin
- School of Medicine, Northwest University, Xi'an, 710069, China
| | - Liu Yanan
- Department of Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xian, 710069, China.
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47
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Zhou Y, Zhang X, Xiong S, Zeng X, Zhang X. Predicted gene 31453 (Gm31453) and the gene encoding carboxypeptidase A5 (Cpa5) are not essential for spermatogenesis and male fertility in the mouse. Reprod Fertil Dev 2021; 33:401-409. [PMID: 33745502 DOI: 10.1071/rd20284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/09/2021] [Indexed: 01/03/2023] Open
Abstract
Numerous long non-coding (lnc) RNAs are highly enriched or exclusively expressed in the mammalian testis, even in spermatids. Spermatid perinuclear RNA-binding protein (STRBP) can bind many RNAs, and loss of STRBP impairs male fertility. However, the functions of lncRNAs interacting with STRBP are unknown. In this study, the roles of one STRBP-interacting lncRNA, namely predicted gene 31453 (Gm31453), and its potential target gene encoding carboxypeptidase A5 (Cpa5) in spermatogenesis were determined using gene-knockout (KO) mice. Gm31453 and Cpa5 are located adjacent to each other on the same chromosome and are highly expressed in the testis. Gm31453 and Cpa5 are primarily expressed from secondary spermatocytes to elongated spermatids, implying their involvement in spermiogenesis. Although deletion of Gm31453 disturbed the expression of both its target and interacting gene, as indicated by decreased Cpa5 and increased Strbp mRNA levels, both Gm31453- and Cpa5-KO mice showed normal spermatogenesis and fertility, and had no detectable abnormalities in terms of testicular and epididymal development, sperm production morphology or motility, pregnancy rate or litter size. Thus, Gm31453 and Cpa5 are dispensable for spermatogenesis and male fertility in mice. Their involvement in spermatogenesis may be a fine-tuning role, regulating gene expression at the molecular level.
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Affiliation(s)
- Yang Zhou
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong 226019, PR China
| | - Xiaona Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, PR China
| | - Suping Xiong
- Institute of Life Science, Nanchang University, Nanchang 330031, PR China
| | - Xuhui Zeng
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong 226019, PR China; and Corresponding authors. ;
| | - Xiaoning Zhang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong 226019, PR China; and Institute of Life Science, Nanchang University, Nanchang 330031, PR China; and Corresponding authors. ;
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48
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Minati L, Firrito C, Del Piano A, Peretti A, Sidoli S, Peroni D, Belli R, Gandolfi F, Romanel A, Bernabo P, Zasso J, Quattrone A, Guella G, Lauria F, Viero G, Clamer M. One-shot analysis of translated mammalian lncRNAs with AHARIBO. eLife 2021; 10:59303. [PMID: 33594971 PMCID: PMC7932693 DOI: 10.7554/elife.59303] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode peptides, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated and peptide-producing lncRNAs. Here, we present AHA-mediated RIBOsome isolation (AHARIBO), a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs, and corresponding de novo synthesized peptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds of lncRNAs.
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Affiliation(s)
| | | | | | | | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
| | - Daniele Peroni
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Romina Belli
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Gandolfi
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Romanel
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Jacopo Zasso
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
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49
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Schlesinger D, Elsässer SJ. Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins. FEBS J 2021; 289:53-74. [PMID: 33595896 DOI: 10.1111/febs.15769] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/17/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023]
Abstract
Short ORFs (sORFs), that is, occurrences of a start and stop codon within 100 codons or less, can be found in organisms of all domains of life, outnumbering annotated protein-coding ORFs by orders of magnitude. Even though functional proteins smaller than 100 amino acids are known, the coding potential of sORFs has often been overlooked, as it is not trivial to predict and test for functionality within the large number of sORFs. Recent advances in ribosome profiling and mass spectrometry approaches, together with refined bioinformatic predictions, have enabled a huge leap forward in this field and identified thousands of likely coding sORFs. A relatively low number of small proteins or microproteins produced from these sORFs have been characterized so far on the molecular, structural, and/or mechanistic level. These however display versatile and, in some cases, essential cellular functions, allowing for the exciting possibility that many more, previously unknown small proteins might be encoded in the genome, waiting to be discovered. This review will give an overview of the steadily growing microprotein field, focusing on eukaryotic small proteins. We will discuss emerging themes in the molecular action of microproteins, as well as advances and challenges in microprotein identification and characterization.
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Affiliation(s)
- Dörte Schlesinger
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
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50
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Katsushima K, Jallo G, Eberhart CG, Perera RJ. Long non-coding RNAs in brain tumors. NAR Cancer 2021; 3:zcaa041. [PMID: 34316694 PMCID: PMC8210177 DOI: 10.1093/narcan/zcaa041] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/09/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been found to be central players in the epigenetic, transcriptional and post-transcriptional regulation of gene expression. There is an accumulation of evidence on newly discovered lncRNAs, their molecular interactions and their roles in the development and progression of human brain tumors. LncRNAs can have either tumor suppressive or oncogenic functions in different brain cancers, making them attractive therapeutic targets and biomarkers for personalized therapy and precision diagnostics. Here, we summarize the current state of knowledge of the lncRNAs that have been implicated in brain cancer pathogenesis, particularly in gliomas and medulloblastomas. We discuss their epigenetic regulation as well as the prospects of using lncRNAs as diagnostic biomarkers and therapeutic targets in patients with brain tumors.
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Affiliation(s)
- Keisuke Katsushima
- Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans St., Baltimore, MD 21231, USA
| | - George Jallo
- Johns Hopkins All Children's Hospital, 600 5th St. South, St Petersburg, FL 33701, USA
| | - Charles G Eberhart
- Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans St., Baltimore, MD 21231, USA
| | - Ranjan J Perera
- Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans St., Baltimore, MD 21231, USA
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