1
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Li K, Xie T, Li Y, Huang X. LncRNAs act as modulators of macrophages within the tumor microenvironment. Carcinogenesis 2024; 45:363-377. [PMID: 38459912 DOI: 10.1093/carcin/bgae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/21/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been established as pivotal players in various cellular processes, encompassing the regulation of transcription, translation and post-translational modulation of proteins, thereby influencing cellular functions. Notably, lncRNAs exert a regulatory influence on diverse biological processes, particularly in the context of tumor development. Tumor-associated macrophages (TAMs) exhibit the M2 phenotype, exerting significant impact on crucial processes such as tumor initiation, angiogenesis, metastasis and immune evasion. Elevated infiltration of TAMs into the tumor microenvironment (TME) is closely associated with a poor prognosis in various cancers. LncRNAs within TAMs play a direct role in regulating cellular processes. Functioning as integral components of tumor-derived exosomes, lncRNAs prompt the M2-like polarization of macrophages. Concurrently, reports indicate that lncRNAs in tumor cells contribute to the expression and release of molecules that modulate TAMs within the TME. These actions of lncRNAs induce the recruitment, infiltration and M2 polarization of TAMs, thereby providing critical support for tumor development. In this review, we survey recent studies elucidating the impact of lncRNAs on macrophage recruitment, polarization and function across different types of cancers.
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Affiliation(s)
- Kangning Li
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
- HuanKui Academy, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Tao Xie
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yong Li
- Department of Anesthesiology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xuan Huang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
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2
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Jasielski P, Zawlik I, Bogaczyk A, Potocka N, Paszek S, Maźniak M, Witkoś A, Korzystka A, Kmieć A, Kluz T. The Promotive and Inhibitory Role of Long Non-Coding RNAs in Endometrial Cancer Course-A Review. Cancers (Basel) 2024; 16:2125. [PMID: 38893244 PMCID: PMC11171405 DOI: 10.3390/cancers16112125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Endometrial cancer is one of the most common malignant tumours in women. The development of this tumour is associated with several genetic disorders, many of which are still unknown. One type of RNA molecules currently being intensively studied in many types of cancer are long non-coding RNAs (lncRNAs). LncRNA-coding genes occupy a large fraction of the human genome. LncRNAs regulate many aspects of cell development, metabolism, and other physiological processes. Diverse types of lncRNA can function as a tumour suppressor or an oncogene that can alter migration, invasion, cell proliferation, apoptosis, and immune system response. Recent studies suggest that selected lncRNAs are important in an endometrial cancer course. Our article describes over 70 lncRNAs involved in the development of endometrial cancer, which were studied via in vivo and in vitro research. It was proved that lncRNAs could both promote and inhibit the development of endometrial cancer. In the future, lncRNAs may become an important therapeutic target. The aim of this study is to review the role of lncRNAs in the development of carcinoma of uterine body.
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Affiliation(s)
- Patryk Jasielski
- Department of Gynecology, Gynecology Oncology and Obstetrics, Fryderyk Chopin University Hospital, 35-055 Rzeszow, Poland
| | - Izabela Zawlik
- Laboratory of Molecular Biology, Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Institute of Medical Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Anna Bogaczyk
- Department of Gynecology, Gynecology Oncology and Obstetrics, Fryderyk Chopin University Hospital, 35-055 Rzeszow, Poland
| | - Natalia Potocka
- Laboratory of Molecular Biology, Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Sylwia Paszek
- Laboratory of Molecular Biology, Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Institute of Medical Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Michał Maźniak
- Department of Gynecology, Gynecology Oncology and Obstetrics, Fryderyk Chopin University Hospital, 35-055 Rzeszow, Poland
| | - Aleksandra Witkoś
- Department of Gynecology, Gynecology Oncology and Obstetrics, Fryderyk Chopin University Hospital, 35-055 Rzeszow, Poland
| | - Adrianna Korzystka
- Department of Gynecology, Gynecology Oncology and Obstetrics, Fryderyk Chopin University Hospital, 35-055 Rzeszow, Poland
| | - Aleksandra Kmieć
- Department of Gynecology, Gynecology Oncology and Obstetrics, Fryderyk Chopin University Hospital, 35-055 Rzeszow, Poland
| | - Tomasz Kluz
- Department of Gynecology, Gynecology Oncology and Obstetrics, Fryderyk Chopin University Hospital, 35-055 Rzeszow, Poland
- Institute of Medical Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
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3
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Leisegang MS, Warwick T, Stötzel J, Brandes RP. RNA-DNA triplexes: molecular mechanisms and functional relevance. Trends Biochem Sci 2024; 49:532-544. [PMID: 38582689 DOI: 10.1016/j.tibs.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024]
Abstract
Interactions of RNA with DNA are principles of gene expression control that have recently gained considerable attention. Among RNA-DNA interactions are R-loops and RNA-DNA hybrid G-quadruplexes, as well as RNA-DNA triplexes. It is proposed that RNA-DNA triplexes guide RNA-associated regulatory proteins to specific genomic locations, influencing transcription and epigenetic decision making. Although triplex formation initially was considered solely an in vitro event, recent progress in computational, biochemical, and biophysical methods support in vivo functionality with relevance for gene expression control. Here, we review the central methodology and biology of triplexes, outline paradigms required for triplex function, and provide examples of physiologically important triplex-forming long non-coding RNAs.
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Affiliation(s)
- Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany.
| | - Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Julia Stötzel
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
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4
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Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol 2024; 25:396-415. [PMID: 38242953 PMCID: PMC11045326 DOI: 10.1038/s41580-023-00694-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets.
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Affiliation(s)
- Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
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5
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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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6
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Ghahramani Almanghadim H, Karimi B, Poursalehi N, Sanavandi M, Atefi Pourfardin S, Ghaedi K. The biological role of lncRNAs in the acute lymphocytic leukemia: An updated review. Gene 2024; 898:148074. [PMID: 38104953 DOI: 10.1016/j.gene.2023.148074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
The cause of leukemia, a common malignancy of the hematological system, is unknown. The structure of long non-coding RNAs (lncRNAs) is similar to mRNA but no ability to encode proteins. Numerous malignancies, including different forms of leukemia, are linked to Lnc-RNAs. It is verified that the carcinogenesis and growth of a variety of human malignancies are significantly influenced by aberrant lncRNA expression. The body of evidence linking various types of lncRNAs to the etiology of leukemia has dramatically increased during the past ten years. Some lncRNAs are therefore anticipated to function as novel therapeutic targets, diagnostic biomarkers, and clinical outcome predictions. Additionally, these lncRNAs may provide new therapeutic options and insight into the pathophysiology of diseases, particularly leukemia. Thus, this review outlines the present comprehension of leukemia-associated lncRNAs.
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Affiliation(s)
| | - Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Negareh Poursalehi
- Department of Medical Biotechnology, School of Medicine Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., 81746-73441 Isfahan, Iran.
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7
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Merici G, Amidani D, Dieci G, Rivetti C. A New Strategy to Investigate RNA:DNA Triplex Using Atomic Force Microscopy. Int J Mol Sci 2024; 25:3035. [PMID: 38474280 DOI: 10.3390/ijms25053035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Over the past decade, long non-coding RNAs (lncRNAs) have been recognized as key players in gene regulation, influencing genome organization and expression. The locus-specific binding of these non-coding RNAs (ncRNAs) to DNA involves either a non-covalent interaction with DNA-bound proteins or a direct sequence-specific interaction through the formation of RNA:DNA triplexes. In an effort to develop a novel strategy for characterizing a triple-helix formation, we employed atomic force microscopy (AFM) to visualize and study a regulatory RNA:DNA triplex formed between the Khps1 lncRNA and the enhancer of the proto-oncogene SPHK1. The analysis demonstrates the successful formation of RNA:DNA triplexes under various conditions of pH and temperature, indicating the effectiveness of the AFM strategy. Despite challenges in discriminating between the triple-helix and R-loop configurations, this approach opens new perspectives for investigating the role of lncRNAs in gene regulation at the single-molecule level.
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Affiliation(s)
- Giovanni Merici
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Davide Amidani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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8
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Chen H, Xiao L, Xie G, Zhang P, Dong P, Bian B, Wang J, Zhou Y, Ma Y, Liu Y, Shen L. LINC00355 promotes gastric carcinogenesis by scaffolding p300 to activate CDC42 transcription and enhancing HNRNPA2B1 to stabilize CDC42 mRNA dependent on m6A. Mol Carcinog 2024; 63:430-447. [PMID: 37983727 DOI: 10.1002/mc.23662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
LINC00355 is involved in the tumorigenesis of several types of cancer. We verified that LINC00355 is upregulated in gastric cancer (GC) and contributes to GC cells' proliferation and metastasis. RNA sequencing (RNA-seq) and rescue assays suggested that LINC00355 controls gastric carcinogenesis by regulating the expression of cell division cycle 42 (CDC42) guanosine triphosphatase (GTPases), thereby activating their downstream pathways. Most previous studies have shown that LINC00355 acts as a ceRNA by sponging miRNAs to modulate downstream gene expression. Our group focus on epigenetic regulatory potential of LINC00355 in gene expression. Mechanistically, LINC00355 binds to p300 histone acetyltransferase, specifying the histone modification pattern on the CDC42 promoter to activate CDC42 transcription, thereby altering GC cell biology. In addition, HNRNPA2B1, which is upregulated by LINC00355, recognizes the N6-methyladenosine (m6A) sites of CDC42 and enhances the stability of CDC42 mRNA transcripts. Therefore, LINC00355 is mechanistically, functionally, and clinically oncogenic in GC cells.
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Affiliation(s)
- Hui Chen
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lanshu Xiao
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Guohua Xie
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Zhang
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Dong
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingxian Bian
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Wang
- Department of Clinical Laboratory, Shanghai Ruijin Rehabilitation Hospital, Shanghai, China
| | - Yunlan Zhou
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanhui Ma
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Liu
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lisong Shen
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Artificial Intelligence Medicine, Shanghai Academy of Experimental Medicine, Shanghai, China
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9
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Hussein MA, Valinezhad K, Adel E, Munirathinam G. MALAT-1 Is a Key Regulator of Epithelial-Mesenchymal Transition in Cancer: A Potential Therapeutic Target for Metastasis. Cancers (Basel) 2024; 16:234. [PMID: 38201661 PMCID: PMC10778055 DOI: 10.3390/cancers16010234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript-1 (MALAT-1) is a long intergenic non-coding RNA (lncRNA) located on chr11q13. It is overexpressed in several cancers and controls gene expression through chromatin modification, transcriptional regulation, and post-transcriptional regulation. Importantly, MALAT-1 stimulates cell proliferation, migration, and metastasis and serves a vital role in driving the epithelial-to-mesenchymal transition (EMT), subsequently acquiring cancer stem cell-like properties and developing drug resistance. MALAT-1 modulates EMT by interacting with various intracellular signaling pathways, notably the phosphoinositide 3-kinase (PI3K)/Akt and Wnt/β-catenin pathways. It also behaves like a sponge for microRNAs, preventing their interaction with target genes and promoting EMT. In addition, we have used bioinformatics online tools to highlight the disparities in the expression of MALAT-1 between normal and cancer samples using data from The Cancer Genome Atlas (TCGA). Furthermore, the intricate interplay of MALAT-1 with several essential targets of cancer progression and metastasis renders it a good candidate for therapeutic interventions. Several innovative approaches have been exploited to target MALAT-1, such as short hairpin RNAs (shRNAs), antisense oligonucleotides (ASOs), and natural products. This review emphasizes the interplay between MALAT-1 and EMT in modulating cancer metastasis, stemness, and chemoresistance in different cancers.
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Affiliation(s)
- Mohamed Ali Hussein
- Department of Pharmaceutical Services, Children’s Cancer Hospital Egypt, Cairo 57357, Egypt;
- Department of Biology, School of Sciences and Engineering, American University in Cairo, New Cairo 11835, Egypt;
| | - Kamyab Valinezhad
- Department of Biomedical Sciences, College of Medicine, University of Illinois, Rockford, IL 61107, USA;
| | - Eman Adel
- Department of Biology, School of Sciences and Engineering, American University in Cairo, New Cairo 11835, Egypt;
| | - Gnanasekar Munirathinam
- Department of Biomedical Sciences, College of Medicine, University of Illinois, Rockford, IL 61107, USA;
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10
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Yildiz CB, Kundu T, Gehrmann J, Koesling J, Ravaei A, Wolff P, Kraft F, Maié T, Jakovcevski M, Pensold D, Zimmermann O, Rossetti G, Costa IG, Zimmer-Bensch G. EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter. Epigenetics Chromatin 2023; 16:42. [PMID: 37880732 PMCID: PMC10601256 DOI: 10.1186/s13072-023-00516-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
Cell-cell communication is mediated by membrane receptors and their ligands, such as the Eph/ephrin system, orchestrating cell migration during development and in diverse cancer types. Epigenetic mechanisms are key for integrating external "signals", e.g., from neighboring cells, into the transcriptome in health and disease. Previously, we reported ephrinA5 to trigger transcriptional changes of lncRNAs and protein-coding genes in cerebellar granule cells, a cell model for medulloblastoma. LncRNAs represent important adaptors for epigenetic writers through which they regulate gene expression. Here, we investigate a lncRNA-mediated targeting of DNMT1 to specific gene loci by the combined power of in silico modeling of RNA/DNA interactions and wet lab approaches, in the context of the clinically relevant use case of ephrinA5-dependent regulation of cellular motility of cerebellar granule cells. We provide evidence that Snhg15, a cancer-related lncRNA, recruits DNMT1 to the Ncam1 promoter through RNA/DNA triplex structure formation and the interaction with DNMT1. This mediates DNA methylation-dependent silencing of Ncam1, being abolished by ephrinA5 stimulation-triggered reduction of Snhg15 expression. Hence, we here propose a triple helix recognition mechanism, underlying cell motility regulation via lncRNA-targeted DNA methylation in a clinically relevant context.
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Affiliation(s)
- Can Bora Yildiz
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- Research Training Group 2416 Multi Senses - Multi Scales, RWTH Aachen University, 52074, Aachen, Germany
| | - Tathagata Kundu
- Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Julia Gehrmann
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, 52074, Aachen, Germany
| | - Jannis Koesling
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Amin Ravaei
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- Department of Neurosciences and Rehabilitation, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Philip Wolff
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany
| | - Tiago Maié
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, 52074, Aachen, Germany
| | - Mira Jakovcevski
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Daniel Pensold
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Olav Zimmermann
- Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Giulia Rossetti
- Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Department of Neurology, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
- Institute of Neuroscience and Medicine (INM-9)/Institute of Advanced Simulations (IAS-5), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, 52074, Aachen, Germany
| | - Geraldine Zimmer-Bensch
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.
- Research Training Group 2416 Multi Senses - Multi Scales, RWTH Aachen University, 52074, Aachen, Germany.
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11
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Zhang HB, Pan JY, Zhu T. A disulfidptosis-related lncRNA prognostic model to predict survival and response to immunotherapy in lung adenocarcinoma. Front Pharmacol 2023; 14:1254119. [PMID: 37822882 PMCID: PMC10563764 DOI: 10.3389/fphar.2023.1254119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/15/2023] [Indexed: 10/13/2023] Open
Abstract
Background: Lung adenocarcinoma (LUAD) is the major subtype of lung cancer and has a poor prognosis. Disulfidptosis is a novel regulated cell death form characterized by aberrant disulfide stress and actin network collapse. This study aimed to identify disulfidptosis-related lncRNAs, and predict LUAD patients' prognosis and response to antitumor therapies by establishing a disulfidptosis-related lncRNA model. Methods: Transcriptome and clinical data of LUAD patients were obtained from the TCGA database. Pearson correlation and Cox regression analysis was used to identify disulfidptosis-related lncRNAs associated with overall survival. LASSO regression analysis was adopted to construct the prognostic model. GO, KEGG and GSEA analysis was used to identify cellular pathways related to this model. Immune cell infiltration was investigated by ESTIMATE and CIBERSORT algorithms. Tumor mutational burden (TMB) and its association with model-derived risk score were analyzed using simple nucleotide variation data. Patients' response to immunotherapy and other antineoplastic drugs was predicted by the TIDE algorithm and GDSC tool, respectively. Results: We identified 127 disulfidptosis-related lncRNAs, and a prognostic model that consists eight of them (KTN1-AS1, AL365181.3, MANCR, LINC01352, AC090559.1, AC093673.1, AP001094.3, and MHENCR) was established and verified. The prognostic model could stratify LUAD patients into two distinct risk-score groups. A high risk score was an independent prognosis factor indicating poor overall survival, and correlated with reduced immune cell infiltration, high TMB, and lower activity of tumor immune response. Immune checkpoint blockade might bring more survival benefits to the high-risk LUAD patients, whereas low-risk patients might be more responsive to targeted therapy and diverse kinase inhibitors. Conclusion: We established a disulfidptosis-related lncRNA model that can be exploited to predict the prognosis, tumor mutational burden, immune cell infiltration landscape, and response to immunotherapy and targeted therapy in LUAD patients.
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Affiliation(s)
- Hai-Bo Zhang
- Department of Pharmacy, Hangzhou Women’s Hospital, Hangzhou Maternity and Child Health Care Hospital, Hangzhou, China
| | - Jian-Yan Pan
- Department of Birth Health and Genetics, The Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Tao Zhu
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Intelligent Pharmacy and Individualized Therapy of Huzhou, Department of Pharmacy, Changxing People’s Hospital, Hangzhou, China
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12
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Di Michele F, Chillón I, Feil R. Imprinted Long Non-Coding RNAs in Mammalian Development and Disease. Int J Mol Sci 2023; 24:13647. [PMID: 37686455 PMCID: PMC10487962 DOI: 10.3390/ijms241713647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Imprinted genes play diverse roles in mammalian development, homeostasis, and disease. Most imprinted chromosomal domains express one or more long non-coding RNAs (lncRNAs). Several of these lncRNAs are strictly nuclear and their mono-allelic expression controls in cis the expression of protein-coding genes, often developmentally regulated. Some imprinted lncRNAs act in trans as well, controlling target gene expression elsewhere in the genome. The regulation of imprinted gene expression-including that of imprinted lncRNAs-is susceptible to stochastic and environmentally triggered epigenetic changes in the early embryo. These aberrant changes persist during subsequent development and have long-term phenotypic consequences. This review focuses on the expression and the cis- and trans-regulatory roles of imprinted lncRNAs and describes human disease syndromes associated with their perturbed expression.
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Affiliation(s)
- Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Isabel Chillón
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
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13
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Khorkova O, Stahl J, Joji A, Volmar CH, Zeier Z, Wahlestedt C. Long non-coding RNA-targeting therapeutics: discovery and development update. Expert Opin Drug Discov 2023; 18:1011-1029. [PMID: 37466388 DOI: 10.1080/17460441.2023.2236552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023]
Abstract
INTRODUCTION lncRNAs are major players in regulatory networks orchestrating multiple cellular functions, such as 3D chromosomal interactions, epigenetic modifications, gene expression and others. Due to progress in the development of nucleic acid-based therapeutics, lncRNAs potentially represent easily accessible therapeutic targets. AREAS COVERED Currently, significant efforts are directed at studies that can tap the enormous therapeutic potential of lncRNAs. This review describes recent developments in this field, particularly focusing on clinical applications. EXPERT OPINION Extensive druggable target range of lncRNA combined with high specificity and accelerated development process of nucleic acid-based therapeutics open new prospects for treatment in areas of extreme unmet medical need, such as genetic diseases, aggressive cancers, protein deficiencies, and subsets of common diseases caused by known mutations. Although currently wide acceptance of lncRNA-targeting nucleic acid-based therapeutics is impeded by the need for parenteral or direct-to-CNS administration, development of less invasive techniques and orally available/BBB-penetrant nucleic acid-based therapeutics is showing early successes. Recently, mRNA-based COVID-19 vaccines have demonstrated clinical safety of all aspects of nucleic acid-based therapeutic technology, including multiple chemical modifications of nucleic acids and nanoparticle delivery. These trends position lncRNA-targeting drugs as significant players in the future of drug development, especially in the area of personalized medicine.
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Affiliation(s)
- Olga Khorkova
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Zane Zeier
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
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14
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Khorkova O, Stahl J, Joji A, Volmar CH, Wahlestedt C. Amplifying gene expression with RNA-targeted therapeutics. Nat Rev Drug Discov 2023; 22:539-561. [PMID: 37253858 PMCID: PMC10227815 DOI: 10.1038/s41573-023-00704-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 06/01/2023]
Abstract
Many diseases are caused by insufficient expression of mutated genes and would benefit from increased expression of the corresponding protein. However, in drug development, it has been historically easier to develop drugs with inhibitory or antagonistic effects. Protein replacement and gene therapy can achieve the goal of increased protein expression but have limitations. Recent discoveries of the extensive regulatory networks formed by non-coding RNAs offer alternative targets and strategies to amplify the production of a specific protein. In addition to RNA-targeting small molecules, new nucleic acid-based therapeutic modalities that allow highly specific modulation of RNA-based regulatory networks are being developed. Such approaches can directly target the stability of mRNAs or modulate non-coding RNA-mediated regulation of transcription and translation. This Review highlights emerging RNA-targeted therapeutics for gene activation, focusing on opportunities and challenges for translation to the clinic.
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Affiliation(s)
- Olga Khorkova
- OPKO Health, Miami, FL, USA
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Chemistry, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA.
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA.
- Department of Chemistry, University of Miami, Miami, FL, USA.
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15
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Duan J, Huang Z, Nice EC, Xie N, Chen M, Huang C. Current advancements and future perspectives of long noncoding RNAs in lipid metabolism and signaling. J Adv Res 2023; 48:105-123. [PMID: 35973552 PMCID: PMC10248733 DOI: 10.1016/j.jare.2022.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The investigation of lncRNAs has provided a novel perspective for elucidating mechanisms underlying diverse physiological and pathological processes. Compelling evidence has revealed an intrinsic link between lncRNAs and lipid metabolism, demonstrating that lncRNAs-induced disruption of lipid metabolism and signaling contribute to the development of multiple cancers and some other diseases, including obesity, fatty liver disease, and cardiovascular disease. AIMOF REVIEW The current review summarizes the recent advances in basic research about lipid metabolism and lipid signaling-related lncRNAs. Meanwhile, the potential and challenges of targeting lncRNA for the therapy of cancers and other lipid metabolism-related diseases are also discussed. KEY SCIENTIFIC CONCEPT OF REVIEW Compared with the substantial number of lncRNA loci, we still know little about the role of lncRNAs in metabolism. A more comprehensive understanding of the function and mechanism of lncRNAs may provide a new standpoint for the study of lipid metabolism and signaling. Developing lncRNA-based therapeutic approaches is an effective strategy for lipid metabolism-related diseases.
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Affiliation(s)
- Jiufei Duan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041 Chengdu, China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041 Chengdu, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041 Chengdu, China.
| | - Mingqing Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, 430079 Wuhan, China.
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041 Chengdu, China.
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16
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 353] [Impact Index Per Article: 353.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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17
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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] [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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18
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Huo Y, Li Q, Yang L, Li X, Sun C, Liu Y, Liu H, Pan Z, Li Q, Du X. SDNOR, a Novel Antioxidative lncRNA, Is Essential for Maintaining the Normal State and Function of Porcine Follicular Granulosa Cells. Antioxidants (Basel) 2023; 12:antiox12040799. [PMID: 37107173 PMCID: PMC10135012 DOI: 10.3390/antiox12040799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Increasing evidence shows that lncRNAs, an important kind of endogenous regulator, are involved in the regulation of follicular development and female fertility, but the mechanism remain largely unknown. In this study, we found that SDNOR, a recently identified antiapoptotic lncRNA, is a potential multifunctional regulator in porcine follicular granulosa cells (GCs) through RNA-seq and multi-dimension analyses. SDNOR-mediated regulatory networks were established and identified that SOX9, a transcription factor inhibited by SDNOR, mediates SDNOR's regulation of the transcription of downstream targets. Functional analyses showed that loss of SDNOR significantly impairs GC morphology, inhibits cell proliferation and viability, reduces E2/P4 index, and suppresses the expression of crucial markers, including PCNA, Ki67, CDK2, CYP11A1, CYP19A1, and StAR. Additionally, after the detection of ROS, SOD, GSH-Px, and MDA, we found that SDNOR elevates the resistance of GCs to oxidative stress (OS) and also inhibits OS-induced apoptosis. Notably, GCs with high SDNOR levels are insensitive to oxidative stress, leading to lower apoptosis rates and higher environmental adaptability. In summary, our findings reveal the regulation of porcine GCs in response to oxidative stress from the perspective of lncRNA and demonstrate that SDNOR is an essential antioxidative lncRNA for maintaining the normal state and function of GCs.
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Affiliation(s)
- Yangan Huo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiqi Li
- College of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College Agriculture and Forestry, Jurong 215314, China
| | - Liu Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoxue Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Sun
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Du
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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19
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Tao X, Li S, Chen G, Wang J, Xu S. Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination. Int J Mol Sci 2023; 24:ijms24065562. [PMID: 36982636 PMCID: PMC10054671 DOI: 10.3390/ijms24065562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are not translated into known functional proteins. This broad definition covers a large collection of transcripts with diverse genomic origins, biogenesis, and modes of action. Thus, it is very important to choose appropriate research methodologies when investigating lncRNAs with biological significance. Multiple reviews to date have summarized the mechanisms of lncRNA biogenesis, their localization, their functions in gene regulation at multiple levels, and also their potential applications. However, little has been reviewed on the leading strategies for lncRNA research. Here, we generalize a basic and systemic mind map for lncRNA research and discuss the mechanisms and the application scenarios of ‘up-to-date’ techniques as applied to molecular function studies of lncRNAs. Taking advantage of documented lncRNA research paradigms as examples, we aim to provide an overview of the developing techniques for elucidating lncRNA interactions with genomic DNA, proteins, and other RNAs. In the end, we propose the future direction and potential technological challenges of lncRNA studies, focusing on techniques and applications.
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Affiliation(s)
- Xiaoyuan Tao
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sujuan Li
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wang
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shengchun Xu
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence:
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20
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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21
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Ntostis P, Swanson G, Kokkali G, Iles D, Huntriss J, Pantou A, Tzetis M, Pantos K, Picton HM, Krawetz SA, Miller D. Trophectoderm non-coding RNAs reflect the higher metabolic and more invasive properties of young maternal age blastocysts. Syst Biol Reprod Med 2023; 69:3-19. [PMID: 36576378 DOI: 10.1080/19396368.2022.2153636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Increasing female age is accompanied by a corresponding fall in her fertility. This decline is influenced by a variety of factors over an individual's life course including background genetics, local environment and diet. Studying both coding and non-coding RNAs of the embryo could aid our understanding of the causes and/or effects of the physiological processes accompanying the decline including the differential expression of sub-cellular biomarkers indicative of various diseases. The current study is a post-hoc analysis of the expression of trophectoderm RNA data derived from a previous high throughput study. Its main aim is to determine the characteristics and potential functionalities that characterize long non-coding RNAs. As reported previously, a maternal age-related component is potentially implicated in implantation success. Trophectoderm samples representing the full range of maternal reproductive ages were considered in relation to embryonic implantation potential, trophectoderm transcriptome dynamics and reproductive maternal age. The long non-coding RNA (lncRNA) biomarkers identified here are consistent with the activities of embryo-endometrial crosstalk, developmental competency and implantation and share common characteristics with markers of neoplasia/cancer invasion. Corresponding genes for expressed lncRNAs were more active in the blastocysts of younger women are associated with metabolic pathways including cholesterol biosynthesis and steroidogenesis.
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Affiliation(s)
- Panagiotis Ntostis
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
- Department of Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Grace Swanson
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Georgia Kokkali
- Genesis Athens Clinic, Reproductive Medicine Unit, Athens, Greece
| | - David Iles
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - John Huntriss
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Agni Pantou
- Genesis Athens Clinic, Reproductive Medicine Unit, Athens, Greece
| | - Maria Tzetis
- Department of Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Helen M Picton
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - David Miller
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
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22
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Mangiavacchi A, Morelli G, Orlando V. Behind the scenes: How RNA orchestrates the epigenetic regulation of gene expression. Front Cell Dev Biol 2023; 11:1123975. [PMID: 36760365 PMCID: PMC9905133 DOI: 10.3389/fcell.2023.1123975] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Non-coding DNA accounts for approximately 98.5% of the human genome. Once labeled as "junk DNA", this portion of the genome has undergone a progressive re-evaluation and it is now clear that some of its transcriptional products, belonging to the non-coding RNAs (ncRNAs), are key players in cell regulatory networks. A growing body of evidence demonstrates the crucial impact of regulatory ncRNAs on mammalian gene expression. Here, we focus on the defined relationship between chromatin-interacting RNAs, particularly long non-coding RNA (lncRNA), enhancer RNA (eRNA), non-coding natural antisense transcript (ncNAT), and circular RNA (circRNA) and epigenome, a common ground where both protein and RNA species converge to regulate cellular functions. Through several examples, this review provides an overview of the variety of targets, interactors, and mechanisms involved in the RNA-mediated modulation of loci-specific epigenetic states, a fundamental evolutive strategy to orchestrate mammalian gene expression in a timely and reversible manner. We will discuss how RNA-mediated epigenetic regulation impacts development and tissue homeostasis and how its alteration contributes to the onset and progression of many different human diseases, particularly cancer.
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23
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Warwick T, Brandes RP, Leisegang MS. Computational Methods to Study DNA:DNA:RNA Triplex Formation by lncRNAs. Noncoding RNA 2023; 9:ncrna9010010. [PMID: 36827543 PMCID: PMC9965544 DOI: 10.3390/ncrna9010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) impact cell function via numerous mechanisms. In the nucleus, interactions between lncRNAs and DNA and the consequent formation of non-canonical nucleic acid structures seems to be particularly relevant. Along with interactions between single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA), such as R-loops, ssRNA can also interact with double-stranded DNA (dsDNA) to form DNA:DNA:RNA triplexes. A major challenge in the study of DNA:DNA:RNA triplexes is the identification of the precise RNA component interacting with specific regions of the dsDNA. As this is a crucial step towards understanding lncRNA function, there exist several computational methods designed to predict these sequences. This review summarises the recent progress in the prediction of triplex formation and highlights important DNA:DNA:RNA triplexes. In particular, different prediction tools (Triplexator, LongTarget, TRIPLEXES, Triplex Domain Finder, TriplexFFP, TriplexAligner and Fasim-LongTarget) will be discussed and their use exemplified by selected lncRNAs, whose DNA:DNA:RNA triplex forming potential was validated experimentally. Collectively, these tools revealed that DNA:DNA:RNA triplexes are likely to be numerous and make important contributions to gene expression regulation.
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Affiliation(s)
- Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site RheinMain, 60590 Frankfurt, Germany
| | - Ralf P. Brandes
- Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site RheinMain, 60590 Frankfurt, Germany
| | - Matthias S. Leisegang
- Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site RheinMain, 60590 Frankfurt, Germany
- Correspondence: ; Tel.: +49-69-6301-6996; Fax: +49-69-6301-7668
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24
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Luo L, Chen X. Exploring the potential of eRNAs in cancer immunotherapy. MOLECULAR THERAPY - ONCOLYTICS 2022; 27:197-199. [PMID: 36381659 PMCID: PMC9647423 DOI: 10.1016/j.omto.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Marakulina D, Vorontsov IE, Kulakovskiy IV, Lennartsson A, Drabløs F, Medvedeva Y. EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes. Nucleic Acids Res 2022; 51:D564-D570. [PMID: 36350659 PMCID: PMC9825597 DOI: 10.1093/nar/gkac989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/30/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
We present an update of EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets, and products which is openly accessible at http://epifactors.autosome.org. An updated version of the EpiFactors contains information on 902 proteins, including 101 histones and protamines, and, as a main update, a newly curated collection of 124 lncRNAs involved in epigenetic regulation. The amount of publications concerning the role of lncRNA in epigenetics is rapidly growing. Yet, the resource that compiles, integrates, organizes, and presents curated information on lncRNAs in epigenetics is missing. EpiFactors fills this gap and provides data on epigenetic regulators in an accessible and user-friendly form. For 820 of the genes in EpiFactors, we include expression estimates across multiple cell types assessed by CAGE-Seq in the FANTOM5 project. In addition, the updated EpiFactors contains information on 73 protein complexes involved in epigenetic regulation. Our resource is practical for a wide range of users, including biologists, bioinformaticians and molecular/systems biologists.
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Affiliation(s)
- Daria Marakulina
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Moscow Region, Russia
| | - Ilya E Vorontsov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ivan V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NEO, Karolinska Institutet, 14157, Huddinge, Sweden
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, PO Box 8905, NO-7491 Trondheim, Norway
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26
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HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex. Nat Commun 2022; 13:6563. [PMID: 36323673 PMCID: PMC9630315 DOI: 10.1038/s41467-022-34252-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/19/2022] [Indexed: 11/07/2022] Open
Abstract
DNA:DNA:RNA triplexes that are formed through Hoogsteen base-pairing of the RNA in the major groove of the DNA duplex have been observed in vitro, but the extent to which these interactions occur in cells and how they impact cellular functions remains elusive. Using a combination of bioinformatic techniques, RNA/DNA pulldown and biophysical studies, we set out to identify functionally important DNA:DNA:RNA triplex-forming long non-coding RNAs (lncRNA) in human endothelial cells. The lncRNA HIF1α-AS1 was retrieved as a top hit. Endogenous HIF1α-AS1 reduces the expression of numerous genes, including EPH Receptor A2 and Adrenomedullin through DNA:DNA:RNA triplex formation by acting as an adapter for the repressive human silencing hub complex (HUSH). Moreover, the oxygen-sensitive HIF1α-AS1 is down-regulated in pulmonary hypertension and loss-of-function approaches not only result in gene de-repression but also enhance angiogenic capacity. As exemplified here with HIF1α-AS1, DNA:DNA:RNA triplex formation is a functionally important mechanism of trans-acting gene expression control.
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27
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Khorkova O, Stahl J, Joji A, Volmar CH, Zeier Z, Wahlestedt C. Natural antisense transcripts as drug targets. Front Mol Biosci 2022; 9:978375. [PMID: 36250017 PMCID: PMC9563854 DOI: 10.3389/fmolb.2022.978375] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
The recent discovery of vast non-coding RNA-based regulatory networks that can be easily modulated by nucleic acid-based drugs has opened numerous new therapeutic possibilities. Long non-coding RNA, and natural antisense transcripts (NATs) in particular, play a significant role in networks that involve a wide variety of disease-relevant biological mechanisms such as transcription, splicing, translation, mRNA degradation and others. Currently, significant efforts are dedicated to harnessing these newly emerging NAT-mediated biological mechanisms for therapeutic purposes. This review will highlight the recent clinical and pre-clinical developments in this field and survey the advances in nucleic acid-based drug technologies that make these developments possible.
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Affiliation(s)
- Olga Khorkova
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Jack Stahl
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Aswathy Joji
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
- Department of Chemistry, University of Miami, Miami, FL, United States
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Zane Zeier
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
- Department of Chemistry, University of Miami, Miami, FL, United States
- *Correspondence: Claes Wahlestedt,
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28
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CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles. Sci Rep 2022; 12:15525. [PMID: 36109624 PMCID: PMC9477841 DOI: 10.1038/s41598-022-19782-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are transcribed from the same genomic locus as their partner gene but from the opposite DNA strand and overlap with the partner gene transcript. Here, we developed a simple and convenient program termed CCIVR (comprehensive cis-NATs identifier via RNA-seq data) that comprehensively identifies all kinds of cis-NATs based on genome annotation with expression data obtained from RNA-seq. Using CCIVR with genome databases, we demonstrated total cis-NAT pairs from 11 model organisms. CCIVR analysis with RNA-seq data from parthenogenetic and androgenetic embryonic stem cells identified well-known imprinted cis-NAT pair, KCNQ1/KCNQ1OT1, ensuring the availability of CCIVR. Finally, CCIVR identified cis-NAT pairs that demonstrate inversely correlated expression upon TGFβ stimulation including cis-NATs that functionally repress their partner genes by introducing epigenetic alteration in the promoters of partner genes. Thus, CCIVR facilitates the investigation of structural characteristics and functions of cis-NATs in numerous processes in various species.
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29
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Kunkler CN, Schiefelbein GE, O'Leary NJ, McCown PJ, Brown JA. A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix. RNA (NEW YORK, N.Y.) 2022; 28:1172-1184. [PMID: 35820700 PMCID: PMC9380742 DOI: 10.1261/rna.079244.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Recent studies suggest noncoding RNAs interact with genomic DNA, forming RNA•DNA-DNA triple helices, as a mechanism to regulate transcription. One way cells could regulate the formation of these triple helices is through RNA modifications. With over 140 naturally occurring RNA modifications, we hypothesize that some modifications stabilize RNA•DNA-DNA triple helices while others destabilize them. Here, we focus on a pyrimidine-motif triple helix composed of canonical U•A-T and C•G-C base triples. We employed electrophoretic mobility shift assays and microscale thermophoresis to examine how 11 different RNA modifications at a single position in an RNA•DNA-DNA triple helix affect stability: 5-methylcytidine (m5C), 5-methyluridine (m5U or rT), 3-methyluridine (m3U), pseudouridine (Ψ), 4-thiouridine (s4U), N 6-methyladenosine (m6A), inosine (I), and each nucleobase with 2'-O-methylation (Nm). Compared to the unmodified U•A-T base triple, some modifications have no significant change in stability (Um•A-T), some have ∼2.5-fold decreases in stability (m5U•A-T, Ψ•A-T, and s4U•A-T), and some completely disrupt triple helix formation (m3U•A-T). To identify potential biological examples of RNA•DNA-DNA triple helices controlled by an RNA modification, we searched RMVar, a database for RNA modifications mapped at single-nucleotide resolution, for lncRNAs containing an RNA modification within a pyrimidine-rich sequence. Using electrophoretic mobility shift assays, the binding of DNA-DNA to a 22-mer segment of human lncRNA Al157886.1 was destabilized by ∼1.7-fold with the substitution of m5C at known m5C sites. Therefore, the formation and stability of cellular RNA•DNA-DNA triple helices could be influenced by RNA modifications.
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Affiliation(s)
- Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Grace E Schiefelbein
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Phillip J McCown
- Michigan Medicine, Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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30
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Liu YC, Lin YH, Chi HC, Huang PS, Liao CJ, Liou YS, Lin CC, Yu CJ, Yeh CT, Huang YH, Lin KH. CRNDE acts as an epigenetic modulator of the p300/YY1 complex to promote HCC progression and therapeutic resistance. Clin Epigenetics 2022; 14:106. [PMID: 35999564 PMCID: PMC9400329 DOI: 10.1186/s13148-022-01326-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common primary liver malignancies worldwide. The long-term prognosis for HCC remains extremely poor, with drug resistance being the major underlying cause of recurrence and mortality. The lncRNA colorectal neoplasia differentially expressed (CRNDE) is an epigenetic mediator and plays an important role to drive proliferation and drug resistance in HCC. However, CRNDE as an epigenetic regulator with influences sorafenib resistance in HCC is unclear. Thus, we explore the potential of targeting the CRNDE/p300/YY1 axis as a novel therapeutic strategy to overcome sorafenib resistance of HCC. Method Detection of the expression level of CRNDE and EGFR in clinical specimens of HCC. CRNDE, EGFR, p300, and YY1expression were altered in HCC cells through transfection with different plasmids, and cell proliferation, migration, invasion, and sorafenib resistance were subsequently observed. Immunoprecipitation, chromatin immunoprecipitation, re-chromatin immunoprecipitation, site-directed mutagenesis, RNA Immunoprecipitation, immune fluorescence, qRT-PCR, and western blotting were performed to uncover the mechanisms of CRNDE regulation. The xenograft nude mice model was used to investigate the tumor growth and sorafenib resistance. Results In this study, we showed that CRNDE expression is significantly positively correlated with that of epidermal growth factor receptor (EGFR) in clinical specimens of HCC and induces proliferation and sorafenib resistance of HCC via EGFR-mediated signaling. Mechanistically, CRNDE stabilized the p300/YY1 complex at the EGFR promoter and simultaneously enhanced histone H3K9 and H3K27 acetylation, which serve as markers of relaxed chromatin. EGFR was positively upregulated by the epigenetic complex, p300/YY1, in a manner dependent on CRNDE expression, leading to enhanced tumor cell proliferation and sorafenib resistance. Furthermore, C646, a p300 inhibitor, suppressed EGFR transcriptional activity by decreasing chromatin relaxation and YY1 binding, which effectively reduced proliferation/sorafenib resistance and prolonged overall survival. Conclusion Our collective findings support the potential of targeting the CRNDE/p300/YY1 axis as a novel therapeutic strategy to overcome sorafenib resistance of HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01326-3.
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Affiliation(s)
- Yu-Chin Liu
- Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1 Road, Taoyuan, Taiwan, Republic of China.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yang-Hsiang Lin
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Hsiang-Cheng Chi
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan
| | - Po-Shuan Huang
- Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1 Road, Taoyuan, Taiwan, Republic of China
| | - Chia-Jung Liao
- Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1 Road, Taoyuan, Taiwan, Republic of China
| | - Yu-Syuan Liou
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1 Road, Taoyuan, Taiwan, Republic of China
| | - Chiao-Chun Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1 Road, Taoyuan, Taiwan, Republic of China
| | - Chia-Jung Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1 Road, Taoyuan, Taiwan, Republic of China.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Thoracic Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Ya-Hui Huang
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Kwang-Huei Lin
- Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan, Taiwan. .,Graduate Institute of Biomedical Sciences, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1 Road, Taoyuan, Taiwan, Republic of China. .,Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan. .,Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan.
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31
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So KKH, Huang Y, Zhang S, Qiao Y, He L, Li Y, Chen X, Sham MH, Sun H, Wang H. seRNA
PAM
controls skeletal muscle satellite cell proliferation and aging through
trans
regulation of
Timp2
expression synergistically with Ddx5. Aging Cell 2022; 21:e13673. [PMID: 35851988 PMCID: PMC9381903 DOI: 10.1111/acel.13673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/20/2022] [Accepted: 07/03/2022] [Indexed: 12/11/2022] Open
Affiliation(s)
- Karl Kam Hei So
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Hong Kong SAR China
- School of Biomedical Sciences The Chinese University of Hong Kong Hong Kong SAR China
| | - Yile Huang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Hong Kong SAR China
| | - Suyang Zhang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Hong Kong SAR China
- Center for Neuromusculoskeletal Restorative Medicine Hong Kong Science Park Hong Kong SAR China
| | - Yulong Qiao
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Hong Kong SAR China
- Center for Neuromusculoskeletal Restorative Medicine Hong Kong Science Park Hong Kong SAR China
| | - Liangqiang He
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Hong Kong SAR China
- Center for Neuromusculoskeletal Restorative Medicine Hong Kong Science Park Hong Kong SAR China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Hong Kong SAR China
| | - Xiaona Chen
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Hong Kong SAR China
- Center for Neuromusculoskeletal Restorative Medicine Hong Kong Science Park Hong Kong SAR China
| | - Mai Har Sham
- School of Biomedical Sciences The Chinese University of Hong Kong Hong Kong SAR China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Hong Kong SAR China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Hong Kong SAR China
- Center for Neuromusculoskeletal Restorative Medicine Hong Kong Science Park Hong Kong SAR China
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32
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Zhang P, Wu S, He Y, Li X, Zhu Y, Lin X, Chen L, Zhao Y, Niu L, Zhang S, Li X, Zhu L, Shen L. LncRNA-Mediated Adipogenesis in Different Adipocytes. Int J Mol Sci 2022; 23:ijms23137488. [PMID: 35806493 PMCID: PMC9267348 DOI: 10.3390/ijms23137488] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/01/2023] Open
Abstract
Long-chain noncoding RNAs (lncRNAs) are RNAs that do not code for proteins, widely present in eukaryotes. They regulate gene expression at multiple levels through different mechanisms at epigenetic, transcription, translation, and the maturation of mRNA transcripts or regulation of the chromatin structure, and compete with microRNAs for binding to endogenous RNA. Adipose tissue is a large and endocrine-rich functional tissue in mammals. Excessive accumulation of white adipose tissue in mammals can cause metabolic diseases. However, unlike white fat, brown and beige fats release energy as heat. In recent years, many lncRNAs associated with adipogenesis have been reported. The molecular mechanisms of how lncRNAs regulate adipogenesis are continually investigated. In this review, we discuss the classification of lncRNAs according to their transcriptional location. lncRNAs that participate in the adipogenesis of white or brown fats are also discussed. The function of lncRNAs as decoy molecules and RNA double-stranded complexes, among other functions, is also discussed.
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Affiliation(s)
- Peiwen Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuang Wu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuxu He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinrong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Zhu
- College of Life Science, China West Normal University, Nanchong 637009, China;
| | - Xutao Lin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.Z.); (L.S.); Tel.: +86-28-8629-1133 (L.Z. & L.S.)
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.Z.); (L.S.); Tel.: +86-28-8629-1133 (L.Z. & L.S.)
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Bezzecchi E, Pagani G, Forte B, Percio S, Zaffaroni N, Dolfini D, Gandellini P. MIR205HG/LEADR Long Noncoding RNA Binds to Primed Proximal Regulatory Regions in Prostate Basal Cells Through a Triplex- and Alu-Mediated Mechanism. Front Cell Dev Biol 2022; 10:909097. [PMID: 35784469 PMCID: PMC9247157 DOI: 10.3389/fcell.2022.909097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/31/2022] [Indexed: 01/11/2023] Open
Abstract
Aside serving as host gene for miR-205, MIR205HG transcribes for a chromatin-associated long noncoding RNA (lncRNA) able to restrain the differentiation of prostate basal cells, thus being reannotated as LEADR (Long Epithelial Alu-interacting Differentiation-related RNA). We previously showed the presence of Alu sequences in the promoters of genes modulated upon MIR205HG/LEADR manipulation. Notably, an Alu element also spans the first and second exons of MIR205HG/LEADR, suggesting its possible involvement in target selection/binding. Here, we performed ChIRP-seq to map MIR205HG/LEADR chromatin occupancy at genome-wide level in prostate basal cells. Our results confirmed preferential binding to regions proximal to gene transcription start site (TSS). Moreover, enrichment of triplex-forming sequences was found upstream of MIR205HG/LEADR-bound genes, peaking at −1,500/−500 bp from TSS. Triplexes formed with one or two putative DNA binding sites within MIR205HG/LEADR sequence, located just upstream of the Alu element. Notably, triplex-forming regions of bound genes were themselves enriched in Alu elements. These data suggest, from one side, that triplex formation may be the prevalent mechanism by which MIR205HG/LEADR selects and physically interacts with target DNA, from the other that direct or protein-mediated Alu (RNA)/Alu (DNA) interaction may represent a further functional requirement. We also found that triplex-forming regions were enriched in specific histone modifications, including H3K4me1 in the absence of H3K27ac, H3K4me3 and H3K27me3, indicating that in prostate basal cells MIR205HG/LEADR may preferentially bind to primed proximal regulatory elements. This may underscore the need for basal cells to keep MIR205HG/LEADR target genes repressed but, at the same time, responsive to differentiation cues.
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Affiliation(s)
- Eugenia Bezzecchi
- Department of Biosciences, University of Milan, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Pagani
- Department of Biosciences, University of Milan, Milan, Italy
| | - Barbara Forte
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano Percio
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, Milan, Italy
- *Correspondence: Paolo Gandellini,
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34
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Integrated lncRNA function upon genomic and epigenomic regulation. Mol Cell 2022; 82:2252-2266. [PMID: 35714586 DOI: 10.1016/j.molcel.2022.05.027] [Citation(s) in RCA: 147] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [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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35
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Winkler L, Jimenez M, Zimmer JT, Williams A, Simon MD, Dimitrova N. Functional elements of the cis-regulatory lincRNA-p21. Cell Rep 2022; 39:110687. [PMID: 35443176 PMCID: PMC9118141 DOI: 10.1016/j.celrep.2022.110687] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 02/10/2022] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
The p53-induced long noncoding RNA (lncRNA) lincRNA-p21 is proposed to act in cis to promote p53-dependent expression of the neighboring cell cycle gene, Cdkn1a/p21. The molecular mechanism through which the transcribed lincRNA-p21 regulatory locus activates p21 expression remains poorly understood. To elucidate the functional elements of cis-regulation, we generate a series of genetic models that disrupt DNA regulatory elements, the transcription of lincRNA-p21, or the accumulation of mature lincRNA-p21. Unexpectedly, we determine that full-length transcription, splicing, and accumulation of lincRNA-p21 are dispensable for the chromatin organization of the locus and for cis-regulation. Instead, we find that production of lincRNA-p21 through conserved regions in exon 1 of lincRNA-p21 promotes cis-activation. These findings demonstrate that the activation of nascent transcription from this lncRNA locus, but not the generation or accumulation of a mature lncRNA transcript, is necessary to enact local gene expression control.
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Affiliation(s)
- Lauren Winkler
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Maria Jimenez
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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36
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Enhancer RNAs (eRNAs) in Cancer: The Jacks of All Trades. Cancers (Basel) 2022; 14:cancers14081978. [PMID: 35454885 PMCID: PMC9030334 DOI: 10.3390/cancers14081978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary This review focuses on eRNAs and the several mechanisms by which they can regulate gene expression. In particular we describe here the most recent examples of eRNAs dysregulated in cancer or involved in the immune escape of tumor cells. Abstract Enhancer RNAs (eRNAs) are non-coding RNAs (ncRNAs) transcribed in enhancer regions. They play an important role in transcriptional regulation, mainly during cellular differentiation. eRNAs are tightly tissue- and cell-type specific and are induced by specific stimuli, activating promoters of target genes in turn. eRNAs usually have a very short half-life but in some cases, once activated, they can be stably expressed and acquire additional functions. Due to their critical role, eRNAs are often dysregulated in cancer and growing number of interactions with chromatin modifiers, transcription factors, and splicing machinery have been described. Enhancer activation and eRNA transcription have particular relevance also in inflammatory response, placing the eRNAs at the interplay between cancer and immune cells. Here, we summarize all the possible molecular mechanisms recently reported in association with eRNAs activity.
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37
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Bencivenga D, Stampone E, Vastante A, Barahmeh M, Della Ragione F, Borriello A. An Unanticipated Modulation of Cyclin-Dependent Kinase Inhibitors: The Role of Long Non-Coding RNAs. Cells 2022; 11:cells11081346. [PMID: 35456025 PMCID: PMC9028986 DOI: 10.3390/cells11081346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022] Open
Abstract
It is now definitively established that a large part of the human genome is transcribed. However, only a scarce percentage of the transcriptome (about 1.2%) consists of RNAs that are translated into proteins, while the large majority of transcripts include a variety of RNA families with different dimensions and functions. Within this heterogeneous RNA world, a significant fraction consists of sequences with a length of more than 200 bases that form the so-called long non-coding RNA family. The functions of long non-coding RNAs range from the regulation of gene transcription to the changes in DNA topology and nucleosome modification and structural organization, to paraspeckle formation and cellular organelles maturation. This review is focused on the role of long non-coding RNAs as regulators of cyclin-dependent kinase inhibitors’ (CDKIs) levels and activities. Cyclin-dependent kinases are enzymes necessary for the tuned progression of the cell division cycle. The control of their activity takes place at various levels. Among these, interaction with CDKIs is a vital mechanism. Through CDKI modulation, long non-coding RNAs implement control over cellular physiology and are associated with numerous pathologies. However, although there are robust data in the literature, the role of long non-coding RNAs in the modulation of CDKIs appears to still be underestimated, as well as their importance in cell proliferation control.
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38
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Regulation of Sox8 through lncRNA Mrhl-Mediated Chromatin Looping in Mouse Spermatogonia. Mol Cell Biol 2022; 42:e0047521. [PMID: 35412350 DOI: 10.1128/mcb.00475-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sox8 is a developmentally important transcription factor that plays an important role in sex maintenance and fertility of adult mice. In the B-type spermatogonial cells, Sox8 is regulated by the long noncoding RNAs (lncRNA) Mrhl in a p68-dependant manner under the control of the Wnt signaling pathway. The downregulation of Mrhl leads to the meiotic commitment of the spermatogonial cells in a Sox8-dependant manner. While the molecular players involved in the regulation of transcription at the Sox8 promoter have been worked out, our current study points to the involvement of the architectural proteins CTCF and cohesin in mediating a chromatin loop that brings the Sox8 promoter in contact with a silencer element present within the gene body in the presence of lncRNA Mrhl concomitant with transcriptional repression. Further, lncRNA Mrhl interacts with the Sox8 locus through the formation of a DNA:DNA:RNA triplex, which is necessary for the recruitment of PRC2 to the locus. The downregulation of lncRNA Mrhl results in the promoter-silencer loop giving way to a promoter-enhancer loop. This active transcription-associated chromatin loop is mediated by YY1 and brings the promoter in contact with the enhancer present downstream of the gene.
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39
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A feedforward circuit between KLF5 and lncRNA KPRT4 contributes to basal-like breast cancer. Cancer Lett 2022; 534:215618. [PMID: 35259457 DOI: 10.1016/j.canlet.2022.215618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 12/21/2022]
Abstract
Basal-like breast cancer (BLBC) is the most aggressive subtype of breast cancer with a poor prognosis. Long noncoding RNAs (lncRNAs) play critical roles in human cancers. Krüppel-like Factor 5 (KLF5) is a key oncogenic transcription factor in BLBC. However, the underlying mechanism of mutual regulation between KLF5 and lncRNA remains largely unknown. Here, we demonstrate that lncRNA KPRT4 promotes BLBC cell proliferation in vitro and in vivo. Mechanistically, KLF5 directly binds to the promoter of KPRT4 to promote KPRT4 transcription. Reciprocally, KPRT4 recruits the YB-1 transcription factor to the KLF5 promoter by interacting with YB-1 at its 5' domain and forming an RNA-DNA-DNA triplex structure at its 3' domain, resulting in enhanced transcription of KLF5 and ultimately establishing a feedforward circuit to promote cell proliferation. Moreover, the antisense oligonucleotide (ASO)-based therapy targeting KPRT4 substantially attenuated tumor growth in vivo. Clinically, the expression levels of YB-1, KLF5 and KPRT4 are positively correlated in clinical breast specimens. Together, our data suggest that KPRT4 is a major molecule for BLBC progression and that the feedforward circuit between KLF5 and KPRT4 may represent a potential therapeutic target in BLBC.
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40
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Characterization of influenza A virus induced transposons reveals a subgroup of transposons likely possessing the regulatory role as eRNAs. Sci Rep 2022; 12:2188. [PMID: 35140280 PMCID: PMC8828846 DOI: 10.1038/s41598-022-06196-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/25/2022] [Indexed: 01/02/2023] Open
Abstract
Although many studies have observed genome-wide host transposon expression alteration during viral infection, the mechanisms of induction and the impact on the host remain unclear. Utilizing recently published influenza A virus (IAV) time series data and ENCODE functional genomics data, we characterized virus induced host differentially expressed transposons (virus-induced-TE) by investigating genome-wide spatial and functional relevance between the virus-induced-TEs and epigenomic markers (e.g. histone modification and chromatin remodelers). We found that a significant fraction of virus-induced-TEs are derived from host enhancer regions, where CHD4 binding and/or H3K27ac occupancy is high or H3K9me3 occupancy is low. By overlapping virus-induced-TEs to human enhancer RNAs (eRNAs), we discovered that a proportion of virus-induced-TEs are either eRNAs or part of enhancer RNAs. Upon further analysis of the eRNA targeted genes, we found that the virus-induced-TE related eRNA targets are overrepresented in differentially expressed host genes of IAV infected samples. Our results suggest that changing chromatin accessibility from repressive to permissive in the transposon docked enhancer regions to regulate host downstream gene expression is potentially one of the virus and host cell interaction mechanisms, where transposons are likely important regulatory genomic elements. Our study provides a new insight into the mechanisms of virus-host interaction and may lead to novel strategies for prevention and therapeutics of IAV and other virus infectious diseases.
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41
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Maldotti M, Lauria A, Anselmi F, Molineris I, Tamburrini A, Meng G, Polignano IL, Scrivano MG, Campestre F, Simon LM, Rapelli S, Morandi E, Incarnato D, Oliviero S. The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. Nucleic Acids Res 2022; 50:2587-2602. [PMID: 35137201 PMCID: PMC8934626 DOI: 10.1093/nar/gkac083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear (1,2). We found 122 lncRNAs that interacts directly with p300. In depth analysis of one of these, lncSmad7, is required to maintain ESC self-renewal and it interacts to the C-terminal domain of p300. lncSmad7 also contains predicted RNA-DNA Hoogsteen forming base pairing. Combined Chromatin Isolation by RNA precipitation followed by sequencing (ChIRP-seq) together with CRISPR/Cas9 mutagenesis of the target sites demonstrate that lncSmad7 binds and recruits p300 to enhancers in trans, to trigger enhancer acetylation and transcriptional activation of its target genes. Thus, these results unveil a new mechanism by which p300 is recruited to the genome.
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Affiliation(s)
- Mara Maldotti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Andrea Lauria
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Francesca Anselmi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Ivan Molineris
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Annalaura Tamburrini
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Guohua Meng
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Isabelle Laurence Polignano
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Mirko Giuseppe Scrivano
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Fabiola Campestre
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Lisa Marie Simon
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Stefania Rapelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Edoardo Morandi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
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42
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The potential of long noncoding RNA therapies. Trends Pharmacol Sci 2022; 43:269-280. [DOI: 10.1016/j.tips.2022.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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43
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Abd El Halim HM, Ali A. Long noncoding RNAs: Emerging players regulating innate immune memory in the red flour beetle. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104304. [PMID: 34756931 DOI: 10.1016/j.dci.2021.104304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/03/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
A variety of strategies have been evolved to eradicate invading microbes. Phagocytes have developed in vertebrates and invertebrates to confer a non-specific immune response to pathogens. Besides, vertebrates have evolved lymphocytes to develop memory cells that can quickly respond upon the next exposure to the same pathogen. Although lymphocytes are absent in invertebrates, historical evidence, dating back to the 1920s, indicated the presence of immune memory in invertebrates. However, the concept of long-lasting non-specific defense predominated until recent evidence has been introduced in the first decade of the 21st century. Although more evidence has been introduced later, the molecular mechanism underlying the innate immune memory is largely undefined in invertebrates. Long noncoding RNAs (lncRNAs) have demonstrated a role in regulating various biological processes, including immune response. In this review, we will explore the potential role of lncRNAs in developing innate immune memory in the red flour beetle (Tribolium castaneum).
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Affiliation(s)
| | - Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742-231, USA; Department of Zoology, Faculty of Science, Benha University, Benha, 13518, Egypt.
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Deogharia M, Gurha P. The "guiding" principles of noncoding RNA function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 13:e1704. [PMID: 34856642 DOI: 10.1002/wrna.1704] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/09/2021] [Accepted: 11/11/2021] [Indexed: 12/25/2022]
Abstract
The human genome is pervasively transcribed and yet only a small fraction of these RNAs (less than 2%) are known to code for proteins. The vast majority of the RNAs are classified as noncoding RNAs (ncRNAs) and are further subgrouped as small (shorter than 200 bases) and long noncoding RNAs. The ncRNAs have been identified in all three domains of life and regulate diverse cellular processes through transcriptional and posttranscriptional gene regulation. Most of these RNAs work in conjunction with proteins forming a wide array of base pairing interactions. The determinants of these base pairing interactions are now becoming more evident and show striking similarities among the diverse group of ncRNAs. Here we present a mechanistic overview of pairing between RNA-RNA or RNA-DNA that dictates the function of ncRNAs; we provide examples to illustrate that ncRNAs work through shared evolutionary mechanisms that encompasses a guide-target interaction, involving not only classical Watson-Crick but also noncanonical Wobble and Hoogsteen base pairing. We also highlight the similarities in target selection, proofreading, and the ruler mechanism of ncRNA-protein complexes that confers target specificity and target site selection. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA-Based Catalysis > RNA-Mediated Cleavage RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Manisha Deogharia
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, Houston, Texas, USA.,University of Texas Health Sciences Center at Houston, Houston, Texas, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, Houston, Texas, USA.,University of Texas Health Sciences Center at Houston, Houston, Texas, USA
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Choudhury SR, Dutta S, Bhaduri U, Rao MRS. LncRNA Hmrhl regulates expression of cancer related genes in chronic myelogenous leukemia through chromatin association. NAR Cancer 2021; 3:zcab042. [PMID: 34734184 PMCID: PMC8559160 DOI: 10.1093/narcan/zcab042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNA has emerged as a key regulator of myriad gene functions. One such lncRNA mrhl, reported by our group, was found to have important role in spermatogenesis and embryonic development in mouse. Recently, its human homolog, Hmrhl was shown to have differential expression in several type of cancers. In the present study, we further characterize molecular features of Hmrhl and gain insight into its functional role in leukemia by gene silencing and transcriptome-based studies. Results indicate its high expression in CML patient samples as well as in K562 cell line. Silencing experiments suggest role of Hmrhl in cell proliferation, migration & invasion. RNA-seq and ChiRP-seq data analysis further revealed its association with important biological processes, including perturbed expression of crucial TFs and cancer-related genes. Among them ZIC1, PDGRFβ and TP53 were identified as regulatory targets, with high possibility of triplex formation by Hmrhl at their promoter site. Further, overexpression of PDGRFβ in Hmrhl silenced cells resulted in rescue effect of cancer associated cellular phenotypes. In addition, we also found TAL-1 to be a potential regulator of Hmrhl expression in K562 cells. Thus, we hypothesize that Hmrhl lncRNA may play a significant role in the pathobiology of CML.
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Affiliation(s)
- Subhendu Roy Choudhury
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, India
| | - Sangeeta Dutta
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, India
| | - Utsa Bhaduri
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, India
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Heterogeneity among enhancer RNAs: origins, consequences and perspectives. Essays Biochem 2021; 65:709-721. [PMID: 34414426 DOI: 10.1042/ebc20200064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Enhancer RNAs (eRNAs) are non-coding RNAs transcribed from distal cis-regulatory elements (i.e. enhancers), which are stereotyped as short, rarely spliced and unstable. In fact, a non-negligible fraction of eRNAs seems to be longer, spliced and more stable, and their cognate enhancers are epigenomically and functionally distinguishable from typical enhancers. In this review, we first summarized the genomic and molecular origins underlying the observed heterogeneity among eRNAs. Then, we discussed how their heterogeneous properties (e.g. stability) affect the modes of interaction with their regulatory partners, from promiscuous cis-interactions to specific trans-interactions. Finally, we highlighted the existence of a seemingly continuous spectrum of eRNA properties and its implications in the genomic origins of non-coding RNA genes from an evolutionary perspective.
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Li X, Zou C, Li M, Fang C, Li K, Liu Z, Li C. Transcriptome Analysis of In Vitro Fertilization and Parthenogenesis Activation during Early Embryonic Development in Pigs. Genes (Basel) 2021; 12:genes12101461. [PMID: 34680856 PMCID: PMC8535918 DOI: 10.3390/genes12101461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
Parthenogenesis activation (PA), as an important artificial breeding method, can stably preserve the dominant genotype of a species. However, the delayed development of PA embryos is still overly severe and largely leads to pre-implantation failure in pigs. The mechanisms underlying the deficiencies of PA embryos have not been completely understood. For further understanding of the molecular mechanism behind PA embryo failure, we performed transcriptome analysis among pig oocytes (meiosis II, MII) and early embryos at three developmental stages (zygote, morula, and blastocyst) in vitro fertilization (IVF) and PA group. Totally, 11,110 differentially expressed genes (DEGs), 4694 differentially expressed lincRNAs (DELs) were identified, and most DEGs enriched the regulation of apoptotic processes. Through cis- and trans-manner functional prediction, we found that hub lincRNAs were mostly involved in abnormal parthenogenesis embryonic development. In addition, twenty DE imprinted genes showed that some paternally imprinted genes in IVF displayed higher expression than that in PA. Notably, we identified that three DELs of imprinted genes (MEST, PLAGL1, and DIRAS3) were up regulated in IVF, and there was no significant change in PA group. Disordered expression of key genes for embryonic development might play key roles in abnormal parthenogenesis embryonic development. Our study indicates that embryos derived from different production techniques have varied in vitro development to the blastocyst stage, and they also affect the transcription level of corresponding genes, such as imprinted genes. This work will help future research on these genes and molecular-assisted breeding for pig parthenotes.
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Affiliation(s)
- Xin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Kui Li
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiguo Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (Z.L.); (C.L.)
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Correspondence: (Z.L.); (C.L.)
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The evolutionary acquisition and mode of functions of promoter-associated non-coding RNAs (pancRNAs) for mammalian development. Essays Biochem 2021; 65:697-708. [PMID: 34328174 DOI: 10.1042/ebc20200143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Increasing evidence has shown that many long non-coding RNAs (lncRNAs) are involved in gene regulation in a variety of ways such as transcriptional, post-transcriptional and epigenetic regulation. Promoter-associated non-coding RNAs (pancRNAs), which are categorized into the most abundant single-copy lncRNA biotype, play vital regulatory roles in finely tuning cellular specification at the epigenomic level. In short, pancRNAs can directly or indirectly regulate downstream genes to participate in the development of organisms in a cell-specific manner. In this review, we will introduce the evolutionarily acquired characteristics of pancRNAs as determined by comparative epigenomics and elaborate on the research progress on pancRNA-involving processes in mammalian embryonic development, including neural differentiation.
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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] [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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Razin SV, Gavrilov AA. Non-coding RNAs in chromatin folding and nuclear organization. Cell Mol Life Sci 2021; 78:5489-5504. [PMID: 34117518 PMCID: PMC11072467 DOI: 10.1007/s00018-021-03876-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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