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Panyushev N, Selitskiy M, Melnichenko V, Lebedev E, Okorokova L, Adonin L. Dynamic Evolution of Repetitive Elements and Chromatin States in Apis mellifera Subspecies. Genes (Basel) 2024; 15:89. [PMID: 38254978 PMCID: PMC10815273 DOI: 10.3390/genes15010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/07/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
In this study, we elucidate the contribution of repetitive DNA sequences to the establishment of social structures in honeybees (Apis mellifera). Despite recent advancements in understanding the molecular mechanisms underlying the formation of honeybee castes, primarily associated with Notch signaling, the comprehensive identification of specific genomic cis-regulatory sequences remains elusive. Our objective is to characterize the repetitive landscape within the genomes of two honeybee subspecies, namely A. m. mellifera and A. m. ligustica. An observed recent burst of repeats in A. m. mellifera highlights a notable distinction between the two subspecies. After that, we transitioned to identifying differentially expressed DNA elements that may function as cis-regulatory elements. Nevertheless, the expression of these sequences showed minimal disparity in the transcriptome during caste differentiation, a pivotal process in honeybee eusocial organization. Despite this, chromatin segmentation, facilitated by ATAC-seq, ChIP-seq, and RNA-seq data, revealed a distinct chromatin state associated with repeats. Lastly, an analysis of sequence divergence among elements indicates successive changes in repeat states, correlating with their respective time of origin. Collectively, these findings propose a potential role of repeats in acquiring novel regulatory functions.
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Affiliation(s)
- Nick Panyushev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
- Bioinformatics Institute, 197342 St. Petersburg, Russia;
| | - Max Selitskiy
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
| | - Vasilina Melnichenko
- International Scientific and Research Institute of Bioengineering, ITMO University, 197101 St. Petersburg, Russia;
| | - Egor Lebedev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
| | | | - Leonid Adonin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
- Institute of Biomedical Chemistry, Group of Mechanisms for Nanosystems Targeted Delivery, 119121 Moscow, Russia
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2
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Ramos TAR, Urquiza-Zurich S, Kim SY, Gillette TG, Hill JA, Lavandero S, do Rêgo TG, Maracaja-Coutinho V. Single-cell transcriptional landscape of long non-coding RNAs orchestrating mouse heart development. Cell Death Dis 2023; 14:841. [PMID: 38110334 PMCID: PMC10728149 DOI: 10.1038/s41419-023-06296-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 10/18/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023]
Abstract
Long non-coding RNAs (lncRNAs) comprise the most representative transcriptional units of the mammalian genome. They are associated with organ development linked with the emergence of cardiovascular diseases. We used bioinformatic approaches, machine learning algorithms, systems biology analyses, and statistical techniques to define co-expression modules linked to heart development and cardiovascular diseases. We also uncovered differentially expressed transcripts in subpopulations of cardiomyocytes. Finally, from this work, we were able to identify eight cardiac cell-types; several new coding, lncRNA, and pcRNA markers; two cardiomyocyte subpopulations at four different time points (ventricle E9.5, left ventricle E11.5, right ventricle E14.5 and left atrium P0) that harbored co-expressed gene modules enriched in mitochondrial, heart development and cardiovascular diseases. Our results evidence the role of particular lncRNAs in heart development and highlight the usage of co-expression modular approaches in the cell-type functional definition.
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Grants
- R01 HL155765 NHLBI NIH HHS
- R01 HL126012 NHLBI NIH HHS
- R01 HL147933 NHLBI NIH HHS
- R01 HL128215 NHLBI NIH HHS
- R01 HL120732 NHLBI NIH HHS
- Agencia Nacional de Investigacion y Desarrollo (ANID, Chile), FONDAP 15130011 (SL), FONDECYT 1200490 (SL)
- the NIH: HL-120732 (JAH), HL-128215 (JAH), HL-126012 (JAH), HL-147933, (JAH), HL-155765 (JAH), 14SFRN20510023 (JAH), 14SFRN20670003 (JAH), Leducq grant number 11CVD04 (JAH), Cancer Prevention and Research Institute of Texas grant RP110486P3 (JAH)
- Agencia Nacional de Investigacion y Desarrollo (ANID, Chile), FONDAP 15130011 (VMC) and FONDECYT 1211731 (VMC).
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Affiliation(s)
- Thaís A R Ramos
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical & Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Programa de Pós-Graduação em Bioinformática, Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, João Pessoa, Brazil
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Sebastián Urquiza-Zurich
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical & Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Soo Young Kim
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center Dallas, Dallas, TX, USA
| | - Thomas G Gillette
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center Dallas, Dallas, TX, USA
| | - Joseph A Hill
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center Dallas, Dallas, TX, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sergio Lavandero
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical & Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile.
- Corporación Centro de Estudios Científicos de las Enfermedades Crónicas (CECEC), Santiago, Chile.
| | - Thaís G do Rêgo
- Programa de Pós-Graduação em Bioinformática, Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, João Pessoa, Brazil.
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil.
| | - Vinicius Maracaja-Coutinho
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Chemical & Pharmaceutical Sciences & Faculty of Medicine, Universidad de Chile, Santiago, Chile.
- Programa de Pós-Graduação em Bioinformática, Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, João Pessoa, Brazil.
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3
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Ao YQ, Gao J, Jiang JH, Wang HK, Wang S, Ding JY. Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village. Mol Ther 2023; 31:3389-3413. [PMID: 37740493 PMCID: PMC10727995 DOI: 10.1016/j.ymthe.2023.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.
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Affiliation(s)
- Yong-Qiang Ao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hai-Kun Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jian-Yong Ding
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
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Modi A, Lopez G, Conkrite KL, Su C, Leung TC, Ramanan S, Manduchi E, Johnson ME, Cheung D, Gadd S, Zhang J, Smith MA, Guidry Auvil JM, Meshinchi S, Perlman EJ, Hunger SP, Maris JM, Wells AD, Grant SF, Diskin SJ. Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors. Cancer Res 2023; 83:3462-3477. [PMID: 37584517 PMCID: PMC10787516 DOI: 10.1158/0008-5472.can-22-3186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/07/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
Abstract
Long noncoding RNAs (lncRNA) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curated RNA sequencing data for 1,044 pediatric leukemia and extracranial solid tumors and integrated paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. A total of 2,657 lncRNAs were robustly expressed across six pediatric cancers, including 1,142 exhibiting histotype-elevated expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multidimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell type-specific transcription factors further implicated distinct histotype-elevated and developmental lncRNAs. Integration of these analyses prioritized lncRNAs for experimental validation, and silencing of TBX2-AS1, the top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming the computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies. SIGNIFICANCE Comprehensive characterization of lncRNAs in pediatric cancer leads to the identification of highly expressed lncRNAs across childhood cancers, annotation of lncRNAs showing histotype-specific elevated expression, and prediction of lncRNA gene regulatory networks.
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Affiliation(s)
- Apexa Modi
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Genomics and Computational Biology Graduate Group, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Gonzalo Lopez
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Karina L. Conkrite
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tsz Ching Leung
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Sathvik Ramanan
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elisabetta Manduchi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew E. Johnson
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daphne Cheung
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois 60208, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Malcolm A. Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland 20892, USA
| | | | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Elizabeth J. Perlman
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois 60208, USA
| | - Stephen P. Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Divisions of Human Genetics and Endocrinology & Diabetes, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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5
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Elsayed AK, Alajez NM, Abdelalim EM. Genome-wide differential expression profiling of long non-coding RNAs in FOXA2 knockout iPSC-derived pancreatic cells. Cell Commun Signal 2023; 21:229. [PMID: 37670346 PMCID: PMC10478503 DOI: 10.1186/s12964-023-01212-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/01/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Our recent studies have demonstrated the crucial involvement of FOXA2 in the development of human pancreas. Reduction of FOXA2 expression during the differentiation of induced pluripotent stem cells (iPSCs) into pancreatic islets has been found to reduce α-and β-cell masses. However, the extent to which such changes are linked to alterations in the expression profile of long non-coding RNAs (lncRNAs) remains unraveled. METHODS Here, we employed our recently established FOXA2-deficient iPSCs (FOXA2-/- iPSCs) to investigate changes in lncRNA profiles and their correlation with dysregulated mRNAs during the pancreatic progenitor (PP) and pancreatic islet stages. Furthermore, we constructed co-expression networks linking significantly downregulated lncRNAs with differentially expressed pancreatic mRNAs. RESULTS Our results showed that 442 lncRNAs were downregulated, and 114 lncRNAs were upregulated in PPs lacking FOXA2 compared to controls. Similarly, 177 lncRNAs were downregulated, and 59 lncRNAs were upregulated in islet cells lacking FOXA2 compared to controls. At both stages, we observed a strong correlation between lncRNAs and several crucial pancreatic genes and TFs during pancreatic differentiation. Correlation analysis revealed 12 DE-lncRNAs that strongly correlated with key downregulated pancreatic genes in both PPs and islet cell stages. Selected DE-lncRNAs were validated using RT-qPCR. CONCLUSIONS Our data indicate that the observed defects in pancreatic islet development due to the FOXA2 loss is associated with significant alterations in the expression profile of lncRNAs. Therefore, our findings provide novel insights into the role of lncRNA and mRNA networks in regulating pancreatic islet development, which warrants further investigations. Video Abstract.
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Affiliation(s)
- Ahmed K Elsayed
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
- Stem Cell Core, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Nehad M Alajez
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Essam M Abdelalim
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.
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6
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Erber J, Herndler-Brandstetter D. Regulation of T cell differentiation and function by long noncoding RNAs in homeostasis and cancer. Front Immunol 2023; 14:1181499. [PMID: 37346034 PMCID: PMC10281531 DOI: 10.3389/fimmu.2023.1181499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) increase in genomes of complex organisms and represent the largest group of RNA genes transcribed in mammalian cells. Previously considered only transcriptional noise, lncRNAs comprise a heterogeneous class of transcripts that are emerging as critical regulators of T cell-mediated immunity. Here we summarize the lncRNA expression landscape of different T cell subsets and highlight recent advances in the role of lncRNAs in regulating T cell differentiation, function and exhaustion during homeostasis and cancer. We discuss the different molecular mechanisms of lncRNAs and highlight lncRNAs that can serve as novel targets to modulate T cell function or to improve the response to cancer immunotherapies by modulating the immunosuppressive tumor microenvironment.
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Zhou Q, Jiang Y, Cai C, Li W, Leow MKS, Yang Y, Liu J, Xu D, Sun L. Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs. Life Sci Alliance 2023; 6:e202302002. [PMID: 37024123 PMCID: PMC10078953 DOI: 10.26508/lsa.202302002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
Although long noncoding RNAs (lncRNAs) experience weaker evolutionary constraints and exhibit lower sequence conservation than coding genes, they can still conserve their features in various aspects. Here, we used multiple approaches to systemically evaluate the conservation between human and mouse lncRNAs from various dimensions including sequences, promoter, global synteny, and local synteny, which led to the identification of 1,731 conserved lncRNAs with 427 high-confidence ones meeting multiple criteria. Conserved lncRNAs, compared with non-conserved ones, generally have longer gene bodies, more exons and transcripts, stronger connections with human diseases, and are more abundant and widespread across different tissues. Transcription factor (TF) profile analysis revealed a significant enrichment of TF types and numbers in the promoters of conserved lncRNAs. We further identified a set of TFs that preferentially bind to conserved lncRNAs and exert stronger regulation on conserved than non-conserved lncRNAs. Our study has reconciled some discrepant interpretations of lncRNA conservation and revealed a new set of transcriptional factors ruling the expression of conserved lncRNAs.
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Affiliation(s)
- Qiuzhong Zhou
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
| | - Yuxi Jiang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chaoqun Cai
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wen Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Melvin Khee-Shing Leow
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Endocrinology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Yi Yang
- Program in Health Services & Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Jin Liu
- Program in Health Services & Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Dan Xu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Sun
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, Singapore, Singapore
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Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science 2023; 380:eabn2937. [PMID: 37104612 PMCID: PMC10259825 DOI: 10.1126/science.abn2937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/09/2023] [Indexed: 04/29/2023]
Abstract
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
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Affiliation(s)
- Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Steven Gazal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xue Li
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Diane P. Genereux
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Jessika Nordin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Chao Wang
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - James Xue
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Center for System Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Quan Sun
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Laura M. Huckins
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alyssa Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kathleen C. Keough
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yun Li
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jessica Johnson
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | | | - Benedict Paten
- UC Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185 Uppsala, Sweden
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Elinor K. Karlsson
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
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9
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Zhang L, Yang Y, Zhang L, Ma J, Sun R, Tian Y, Yuan X, Liu B, Yu T, Jiang Z. Identification of long non-coding RNA in formaldehyde-induced cardiac dysplasia in rats. Food Chem Toxicol 2023; 174:113653. [PMID: 36758786 DOI: 10.1016/j.fct.2023.113653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/09/2023]
Abstract
Formaldehyde exposure during pregnancy can cause fetal congenital heart disease (CHD). However, the regulatory mechanism remains unclear. Studies on the biology of long non-coding RNAs (lncRNAs) show that lncRNAs can influence cardiac development and disease. However, expression patterns and regulatory mechanisms of action of lncRNAs in formaldehyde-induced CHD remain unclear. We used high-throughput sequencing strategies as a means of identifying lncRNA expression profiles in heart tissues of normal and formaldehyde-exposed newborn rats. Overall, 763 differentially expressed lncRNAs were identified, including 325 and 438 that were respectively up-regulated and down-regulated. GO and KEGG analyses indicated that the Ras and hedgehog signaling pathways may be important regulatory pathways in CHD caused by exposure to formaldehyde. A lncRNA-miRNA-mRNA co-expression network was constructed and a key miRNA, rno-miR-665, was identified. Furthermore, qRT-PCR analysis verified that the novel lncRNAs: MSTRG.27313.2, MSTRG.30629.2, MSTRG.36520.33, MSTRG.91234.1, and MSTRG.91233.9, were upregulated in the formaldehyde-exposed group. These differentially expressed lncRNAs identified during formaldehyde-induced CHD in newborn rats help explain CHD pathogenesis and provide an effective reference for diagnosing and treating CHD.
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Affiliation(s)
- Lu Zhang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, PR China
| | - Yanyan Yang
- Department of Immunology, Basic Medicine School, Qingdao University, No. 308 Ningxia Road, Qingdao, 266071, PR China
| | - Lin Zhang
- Department of Microbiology, Linyi Center for Disease Control and Prevention, Linyi, 276000, PR China
| | - Jianmin Ma
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, PR China
| | - Ruicong Sun
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, PR China
| | - Yu Tian
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, PR China
| | - Xiaoli Yuan
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, PR China
| | - Bingyu Liu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, PR China
| | - Tao Yu
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, PR China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Road No. 38 Dengzhou, Qingdao, 266021, PR China.
| | - Zhirong Jiang
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Road No. 59 Haier, Qingdao, 266100, Shandong, PR China.
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10
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Man HSJ, Subramaniam N, Downs T, Sukumar AN, Saha AD, Nair R, Chen L, Teitelbaum D, Turgeon PJ, Ku KH, Tran E, de Perrot M, Marsden PA. Long noncoding RNA GATA2-AS1 augments endothelial Hypoxia Inducible Factor 1-α induction and regulates hypoxic signaling. J Biol Chem 2023; 299:103029. [PMID: 36806681 PMCID: PMC10148162 DOI: 10.1016/j.jbc.2023.103029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/18/2023] Open
Abstract
Vascular endothelial cells form the inner cellular lining of blood vessels and have myriad physiologic functions including angiogenesis and response to hypoxia. We recently identified a set of endothelial cell (EC)-enriched long noncoding RNAs (lncRNAs) in differentiated human primary cell types and described the role of the STEEL lncRNA in angiogenic patterning. We sought to further understand the role of EC-enriched lncRNAs in physiologic adaptation of the vascular endothelium. In this work, we describe an abundant, cytoplasmic, and EC-enriched lncRNA, GATA2-AS1, that is divergently transcribed from the EC-enriched developmental regulator, GATA2. While GATA2-AS1 is largely co-expressed with GATA2 in ECs, GATA2-AS1 and GATA2 appear to be complementary rather than synergistic as they have mostly distinct target genes. Common single nucleotide variants (SNVs) in GATA2-AS1 exons are associated with early onset coronary artery disease (CAD) and decreased expression of GATA2-AS1 in endothelial cell lines. In most cells, HIF1-α is central to the transcriptional response to hypoxia, while in ECs, both HIF1-α and HIF2-α are required to coordinate an acute and chronic response respectively. In this setting, GATA2-AS1 contributes to the "HIF switch" and augments HIF1-α induction in acute hypoxia to regulate HIF1-α/ HIF2-α balance. In hypoxia, GATA2-AS1 orchestrates HIF1-α-dependent induction of the glycolytic pathway, and HIF1-α-independent maintenance of mitochondrial biogenesis. Similarly, GATA2-AS1 coordinates both metabolism and "tip/stalk" cell signaling to regulate angiogenesis in hypoxic ECs. Furthermore, we find that GATA2-AS1 expression patterns are perturbed in atherosclerotic disease. Together, these results define a role for GATA2-AS1 in the EC-specific response to hypoxia.
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Affiliation(s)
- H S Jeffrey Man
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Department of Respirology, University Health Network, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Noeline Subramaniam
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Tiana Downs
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aravin N Sukumar
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Aninda D Saha
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Ranju Nair
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lucy Chen
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Teitelbaum
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Paul J Turgeon
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kyung Ha Ku
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Eileen Tran
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Marc de Perrot
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Division of Thoracic Surgery, Toronto General Hospital, Toronto, Ontario, Canada
| | - Philip A Marsden
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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11
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Sun J, Li X, Yin J, Chen X, Zhu Z, Wu R, Yu E, Mao Z. Long non coding RNA COX10-DT promotes the progression of breast cancer via the COX10-DT/miR-206/BDNF axis. Biochem Biophys Res Commun 2023; 639:46-53. [PMID: 36463760 DOI: 10.1016/j.bbrc.2022.11.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators in the biological development of breast cancer. In this study, we aimed to determine the roles and mechanisms of the lncRNA COX10 divergent transcript (COX10-DT) in breast cancer progression. The relative expression level of COX10-DT was calculated in matched breast cancer tissues and adjacent normal tissues using quantitative real-time PCR. Gain-of-function and loss-of-function approaches further revealed the functions and mechanisms of COX10-DT in breast cancer cells. Clinically, we found that the lncRNA COX10-DT was commonly overexpressed in breast cancer tissues compared to paired peritumoural tissues. Functionally, the lncRNA COX10-DT might promote the proliferation and migration of breast cancer cells. Mechanistically, the lncRNA COX10-DT did not play a role by regulating the expression of its divergent gene COX10 but acted as a competitive endogenous RNA (ceRNA) by directly sponging miR-206, which further regulated the expression of brain-derived neurotrophic factor (BDNF). Taken together, our results proved that the lncRNA COX10-DT could function via the COX10-DT/miR-206/BDNF axis, thereby promoting the development of breast cancer. These findings indicated that the lncRNA COX10-DT might be a potential biomarker and therapeutic target for breast cancer.
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Affiliation(s)
- Jie Sun
- Department of Breast Surgery of the First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, 215006, China
| | - Xiaohua Li
- Department of Breast Surgery of Wuzhong People's Hospital, Suzhou, 215218, China
| | - Jun Yin
- Department of General Surgery of the First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, 215006, China
| | - Xin Chen
- Department of General Surgery of the First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, 215006, China
| | - Zheng Zhu
- Department of General Surgery of the First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, 215006, China
| | - Runda Wu
- Department of General Surgery of the First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, 215006, China
| | - EnQiao Yu
- Department of Breast Surgery of the First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, 215006, China.
| | - Zhongqi Mao
- Department of General Surgery of the First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, 215006, China.
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12
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Hao Y, Xie B, Fu X, Xu R, Yang Y. New Insights into lncRNAs in Aβ Cascade Hypothesis of Alzheimer's Disease. Biomolecules 2022; 12:biom12121802. [PMID: 36551230 PMCID: PMC9775548 DOI: 10.3390/biom12121802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Alzheimer's disease (AD) is the most common type of dementia, but its pathogenesis is not fully understood, and effective drugs to treat or reverse the progression of the disease are lacking. Long noncoding RNAs (lncRNAs) are abnormally expressed and deregulated in AD and are closely related to the occurrence and development of AD. In addition, the high tissue specificity and spatiotemporal specificity make lncRNAs particularly attractive as diagnostic biomarkers and specific therapeutic targets. Therefore, an in-depth understanding of the regulatory mechanisms of lncRNAs in AD is essential for developing new treatment strategies. In this review, we discuss the unique regulatory functions of lncRNAs in AD, ranging from Aβ production to clearance, with a focus on their interaction with critical molecules. Additionally, we highlight the advantages and challenges of using lncRNAs as biomarkers for diagnosis or therapeutic targets in AD and present future perspectives in clinical practice.
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Affiliation(s)
- Yitong Hao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Bo Xie
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Xiaoshu Fu
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Rong Xu
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun 130021, China
| | - Yu Yang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
- Correspondence:
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13
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Conceição IMCAD, Luscher-dias T, Queiroz LR, de Melo AGB, Machado CR, Gomes KB, Souza RP, Luizon MR, Franco GR. Metformin Treatment Modulates Long Non-Coding RNA Isoforms Expression in Human Cells. Noncoding RNA 2022; 8:68. [PMID: 36287120 PMCID: PMC9607547 DOI: 10.3390/ncrna8050068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) undergo splicing and have multiple transcribed isoforms. Nevertheless, for lncRNAs, as well as for mRNA, measurements of expression are routinely performed only at the gene level. Metformin is the first-line oral therapy for type 2 diabetes mellitus and other metabolic diseases. However, its mechanism of action remains not thoroughly explained. Transcriptomic analyses using metformin in different cell types reveal that only protein-coding genes are considered. We aimed to characterize lncRNA isoforms that were differentially affected by metformin treatment on multiple human cell types (three cancer, two non-cancer) and to provide insights into the lncRNA regulation by this drug. We selected six series to perform a differential expression (DE) isoform analysis. We also inferred the biological roles for lncRNA DE isoforms using in silico tools. We found the same isoform of an lncRNA (AC016831.6-205) highly expressed in all six metformin series, which has a second exon putatively coding for a peptide with relevance to the drug action. Moreover, the other two lncRNA isoforms (ZBED5-AS1-207 and AC125807.2-201) may also behave as cis-regulatory elements to the expression of transcripts in their vicinity. Our results strongly reinforce the importance of considering DE isoforms of lncRNA for understanding metformin mechanisms at the molecular level.
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14
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Ward Z, Schmeier S, Pearson J, Cameron VA, Frampton CM, Troughton RW, Doughty RN, Richards AM, Pilbrow AP. Identifying Candidate Circulating RNA Markers for Coronary Artery Disease by Deep RNA-Sequencing in Human Plasma. Cells 2022; 11:3191. [PMID: 36291058 PMCID: PMC9599983 DOI: 10.3390/cells11203191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2023] Open
Abstract
Advances in RNA sequencing (RNA-Seq) have facilitated transcriptomic analysis of plasma for the discovery of new diagnostic and prognostic markers for disease. We aimed to develop a short-read RNA-Seq protocol to detect mRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in plasma for the discovery of novel markers for coronary artery disease (CAD) and heart failure (HF). Circulating cell-free RNA from 59 patients with stable CAD (half of whom developed HF within 3 years) and 30 controls was sequenced to a median depth of 108 paired reads per sample. We identified fragments from 3986 messenger RNAs (mRNAs), 164 long non-coding RNAs (lncRNAs), 405 putative novel lncRNAs and 227 circular RNAs in plasma. Circulating levels of 160 mRNAs, 10 lncRNAs and 2 putative novel lncRNAs were altered in patients compared with controls (absolute fold change >1.2, p < 0.01 adjusted for multiple comparisons). The most differentially abundant transcripts were enriched in mRNAs encoded by the mitochondrial genome. We did not detect any differences in the plasma RNA profile between patients who developed HF compared with those who did not. In summary, we show that mRNAs, lncRNAs and circular RNAs can be reliably detected in plasma by deep RNA-Seq. Multiple coding and non-coding transcripts were altered in association with CAD, including several mitochondrial mRNAs, which may indicate underlying myocardial ischaemia and oxidative stress. If validated, circulating levels of these transcripts could potentially be used to help identify asymptomatic individuals with established CAD prior to an acute coronary event.
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Affiliation(s)
- Zoe Ward
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Sebastian Schmeier
- School of Natural and Computational Sciences, Massey University, Auckland 0632, New Zealand
- Evotec SE, Essener Bogen 7, 22419 Hamburg, Germany
| | - John Pearson
- Biostatistics and Computational Biology Unit, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Vicky A Cameron
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Chris M Frampton
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Richard W Troughton
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Rob N Doughty
- Heart Health Research Group, University of Auckland, Auckland 1023, New Zealand
| | - A. Mark Richards
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
- Cardiovascular Research Institute, National University of Singapore, Singapore 119228, Singapore
| | - Anna P Pilbrow
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
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15
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Mahale S, Setia M, Prajapati B, Subhash S, Yadav MP, Thankaswamy Kosalai S, Deshpande A, Kuchlyan J, Di Marco M, Westerlund F, Wilhelmsson LM, Kanduri C, Kanduri M. HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells. Nat Commun 2022; 13:4865. [PMID: 36038571 PMCID: PMC9424213 DOI: 10.1038/s41467-022-32537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/04/2022] [Indexed: 11/09/2022] Open
Abstract
Although antisense transcription is a widespread event in the mammalian genome, double-stranded RNA (dsRNA) formation between sense and antisense transcripts is very rare and mechanisms that control dsRNA remain unknown. By characterizing the FGF-2 regulated transcriptome in normal and cancer cells, we identified sense and antisense transcripts IER3 and IER3-AS1 that play a critical role in FGF-2 controlled oncogenic pathways. We show that IER3 and IER3-AS1 regulate each other's transcription through HnRNPK-mediated post-transcriptional regulation. HnRNPK controls the mRNA stability and colocalization of IER3 and IER3-AS1. HnRNPK interaction with IER3 and IER3-AS1 determines their oncogenic functions by maintaining them in a single-stranded form. hnRNPK depletion neutralizes their oncogenic functions through promoting dsRNA formation and cytoplasmic accumulation. Intriguingly, hnRNPK loss-of-function and gain-of-function experiments reveal its role in maintaining global single- and double-stranded RNA. Thus, our data unveil the critical role of HnRNPK in maintaining single-stranded RNAs and their physiological functions by blocking RNA-RNA interactions.
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Affiliation(s)
- Sagar Mahale
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Meenakshi Setia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Bharat Prajapati
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Mukesh Pratap Yadav
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Ananya Deshpande
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Jagannath Kuchlyan
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Mirco Di Marco
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden.
| | - Meena Kanduri
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden.
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16
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Khan A, Zhang X. Function of the Long Noncoding RNAs in Hepatocellular Carcinoma: Classification, Molecular Mechanisms, and Significant Therapeutic Potentials. Bioengineering (Basel) 2022; 9:406. [PMID: 36004931 PMCID: PMC9405066 DOI: 10.3390/bioengineering9080406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common and serious type of primary liver cancer. HCC patients have a high death rate and poor prognosis due to the lack of clear signs and inadequate treatment interventions. However, the molecular pathways that underpin HCC pathogenesis remain unclear. Long non-coding RNAs (lncRNAs), a new type of RNAs, have been found to play important roles in HCC. LncRNAs have the ability to influence gene expression and protein activity. Dysregulation of lncRNAs has been linked to a growing number of liver disorders, including HCC. As a result, improved understanding of lncRNAs could lead to new insights into HCC etiology, as well as new approaches for the early detection and treatment of HCC. The latest results with respect to the role of lncRNAs in controlling multiple pathways of HCC were summarized in this study. The processes by which lncRNAs influence HCC advancement by interacting with chromatin, RNAs, and proteins at the epigenetic, transcriptional, and post-transcriptional levels were examined. This critical review also highlights recent breakthroughs in lncRNA signaling pathways in HCC progression, shedding light on the potential applications of lncRNAs for HCC diagnosis and therapy.
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17
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Ross CJ, Ulitsky I. Discovering functional motifs in long noncoding RNAs. Wiley Interdiscip Rev RNA 2022; 13:e1708. [PMID: 34981665 DOI: 10.1002/wrna.1708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 12/27/2022]
Abstract
Long noncoding RNAs (lncRNAs) are products of pervasive transcription that closely resemble messenger RNAs on the molecular level, yet function through largely unknown modes of action. The current model is that the function of lncRNAs often relies on specific, typically short, conserved elements, connected by linkers in which specific sequences and/or structures are less important. This notion has fueled the development of both computational and experimental methods focused on the discovery of functional elements within lncRNA genes, based on diverse signals such as evolutionary conservation, predicted structural elements, or the ability to rescue loss-of-function phenotypes. In this review, we outline the main challenges that the different methods need to overcome, describe the recently developed approaches, and discuss their respective limitations. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Caroline Jane Ross
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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18
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Herman AB, Tsitsipatis D, Gorospe M. Integrated lncRNA function upon genomic and epigenomic regulation. Mol Cell 2022; 82:2252-66. [PMID: 35714586 DOI: 10.1016/j.molcel.2022.05.027] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/09/2022] [Accepted: 05/23/2022] [Indexed: 12/20/2022]
Abstract
Although some long noncoding (lnc)RNAs are known since the 1950s, the past 25 years have uncovered myriad lncRNAs with diverse sequences, structures, and functions. The advent of high-throughput and sensitive technologies has further uncovered the vast heterogeneity of lncRNA-interacting molecules and patterns of expressed lncRNAs. We propose a unifying functional theme for the expansive family of lncRNAs. At an elementary level, the genomic program of gene expression is elicited via canonical transcription and post-transcriptional mRNA assembly, turnover, and translation. Building upon this regulation, an epigenomic program refines the basic genomic control by modifying chromatin architecture as well as DNA and RNA chemistry. Superimposed over the genomic and epigenomic programs, lncRNAs create an additional regulatory dimension: by interacting with the proteins and nucleic acids that regulate gene expression in the nucleus and cytoplasm, lncRNAs help establish robust, nimble, and specific transcriptional and post-transcriptional control. We describe our present understanding of lncRNA-coordinated control of protein programs and cell fate and discuss challenges and opportunities as we embark on the next 25 years of lncRNA discovery.
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Kraft K, Yost KE, Murphy SE, Magg A, Long Y, Corces MR, Granja JM, Wittler L, Mundlos S, Cech TR, Boettiger AN, Chang HY. Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation. Proc Natl Acad Sci U S A 2022; 119:e2201883119. [PMID: 35617427 PMCID: PMC9295753 DOI: 10.1073/pnas.2201883119] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cell (ESC) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling progressive spreading of H3K27me3 on the linear genome. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remain unclear. Here, we apply H3K27me3 HiChIP, a protein-directed chromosome conformation method, and optical reconstruction of chromatin architecture to profile long-range Polycomb-associated DNA loops that span tens to hundreds of megabases across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. We find that H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes. Genetic deletion of H3K27me3 loop anchors results in disruption of spatial contact between distant loci and altered H3K27me3 in cis, both locally and megabases away on the same chromosome. In mouse embryos, loop anchor deletion leads to ectopic activation of the partner gene, suggesting that Polycomb-associated loops control gene silencing during development. Further, we find that alterations in PRC2 occupancy resulting from an RNA binding–deficient EZH2 mutant are accompanied by loss of Polycomb-associated DNA looping. Together, these results suggest PRC2 uses RNA binding to enhance long-range chromosome folding and H3K27me3 spreading. Developmental gene loci have unique roles in Polycomb spreading, emerging as important architectural elements of the epigenome.
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Affiliation(s)
- Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
| | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Andreas Magg
- Research Group of Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin, 10117 Berlin, Germany
| | - Yicheng Long
- HHMI, University of Colorado, Boulder, CO 80309
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309
| | - M. Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
| | - Jeffrey M. Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Mundlos
- Research Group of Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin, 10117 Berlin, Germany
| | - Thomas R. Cech
- HHMI, University of Colorado, Boulder, CO 80309
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309
| | | | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305
- HHMI, Stanford University School of Medicine, Stanford, CA 94305
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20
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Pan Y, Xu L, Huang H. Expression, functional mechanism and therapy application of long noncoding RNA in β-thalassemia. Zhong Nan Da Xue Xue Bao Yi Xue Ban 2022; 47:252-257. [PMID: 35545416 PMCID: PMC10930521 DOI: 10.11817/j.issn.1672-7347.2022.210411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 06/15/2023]
Abstract
β-thalassemia (β-thal) is one of the most common genetic diseases in the world, its pathogenesis is extremely complex and there is no effective treatment at present. The birth of children with moderate and severe β-thal brings economic pressure to families, social medical and health services. Long noncoding RNA (lncRNA) is a type of noncoding protein transcripts with a length greater than 200 nucleotides, which is involved in a variety of biological processes, such as cell proliferation, differentiation and chromosome variation and plays an important role in the epigenetic and post-transcriptional regulation of genes. It has potential value in the diagnosis, prevention and treatment of β-thal. LncRNA possesses the characteristics such as tissue specificity, cell specificity, developmental stage specificity, space-time specificity and disease specificity, and its complex interaction network has become a challenge to translate research results into clinical practice. Taking lncRNA as an entry point, in-depth understanding of the function of lncRNA in β-thal and explanation of its related regulatory mechanisms will provide theoretical basis for targeting treatment of β-thal, which can improve the diagnosis and treatment of β-thal.
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Affiliation(s)
- Yali Pan
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital/Affiliated Hospital of Fujian Medical University; Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou 350001.
- School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350004, China.
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital/Affiliated Hospital of Fujian Medical University; Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou 350001
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital/Affiliated Hospital of Fujian Medical University; Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou 350001.
- School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350004, China.
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21
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Mercer TR, Munro T, Mattick JS. The potential of long noncoding RNA therapies. Trends Pharmacol Sci 2022. [DOI: 10.1016/j.tips.2022.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 02/06/2023]
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22
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Venegas-Zamora L, Bravo-Acuña F, Sigcho F, Gomez W, Bustamante-Salazar J, Pedrozo Z, Parra V. New Molecular and Organelle Alterations Linked to Down Syndrome Heart Disease. Front Genet 2022; 12:792231. [PMID: 35126461 PMCID: PMC8808411 DOI: 10.3389/fgene.2021.792231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
Down syndrome (DS) is a genetic disorder caused by a trisomy of the human chromosome 21 (Hsa21). Overexpression of Hsa21 genes that encode proteins and non-coding RNAs (ncRNAs) can disrupt several cellular functions and biological processes, especially in the heart. Congenital heart defects (CHDs) are present in 45–50% of individuals with DS. Here, we describe the genetic background of this condition (Hsa21 and non-Hsa21 genes), including the role of ncRNAs, and the relevance of these new players in the study of the pathophysiology of DS heart diseases. Additionally, we discuss several distinct pathways in cardiomyocytes which help maintain a functional heart, but that might trigger hypertrophy and oxidative stress when altered. Moreover, we highlight the importance of investigating how mitochondrial and lysosomal dysfunction could eventually contribute to understanding impaired heart function and development in subjects with the Hsa21 trisomy. Altogether, this review focuses on the newest insights about the gene expression, molecular pathways, and organelle alterations involved in the cardiac phenotype of DS.
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Affiliation(s)
- Leslye Venegas-Zamora
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Francisco Bravo-Acuña
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Francisco Sigcho
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Wileidy Gomez
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - José Bustamante-Salazar
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Zully Pedrozo
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Programa de Fisiología y Biofísica, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Red para El Estudio de Enfermedades Cardiopulmonares de Alta Letalidad (REECPAL), Universidad de Chile, Santiago, Chile
- *Correspondence: Zully Pedrozo, ; Valentina Parra,
| | - Valentina Parra
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- Red para El Estudio de Enfermedades Cardiopulmonares de Alta Letalidad (REECPAL), Universidad de Chile, Santiago, Chile
- *Correspondence: Zully Pedrozo, ; Valentina Parra,
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Mathy NW, Deng S, Gong AY, Li M, Wang Y, Burleigh O, Kochvar A, Whiteford ER, Shibata A, Chen XM. The Long Non-Coding RNA Nostrill Regulates Transcription of Irf7 Through Interaction With NF-κB p65 to Enhance Intestinal Epithelial Defense Against Cryptosporidium parvum. Front Immunol 2022; 13:863957. [PMID: 35464447 PMCID: PMC9021721 DOI: 10.3389/fimmu.2022.863957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/17/2022] [Indexed: 11/28/2022] Open
Abstract
The cells of the intestinal epithelium establish the frontline for host defense against pathogens in the gastrointestinal tract and play a vital role in the initiation of the immune response. Increasing evidence supports the role of long non-coding RNAs (lncRNAs) as critical regulators of diverse cellular processes, however, their role in antimicrobial host defense is incompletely understood. In this study, we provide evidence that the lncRNA Nostrill is upregulated in the intestinal epithelium following infection by Cryptosporidium parvum, a globally prevalent apicomplexan parasite that causes significant diarrheal disease and an important opportunistic pathogen in the immunocompromised and AIDS patients. Induction of Nostrill in infected intestinal epithelial cells was triggered by NF-κB signaling and was observed to enhance epithelial defense by decreasing parasitic infection burden. Nostrill participates in the transcriptional regulation of C. parvum-induced Irf7 expression through interactions with NF-κB p65, and induction of Nostrill promotes epigenetic histone modifications and occupancy of RNA polymerase II at the Irf7 promoter. Our data suggest that the induction of Nostrill promotes antiparasitic defense against C. parvum and enhances intestinal epithelial antimicrobial defense through contributions to transcriptional regulation of immune-related genes, such as Irf7.
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Affiliation(s)
- Nicholas W Mathy
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, United States
| | - Silu Deng
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, United States
| | - Ai-Yu Gong
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, United States.,Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, United States
| | - Min Li
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, United States
| | - Yang Wang
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, United States
| | - Olivia Burleigh
- Department of Biology, Creighton University, Omaha, NE, United States
| | - Andrew Kochvar
- Department of Biology, Creighton University, Omaha, NE, United States
| | - Erin R Whiteford
- Creighton University, School of Medicine, Omaha, NE, United States
| | - Annemarie Shibata
- Department of Biology, Creighton University, Omaha, NE, United States
| | - Xian-Ming Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, United States.,Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, United States
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Silveira GO, Coelho HS, Amaral MS, Verjovski-Almeida S. Long non-coding RNAs as possible therapeutic targets in protozoa, and in Schistosoma and other helminths. Parasitol Res 2021; 121:1091-1115. [PMID: 34859292 DOI: 10.1007/s00436-021-07384-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/14/2021] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) emerged in the past 20 years due to massive amounts of scientific data regarding transcriptomic analyses. They have been implicated in a plethora of cellular processes in higher eukaryotes. However, little is known about lncRNA possible involvement in parasitic diseases, with most studies only detecting their presence in parasites of human medical importance. Here, we review the progress on lncRNA studies and their functions in protozoans and helminths. In addition, we show an example of knockdown of one lncRNA in Schistosoma mansoni, SmLINC156349, which led to in vitro parasite adhesion, motility, and pairing impairment, with a 20% decrease in parasite viability and 33% reduction in female oviposition. Other observed phenotypes were a decrease in the proliferation rate of both male and female worms and their gonads, and reduced female lipid and vitelline droplets that are markers for well-developed vitellaria. Impairment of female worms' vitellaria in SmLINC156349-silenced worms led to egg development deficiency. All those results demonstrate the great potential of the tools and methods to characterize lncRNAs as potential new therapeutic targets. Further, we discuss the challenges and limitations of current methods for studying lncRNAs in parasites and possible solutions to overcome them, and we highlight the future directions of this exciting field.
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Affiliation(s)
- Gilbert O Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Helena S Coelho
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Murilo S Amaral
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.
| | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil. .,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
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25
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Zhang Z, Wu Y, Yu C, Li Z, Xu L. Comprehensive analysis of immune related lncRNAs in the tumor microenvironment of stage II-III colorectal cancer. J Gastrointest Oncol 2021; 12:2232-2243. [PMID: 34790388 DOI: 10.21037/jgo-21-594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/19/2021] [Indexed: 11/06/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) associated with immunological function have increasingly been found to act as effective prognostic biomarkers of the overall survival (OS) of colorectal cancer (CRC) patients. We sought to identify a signature of immune-related lncRNAs that offered value as a tool for the prospective prognostic evaluation of patients with stage II-III CRC. Methods The clinical and gene expression data of CRC patients in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases was obtained and separated into a training cohort composed of 202 samples, a test cohort of 124 samples from the GSE72970 dataset, and a validation cohort of 91 samples from the GSE143985 dataset. Results We firstly evaluated intratumoral immune cell infiltration by conducting a Single-sample gene set enrichment analyses (ssGSEA) analysis to separate patient tumors into those with low immune cell infiltration and those with high immune cell infiltration. We then compared lncRNA and mRNA expression profiles between these two tumor types, leading us to focus on eight lncRNAs identified within the resultant mRNA-lncRNA co-expression network. Multivariate Cox regression models were then utilized to detect an immune-associated lncRNA signature that offered value for prognostic model construction. Functional analyses revealed this lncRNA signature to be associated with key immunological pathways including the JAK-STAT signaling, T cell receptor signaling, and Rap1 signaling pathways. Conclusions Together, our results suggest that our immune-related 4 lncRNA signature can reliably predict stage II-III CRC patient prognosis, thereby guiding efforts to better understand this disease and to effectively treat it.
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Affiliation(s)
- Zan Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yixin Wu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zhengtai Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lida Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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26
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Li S, Sun X, Li J, Zheng A, Cao Y, Guo Y, Jin F. A Novel Prognostic Signature of Immune-Related Long Noncoding RNA Pairs for Tumor-Infiltrating Immune Cells and Drug Susceptibility in Breast Cancer. DNA Cell Biol 2021; 41:103-115. [PMID: 34762509 DOI: 10.1089/dna.2021.0489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Prognostic signatures of specific immune-related long noncoding RNAs (irlncRNAs) have been elucidated with the development of immunotherapy for breast cancer, but the heterogeneity of gene expression in different patients still limits their effectiveness. We constructed a new prognostic signature based on the relative expression of differentially expressed irlncRNA (DEirlncRNA) pairs and analyzed its clinical application in 1069 patients from The Cancer Genome Atlas-Breast Cancer (TCGA-BRCA) containing 745 White patients, 180 Black and African American patients, 58 Asian patients, 181 stage I patients, 606 stage II patients, 240 stage III patients, and 20 stage IV patients. Data from TCGA-BRCA and ImmPort were used to screen DEirlncRNAs, and the DEirlncRNA pairs were established by cyclical single comparison of each DEirlncRNA. After the data optimization, we constructed a signature containing 24 DEirlncRNA pairs. Risk groups of this signature were defined using the cutoff value from the 10-year survival receiver operating characteristic curve, and Kaplan-Meier analysis verified its prognostic effectiveness. Furthermore, we confirmed this signature as an independent prognostic factor and confirmed its close association with traditional clinicopathological factors. Moreover, this risk signature was closely related to tumor-infiltrating immune cells and drug susceptibility. In short, we successfully constructed a risk signature of DEirlncRNA pairs, which might provide new insights for breast cancer precision therapy.
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Affiliation(s)
- Shan Li
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaoyu Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China
| | - Jiahong Li
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ang Zheng
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yu Cao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yang Guo
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Feng Jin
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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Di Pietro L, Barba M, Palacios D, Tiberio F, Prampolini C, Baranzini M, Parolini O, Arcovito A, Lattanzi W. Shaping modern human skull through epigenetic, transcriptional and post-transcriptional regulation of the RUNX2 master bone gene. Sci Rep 2021; 11:21316. [PMID: 34716352 PMCID: PMC8556228 DOI: 10.1038/s41598-021-00511-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/13/2021] [Indexed: 01/13/2023] Open
Abstract
RUNX2 encodes the master bone transcription factor driving skeletal development in vertebrates, and playing a specific role in craniofacial and skull morphogenesis. The anatomically modern human (AMH) features sequence changes in the RUNX2 locus compared with archaic hominins' species. We aimed to understand how these changes may have contributed to human skull globularization occurred in recent evolution. We compared in silico AMH and archaic hominins' genomes, and used mesenchymal stromal cells isolated from skull sutures of craniosynostosis patients for in vitro functional assays. We detected 459 and 470 nucleotide changes in noncoding regions of the AMH RUNX2 locus, compared with the Neandertal and Denisovan genomes, respectively. Three nucleotide changes in the proximal promoter were predicted to alter the binding of the zinc finger protein Znf263 and long-distance interactions with other cis-regulatory regions. By surface plasmon resonance, we selected nucleotide substitutions in the 3'UTRs able to affect miRNA binding affinity. Specifically, miR-3150a-3p and miR-6785-5p expression inversely correlated with RUNX2 expression during in vitro osteogenic differentiation. The expression of two long non-coding RNAs, AL096865.1 and RUNX2-AS1, within the same locus, was modulated during in vitro osteogenic differentiation and correlated with the expression of specific RUNX2 isoforms. Our data suggest that RUNX2 may have undergone adaptive phenotypic evolution caused by epigenetic and post-transcriptional regulatory mechanisms, which may explain the delayed suture fusion leading to the present-day globular skull shape.
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Affiliation(s)
- Lorena Di Pietro
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marta Barba
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Daniela Palacios
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Federica Tiberio
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Chiara Prampolini
- Dipartimento Testa-Collo e Organi di Senso, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Mirko Baranzini
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ornella Parolini
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alessandro Arcovito
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Wanda Lattanzi
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy.
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
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Lüscher-Dias T, Conceição IM, Schuch V, Maracaja-Coutinho V, Amaral PP, Nakaya HI. Long non-coding RNAs associated with infection and vaccine-induced immunity. Essays Biochem 2021; 65:657-69. [PMID: 34528687 DOI: 10.1042/EBC20200072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 08/01/2021] [Accepted: 08/10/2021] [Indexed: 12/31/2022]
Abstract
The immune system responds to infection or vaccination through a dynamic and complex process that involves several molecular and cellular factors. Among these factors, long non-coding RNAs (lncRNAs) have emerged as significant players in all areas of biology, particularly in immunology. Most of the mammalian genome is transcribed in a highly regulated manner, generating a diversity of lncRNAs that impact the differentiation and activation of immune cells and affect innate and adaptive immunity. Here, we have reviewed the range of functions and mechanisms of lncRNAs in response to infectious disease, including pathogen recognition, interferon (IFN) response, and inflammation. We describe examples of lncRNAs exploited by pathogenic agents during infection, which indicate that lncRNAs are a fundamental part of the arms race between hosts and pathogens. We also discuss lncRNAs potentially implicated in vaccine-induced immunity and present examples of lncRNAs associated with the antibody response of subjects receiving Influenza or Yellow Fever vaccines. Elucidating the widespread involvement of lncRNAs in the immune system will improve our understanding of the factors affecting immune response to different pathogenic agents, to better prevent and treat disease.
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Trigiante G, Blanes Ruiz N, Cerase A. Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression. Front Cell Dev Biol 2021; 9:735527. [PMID: 34722514 PMCID: PMC8552494 DOI: 10.3389/fcell.2021.735527] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic repeats have been intensely studied as regulatory elements controlling gene transcription, splicing and genome architecture. Our understanding of the role of the repetitive RNA such as the RNA coming from genomic repeats, or repetitive sequences embedded in mRNA/lncRNAs, in nuclear and cellular functions is instead still limited. In this review we discuss evidence supporting the multifaceted roles of repetitive RNA and RNA binding proteins in nuclear organization, gene regulation, and in the formation of dynamic membrane-less aggregates. We hope that our review will further stimulate research in the consolidating field of repetitive RNA biology.
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Affiliation(s)
| | | | - Andrea Cerase
- Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, United Kingdom
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30
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Gandhi S, Witten A, De Majo F, Gilbers M, Maessen J, Schotten U, de Windt LJ, Stoll M. Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology. Genomics 2021; 113:3782-3792. [PMID: 34506887 DOI: 10.1016/j.ygeno.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/17/2021] [Accepted: 09/05/2021] [Indexed: 12/14/2022]
Abstract
Cardiovascular disease (CVD) remains the leading cause of death worldwide. A deeper characterization of regional transcription patterns within different heart chambers may aid to improve our understanding of the molecular mechanisms involved in myocardial function and further, our ability to develop novel therapeutic strategies. Here, we used RNA sequencing to determine differentially expressed protein coding (PC) and long non-coding (lncRNA) transcripts within the heart chambers across seven vertebrate species and identified evolutionarily conserved chamber specific genes, lncRNAs and pathways. We investigated lncRNA homologs based on sequence, secondary structure, synteny and expressional conservation and found most lncRNAs to be conserved by synteny. Regional co-expression patterns of transcripts are modulated by multiple factors, including genomic overlap, strandedness and transcript biotype. Finally, we provide a community resource designated EvoACTG, which informs researchers on the conserved yet intertwined nature of the coding and non-coding cardiac transcriptome across popular model organisms in CVD research.
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Affiliation(s)
- Shrey Gandhi
- Institute of Human Genetics, Division of Genetic Epidemiology, University of Muenster, Muenster, Germany
| | - Anika Witten
- Institute of Human Genetics, Division of Genetic Epidemiology, University of Muenster, Muenster, Germany
| | - Federica De Majo
- Department of Molecular Genetics, Maastricht University, Maastricht, the Netherlands
| | - Martijn Gilbers
- Department of Cardiothoracic Surgery, CARIM School for Cardiovascular Diseases, Maastricht University Medical Centre+, Maastricht, the Netherlands
| | - Jos Maessen
- Department of Cardiothoracic Surgery, CARIM School for Cardiovascular Diseases, Maastricht University Medical Centre+, Maastricht, the Netherlands
| | - Ulrich Schotten
- Department of Physiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | - Leon J de Windt
- Department of Molecular Genetics, Maastricht University, Maastricht, the Netherlands
| | - Monika Stoll
- Institute of Human Genetics, Division of Genetic Epidemiology, University of Muenster, Muenster, Germany; Department of Biochemistry, Genetic Epidemiology and Statistical Genetics, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands.
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31
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Xie Y, Wei Y. A Novel Regulatory Player in the Innate Immune System: Long Non-Coding RNAs. Int J Mol Sci 2021; 22:9535. [PMID: 34502451 DOI: 10.3390/ijms22179535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) represent crucial transcriptional and post-transcriptional gene regulators during antimicrobial responses in the host innate immune system. Studies have shown that lncRNAs are expressed in a highly tissue- and cell-specific- manner and are involved in the differentiation and function of innate immune cells, as well as inflammatory and antiviral processes, through versatile molecular mechanisms. These lncRNAs function via the interactions with DNA, RNA, or protein in either cis or trans pattern, relying on their specific sequences or their transcriptions and processing. The dysregulation of lncRNA function is associated with various human non-infectious diseases, such as inflammatory bowel disease, cardiovascular diseases, and diabetes mellitus. Here, we provide an overview of the regulation and mechanisms of lncRNA function in the development and differentiation of innate immune cells, and during the activation or repression of innate immune responses. These elucidations might be beneficial for the development of therapeutic strategies targeting inflammatory and innate immune-mediated diseases.
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32
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Singh N. Role of mammalian long non-coding RNAs in normal and neuro oncological disorders. Genomics 2021; 113:3250-3273. [PMID: 34302945 DOI: 10.1016/j.ygeno.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/09/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes but have a crucial role in gene regulation. LncRNA is distinct, they are being transcribed using RNA polymerase II, and their functionality depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer. To date, ~40% of lncRNAs have been reported in the nervous system (NS) and are involved in the early development/differentiation of the NS to synaptogenesis. LncRNA expression patterns in the most common adult and pediatric tumor suggest them as potential biomarkers and provide a rationale for targeting them pharmaceutically. Here, we discuss the mechanisms of lncRNA synthesis, localization, and functions in transcriptional, post-transcriptional, and other forms of gene regulation, methods of lncRNA identification, and their potential therapeutic applications in neuro oncological disorders as explained by molecular mechanisms in other malignant disorders.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Department of Centre for Advance Research, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India.
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33
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Razin SV, Gavrilov AA. Non-coding RNAs in chromatin folding and nuclear organization. Cell Mol Life Sci 2021; 78:5489-5504. [PMID: 34117518 DOI: 10.1007/s00018-021-03876-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/24/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022]
Abstract
One of the most intriguing questions facing modern biology concerns how the genome directs the construction of cells, tissues, and whole organisms. It is tempting to suggest that the part of the genome that does not encode proteins contains architectural plans. We are still far from understanding how these plans work at the level of building tissues and the body as a whole. However, the results of recent studies demonstrate that at the cellular level, special non-coding RNAs serve as scaffolds for the construction of various intracellular structures. The term "architectural RNAs" was proposed to designate this subset of non-coding RNAs. In this review, we discuss the role of architectural RNAs in the construction of the cell nucleus and maintenance of the three-dimensional organization of the genome.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119234, Moscow, Russia.
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
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34
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Cai D, Han JDJ. Aging-associated lncRNAs are evolutionarily conserved and participate in NFκB signaling. Nat Aging 2021; 1:438-453. [PMID: 37118014 DOI: 10.1038/s43587-021-00056-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/10/2021] [Indexed: 04/30/2023]
Abstract
The transcriptome undergoes global changes during aging, including both protein-coding and noncoding RNAs. Using comparative genomics, we identify aging-associated long noncoding RNAs (lncRNAs) that are under evolutionary constraint and are more conserved than lncRNAs that do not change with age. Aging-associated lncRNAs are enriched for functional elements, including binding sites for RNA-binding proteins and transcription factors, in particular nuclear factor kappa B (NFκB). Using CRISPR screening, we discovered that 13 of the aging-associated lncRNAs were regulators of the NFκB pathway, and we named this family 'NFκB modulating aging-related lncRNAs (NFKBMARLs)'. Further characterization of NFκBMARL-1 reveals it can be traced to 29 Ma before humans and is induced by NFκB during aging, inflammation and senescence. Reciprocally, NFκBMARL-1 directly regulates transcription of the NFκB inhibitor NFKBIZ in cis within the same topologically associated domain by binding to the NFKBIZ enhancer and recruiting RELA to the NFKBIZ promoter. These findings reveal many aging-associated lncRNAs are evolutionarily conserved components of the NFκB pathway.
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Affiliation(s)
- Donghong Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing-Dong J Han
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China.
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35
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Szcześniak MW, Kubiak MR, Wanowska E, Makałowska I. Comparative genomics in the search for conserved long noncoding RNAs. Essays Biochem 2021:EBC20200069. [PMID: 33885137 DOI: 10.1042/EBC20200069] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/15/2021] [Accepted: 03/15/2021] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as prominent regulators of gene expression in eukaryotes. The identification of lncRNA orthologs is essential in efforts to decipher their roles across model organisms, as homologous genes tend to have similar molecular and biological functions. The relatively high sequence plasticity of lncRNA genes compared with protein-coding genes, makes the identification of their orthologs a challenging task. This is why comparative genomics of lncRNAs requires the development of specific and, sometimes, complex approaches. Here, we briefly review current advancements and challenges associated with four levels of lncRNA conservation: genomic sequences, splicing signals, secondary structures and syntenic transcription.
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36
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Pisignano G, Ladomery M. Epigenetic Regulation of Alternative Splicing: How LncRNAs Tailor the Message. Noncoding RNA 2021; 7:ncrna7010021. [PMID: 33799493 PMCID: PMC8005942 DOI: 10.3390/ncrna7010021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/23/2022] Open
Abstract
Alternative splicing is a highly fine-tuned regulated process and one of the main drivers of proteomic diversity across eukaryotes. The vast majority of human multi-exon genes is alternatively spliced in a cell type- and tissue-specific manner, and defects in alternative splicing can dramatically alter RNA and protein functions and lead to disease. The eukaryotic genome is also intensively transcribed into long and short non-coding RNAs which account for up to 90% of the entire transcriptome. Over the years, lncRNAs have received considerable attention as important players in the regulation of cellular processes including alternative splicing. In this review, we focus on recent discoveries that show how lncRNAs contribute significantly to the regulation of alternative splicing and explore how they are able to shape the expression of a diverse set of splice isoforms through several mechanisms. With the increasing number of lncRNAs being discovered and characterized, the contribution of lncRNAs to the regulation of alternative splicing is likely to grow significantly.
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Affiliation(s)
- Giuseppina Pisignano
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
- Correspondence: (G.P.); (M.L.)
| | - Michael Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Frenchay, Bristol BS16 1QY, UK
- Correspondence: (G.P.); (M.L.)
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37
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Arrey-Salas O, Caris-Maldonado JC, Hernández-Rojas B, Gonzalez E. Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine ( Vitis vinifera L.): Insights into the Roles in the Pollen Development Regulation. Genes (Basel) 2021; 12:302. [PMID: 33672655 PMCID: PMC7924211 DOI: 10.3390/genes12020302] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/02/2023] Open
Abstract
Some C2H2 zinc-finger proteins (ZFP) transcription factors are involved in the development of pollen in plants. In grapevine (Vitis vinifera L.), it has been suggested that abnormalities in pollen development lead to the phenomenon called parthenocarpy that occurs in some varieties of this cultivar. At present, a network involving several transcription factors types has been revealed and key roles have been assigned to members of the C2H2 zinc-finger proteins (ZFP) family in model plants. However, particularities of the regulatory mechanisms controlling pollen formation in grapevine remain unknown. In order to gain insight into the participation of ZFPs in grapevine gametophyte development, we performed a genome-wide identification and characterization of genes encoding ZFP (VviZFP family). A total of 98 genes were identified and renamed based on the gene distribution into grapevine genome. The analysis performed indicate significant changes throughout VviZFP genes evolution explained by high heterogeneity in sequence, length, number of ZF and presence of another conserved domains. Moreover, segmental duplication participated in the gene family expansion in grapevine. The VviZFPs were classified based on domain and phylogenetic analysis into three sets and different groups. Heat-map demonstrated differential and tissue-specific expression patterns of these genes and k-means clustering allowed to identify a group of putative orthologs to some ZFPs related to pollen development. In transgenic plants carrying the promVviZFP13::GUS and promVviZFP68::GUS constructs, GUS signals were detectable in the anther and mature pollen grains. Expression profiling of selected VviZFP genes showed differential expression pattern during flower development and provides a basis for deepening in the understanding of VviZFPs role on grapevine reproductive development.
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Affiliation(s)
- Oscar Arrey-Salas
- Laboratorio de Genómica Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile;
| | | | - Bairon Hernández-Rojas
- Ph.D Program in Sciences Mention in Modeling of Chemical and Biological Systems, Faculty of Engineering, University of Talca, Calle 1 Poniente, 1141, 3462227 Talca, Chile;
| | - Enrique Gonzalez
- Laboratorio de Genómica Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile;
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38
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Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent malignancies around the world. The self-renewal, proliferation, differentiation, and tumorigenic potential of liver cancer stem cells (LCSCs) may account for the high recurrence rate and the refractory feature of HCC. Despite extensive researches, the underlying regulatory mechanism of LCSCs has not been fully disclosed. Long nonprotein coding RNAs (lncRNAs) may exert an essential role in regulating various biological functions of LCSCs, such as maintaining the stemness of cancer stem cells (CSCs) and promoting tumor development. Therefore, it is highly critical to determine which lncRNAs can control LCSCs functions and understand how LCSCs are regulated by lncRNAs. Herein, we summarized lncRNAs and the main signaling pathways involved in the regulation of LCSCs found in recent years. Moreover, we shed light on the existence of the network system of lncRNAs and LCSCs, which may provide valuable clues on targeting LCSCs.
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Affiliation(s)
- Xiaoli Zhang
- Liver Disease Center of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, People's Republic of China
| | - Ying Zhu
- Liver Disease Center of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, People's Republic of China
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39
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Abstract
Subcellular localization of RNAs has gained attention in recent years as a prevalent phenomenon that influences numerous cellular processes. This is also evident for the large and relatively novel class of long noncoding RNAs (lncRNAs). Because lncRNAs are defined as RNA transcripts >200 nucleotides that do not encode protein, they are themselves the functional units, making their subcellular localization critical to their function. The discovery of tens of thousands of lncRNAs and the cumulative evidence involving them in almost every cellular activity render assessment of their subcellular localization essential to fully understanding their biology. In this review, we summarize current knowledge of lncRNA subcellular localization, factors controlling their localization, emerging themes, including the role of lncRNA isoforms and the involvement of lncRNAs in phase separation bodies, and the implications of lncRNA localization on their function and on cellular behavior. We also discuss gaps in the current knowledge as well as opportunities that these provide for novel avenues of investigation.
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Affiliation(s)
| | | | - Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC
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Guo F, Li L, Yang W, Hu JF, Cui J. Long noncoding RNA: A resident staff of genomic instability regulation in tumorigenesis. Cancer Lett 2021; 503:103-9. [PMID: 33516792 DOI: 10.1016/j.canlet.2021.01.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 01/07/2023]
Abstract
Genomic instability is an important characteristic of cancer, which promotes clonal evolution and tumorigenesis by increasing the frequency of gene destruction and loss of genome integrity. Generally, the maintenance of genomic stability depends significantly on the accurate regulation and timely repair of different genomic scales, ranging from DNA sequence to chromatin higher-order structures to chromosomes. Once irreversible damage and imperfect repair occurred, the resulting genomic instability can lead to a higher risk of tumorigenesis. However, how these factors disrupt genomic stability and their specific tumorigenic mechanisms remain unclear. Inspiringly, numerous studies have confirmed that long noncoding RNAs (lncRNAs), an important regulator of epigenetic inheritance, are functional in such process. Thus, this review aimed to discuss the vital factors that may lead to genomic instability at these multiple genomic scales, with an emphasis on the role of lncRNAs in it.
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41
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Abstract
Long non-coding RNAs (lncRNAs) are emerging as key regulators in inflammation. However, their functions and profiles in LPS-induced inflammation in pigs are largely unknown. In this study, we profiled global lncRNA and mRNA expression changes in PBMCs treated with LPS using the lncRNA-seq technique. In total 43 differentially expressed (DE) lncRNAs and 1082 DE mRNAs were identified in porcine PBMCs after LPS stimulation. Functional enrichment analysis on DE mRNAs indicated these genes were involved in inflammation-related signaling pathways, including cytokine–cytokine receptor interaction, TNF-α, NF-κB, Jak-STAT and TLR signaling pathways. In addition, co-expression network and function analysis identified the potential lncRNAs related to inflammatory response and immune response. The expressions of eight lncRNAs (ENSSSCT00000045208, ENSSSCT00000051636, ENSSSCT00000049770, ENSSSCT00000050966, ENSSSCT00000047491, ENSSSCT00000049750, ENSSSCT00000054262 and ENSSSCT00000044651) were validated in the LPS-treated PBMCs by quantitative real-time PCR (qRT-PCR). In LPS-challenged piglets, we identified that expression of three lncRNAs (ENSSSCT00000051636, ENSSSCT00000049770, and ENSSSCT00000047491) was significantly up-regulated in liver, spleen and jejunum tissues after LPS challenge, which indicated that these lncRNAs might be important regulators for inflammation. This study provides the first lncRNA and mRNA transcriptomic landscape of LPS-mediated changes in porcine PBMCs, which might provide potential insights into lncRNAs involved in regulating inflammation in pigs.
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Affiliation(s)
- Jing Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutrition Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Xin Xu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutrition Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Hongbo Chen
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutrition Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Ping Kang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutrition Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Huiling Zhu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutrition Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Hongyan Ren
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yulan Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutrition Engineering, Wuhan Polytechnic University, Wuhan, China
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42
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Abstract
Recent advances in sequencing technologies have uncovered the existence of thousands of long noncoding RNAs (lncRNAs) with dysregulated expression in cancer. As a result, there is burgeoning interest in understanding their function and biological significance in both homeostasis and disease. RNA interference (RNAi) enables sequence-specific gene silencing and can, in principle, be employed to silence virtually any gene. However, when applied to lncRNAs, it is important to consider current limitations in their annotation and current principles regarding lncRNA regulation and function when assessing their phenotype in cancer cell lines. In this chapter we describe the analysis of lncRNA splicing variant expression, including subcellular localization, transfection of siRNAs in cancer cell lines, and validation of gene silencing by quantitative PCR and single molecule in situ hybridization. All protocols can be performed in a laboratory with essential equipment for cell culture, molecular biology, and imaging.
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43
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Abstract
Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.
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44
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Abstract
The three-dimensional (3D) organization of the human genome is of crucial importance for gene regulation, and the CCCTC-binding factor (CTCF) plays an important role in chromatin interactions. However, it is still unclear what sequence patterns in addition to CTCF motif pairs determine chromatin loop formation. To discover the underlying sequence patterns, we have developed a deep learning model, called DeepCTCFLoop, to predict whether a chromatin loop can be formed between a pair of convergent or tandem CTCF motifs using only the DNA sequences of the motifs and their flanking regions. Our results suggest that DeepCTCFLoop can accurately distinguish the CTCF motif pairs forming chromatin loops from the ones not forming loops. It significantly outperforms CTCF-MP, a machine learning model based on word2vec and boosted trees, when using DNA sequences only. Furthermore, we show that DNA motifs binding to several transcription factors, including ZNF384, ZNF263, ASCL1, SP1, and ZEB1, may constitute the complex sequence patterns for CTCF-mediated chromatin loop formation. DeepCTCFLoop has also been applied to disease-associated sequence variants to identify candidates that may disrupt chromatin loop formation. Therefore, our results provide useful information for understanding the mechanism of 3D genome organization and may also help annotate and prioritize the noncoding sequence variants associated with human diseases.
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Affiliation(s)
- Shuzhen Kuang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA.,Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
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45
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Abstract
RNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA abundance of other genes act by mechanisms similar to and in concert with protein factors that control transcription. Through recruitment or blocking of activating and silencing complexes to specific genomic loci, RNA and protein factors can favor transcription or lower the local gene expression potential. Most regulatory proteins enter nuclei from all directions to start the search for increased affinity to specific DNA sequences or to other proteins nearby genuine gene targets. In contrast, RNAs emerge from spatial point sources within nuclei, their encoding genes. A transcriptional burst can result in the local appearance of multiple nascent RNA copies at once, in turn increasing local nucleic acid density and RNA motif abundance before diffusion into the nuclear neighborhood. The confined initial localization of regulatory RNAs causing accumulation of protein co-factors raises the intriguing possibility that target specificity of non-coding, and probably coding, RNAs is achieved through gene/RNA positioning and spatial proximity to regulated genomic regions. Here we review examples of positional cis conservation of regulatory RNAs with respect to target genes, spatial proximity of enhancer RNAs to promoters through DNA looping and RNA-mediated formation of membrane-less structures to control chromatin structure and expression. We speculate that linear and spatial proximity between regulatory RNA-encoding genes and gene targets could possibly ease the evolutionary pressure on maintaining regulatory RNA sequence conservation.
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Affiliation(s)
- Jörg Morf
- Jeffrey Cheah Biomedical Centre, Wellcome - Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Srinjan Basu
- Jeffrey Cheah Biomedical Centre, Wellcome - Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Paulo P Amaral
- Jeffrey Cheah Biomedical Centre, The Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
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46
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Abstract
Guo and colleagues discover a new layer of complexity to the lncRNA evolution where positionally conserved lncRNAs in human ESCs are broadly spliced and exported to the cytoplasm contrary to their mouse counterpart that are predominantly unspliced and nuclear retained. Distinct processing leads to species-specific lncRNA function in pluripotency maintenance.
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Affiliation(s)
- Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
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47
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Wang WJ, Li LY, Cui JW. Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis. Epigenetics Chromatin 2020; 13:49. [PMID: 33168103 PMCID: PMC7654176 DOI: 10.1186/s13072-020-00371-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/29/2020] [Indexed: 12/23/2022] Open
Abstract
With the rapid development of next-generation sequencing technology, chromosome structural variation has gradually gained increased clinical significance in tumorigenesis. However, the molecular mechanism(s) underlying this structural variation remain poorly understood. A search of the literature shows that a three-dimensional chromatin state plays a vital role in inducing structural variation and in the gene expression profiles in tumorigenesis. Structural variants may result in changes in copy number or deletions of coding sequences, as well as the perturbation of structural chromatin features, especially topological domains, and disruption of interactions between genes and their regulatory elements. This review focuses recent work aiming at elucidating how structural variations develop and misregulate oncogenes and tumor suppressors, to provide general insights into tumor formation mechanisms and to provide potential targets for future anticancer therapies.
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Affiliation(s)
- Wen-Jun Wang
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021, Jilin, China
| | - Ling-Yu Li
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021, Jilin, China
| | - Jiu-Wei Cui
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021, Jilin, China.
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Kim SY, Zhang X, Schiattarella GG, Altamirano F, Ramos TAR, French KM, Jiang N, Szweda PA, Evers BM, May HI, Luo X, Li H, Szweda LI, Maracaja-Coutinho V, Lavandero S, Gillette TG, Hill JA. Epigenetic Reader BRD4 (Bromodomain-Containing Protein 4) Governs Nucleus-Encoded Mitochondrial Transcriptome to Regulate Cardiac Function. Circulation 2020; 142:2356-2370. [PMID: 33113340 DOI: 10.1161/circulationaha.120.047239] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND BET (bromodomain and extraterminal) epigenetic reader proteins, in particular BRD4 (bromodomain-containing protein 4), have emerged as potential therapeutic targets in a number of pathological conditions, including cancer and cardiovascular disease. Small-molecule BET protein inhibitors such as JQ1 have demonstrated efficacy in reversing cardiac hypertrophy and heart failure in preclinical models. Yet, genetic studies elucidating the biology of BET proteins in the heart have not been conducted to validate pharmacological findings and to unveil potential pharmacological side effects. METHODS By engineering a cardiomyocyte-specific BRD4 knockout mouse, we investigated the role of BRD4 in cardiac pathophysiology. We performed functional, transcriptomic, and mitochondrial analyses to evaluate BRD4 function in developing and mature hearts. RESULTS Unlike pharmacological inhibition, loss of BRD4 protein triggered progressive declines in myocardial function, culminating in dilated cardiomyopathy. Transcriptome analysis of BRD4 knockout mouse heart tissue identified early and specific disruption of genes essential to mitochondrial energy production and homeostasis. Functional analysis of isolated mitochondria from these hearts confirmed that BRD4 ablation triggered significant changes in mitochondrial electron transport chain protein expression and activity. Computational analysis identified candidate transcription factors participating in the BRD4-regulated transcriptome. In particular, estrogen-related receptor α, a key nuclear receptor in metabolic gene regulation, was enriched in promoters of BRD4-regulated mitochondrial genes. CONCLUSIONS In aggregate, we describe a previously unrecognized role for BRD4 in regulating cardiomyocyte mitochondrial homeostasis, observing that its function is indispensable to the maintenance of normal cardiac function.
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MESH Headings
- Animals
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/metabolism
- Cardiomyopathy, Dilated/pathology
- Cardiomyopathy, Dilated/physiopathology
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cell Nucleus/pathology
- Electron Transport Chain Complex Proteins/genetics
- Electron Transport Chain Complex Proteins/metabolism
- Energy Metabolism/genetics
- Epigenesis, Genetic
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Gene Expression Profiling
- Heart Failure/genetics
- Heart Failure/metabolism
- Heart Failure/pathology
- Heart Failure/physiopathology
- Mice, Knockout
- Mitochondria, Heart/genetics
- Mitochondria, Heart/metabolism
- Mitochondria, Heart/pathology
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcriptome
- Ventricular Dysfunction, Left/genetics
- Ventricular Dysfunction, Left/metabolism
- Ventricular Dysfunction, Left/pathology
- Ventricular Dysfunction, Left/physiopathology
- Ventricular Function, Left/genetics
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Affiliation(s)
- Soo Young Kim
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
| | - Xin Zhang
- Institute of Model Animal, Wuhan University, China (X.Z., H.L.)
| | - Gabriele G Schiattarella
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
| | - Francisco Altamirano
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, TX (F.A.)
| | - Thais A R Ramos
- Advanced Center for Chronic Disease, Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, University of Chile, Santiago (T.A.R.R., V.M.-C., S.L.)
- Bioinformatics Multidisciplinary Environment, Digital Metropolis Institute, Federal University of Rio Grande do Norte, Natal, Brazil (T.A.R.R., V.M.-C.)
| | - Kristin M French
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
| | - Nan Jiang
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
| | - Pamela A Szweda
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
| | - Bret M Evers
- Department of Pathology (B.M.E.), University of Texas Southwestern, Dallas
| | - Herman I May
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
| | - Xiang Luo
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
| | - Hongliang Li
- Institute of Model Animal, Wuhan University, China (X.Z., H.L.)
| | - Luke I Szweda
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
| | - Vinicius Maracaja-Coutinho
- Advanced Center for Chronic Disease, Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, University of Chile, Santiago (T.A.R.R., V.M.-C., S.L.)
- Bioinformatics Multidisciplinary Environment, Digital Metropolis Institute, Federal University of Rio Grande do Norte, Natal, Brazil (T.A.R.R., V.M.-C.)
| | - Sergio Lavandero
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
- Advanced Center for Chronic Disease, Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, University of Chile, Santiago (T.A.R.R., V.M.-C., S.L.)
| | - Thomas G Gillette
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
| | - Joseph A Hill
- Division of Cardiology, Department of Internal Medicine (S.Y.K., G.G.S., F.A., K.M.F., N.J., P.A.S., H.I.M., X.L., L.I.S., S.L., T.G.G., J.A.H.), University of Texas Southwestern, Dallas
- Department of Molecular Biology (J.A.H.), University of Texas Southwestern, Dallas
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Zhang X, Bao Q, Jia C, Li C, Chang Y, Wu X, Liang C, Bao P, Yan P. Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak. BMC Genomics 2020; 21:681. [PMID: 32998696 DOI: 10.1186/s12864-020-07082-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 09/18/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Long non-coding RNA (lncRNA) as an important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profile in the HFs cycle of yak are yet unknown. Only a few functional lncRNAs have been identified, partly due to the low sequence conservation and lack of identified conserved properties in lncRNAs. Here, lncRNA-seq was employed to detect the expression profile of lncRNAs during the HFs cycle of yak, and the sequence conservation of two datasets between yak and cashmere goat during the HFs cycle was analyzed. RESULTS A total of 2884 lncRNAs were identified in 5 phases (Jan., Mar., Jun., Aug., and Oct.) during the HFs cycle of yak. Then, differential expression analysis between 3 phases (Jan., Mar., and Oct.) was performed, revealing that 198 differentially expressed lncRNAs (DELs) were obtained in the Oct.-vs-Jan. group, 280 DELs were obtained in the Jan.-vs-Mar. group, and 340 DELs were obtained in the Mar.-vs-Oct. group. Subsequently, the nearest genes of lncRNAs were searched as the potential target genes and used to explore the function of DELs by GO and KEGG enrichment analysis. Several critical pathways involved in HFs development such as Wnt signaling pathway, VEGF signaling pathway, and signaling pathways regulating pluripotency of stem cells, were enriched. To further screen key lncRNAs influencing the HFs cycle, 24 DELs with differ degree of sequence conservation were obtained via a comparative analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in the HFs cycle using NCBI BLAST-2.9.0+, and 3 DELs of them were randomly selected for further detailed analysis of the sequence conservation properties. CONCLUSIONS This study revealed the expression pattern and potential function of lncRNAs during HFs cycle of yak, which would expand the knowledge about the role of lncRNAs in the HFs cycle. The findings related to sequence conservation properties of lncRNAs in the HFs cycle between the two species may provide valuable insights into the study of lncRNA functionality and mechanism.
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50
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Kantidze OL, Razin SV. Weak interactions in higher-order chromatin organization. Nucleic Acids Res 2020; 48:4614-4626. [PMID: 32313950 PMCID: PMC7229822 DOI: 10.1093/nar/gkaa261] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are involved in their establishment and maintenance have been characterized. Generally, protein-protein and protein-DNA interactions underlie the spatial genome organization in eukaryotes. However, it is becoming increasingly evident that weak interactions, which exist in biological systems, also contribute to the 3D genome. Here, we provide a snapshot of our current understanding of the role of the weak interactions in the establishment and maintenance of the 3D genome organization. We discuss how weak biological forces, such as entropic forces operating in crowded solutions, electrostatic interactions of the biomolecules, liquid-liquid phase separation, DNA supercoiling, and RNA environment participate in chromosome segregation into structural and functional units and drive intranuclear functional compartmentalization.
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Affiliation(s)
- Omar L Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
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