1
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Matsuoka T, Yashiro M. Bioinformatics Analysis and Validation of Potential Markers Associated with Prediction and Prognosis of Gastric Cancer. Int J Mol Sci 2024; 25:5880. [PMID: 38892067 PMCID: PMC11172243 DOI: 10.3390/ijms25115880] [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: 04/18/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Gastric cancer (GC) is one of the most common cancers worldwide. Most patients are diagnosed at the progressive stage of the disease, and current anticancer drug advancements are still lacking. Therefore, it is crucial to find relevant biomarkers with the accurate prediction of prognoses and good predictive accuracy to select appropriate patients with GC. Recent advances in molecular profiling technologies, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, have enabled the approach of GC biology at multiple levels of omics interaction networks. Systemic biological analyses, such as computational inference of "big data" and advanced bioinformatic approaches, are emerging to identify the key molecular biomarkers of GC, which would benefit targeted therapies. This review summarizes the current status of how bioinformatics analysis contributes to biomarker discovery for prognosis and prediction of therapeutic efficacy in GC based on a search of the medical literature. We highlight emerging individual multi-omics datasets, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics, for validating putative markers. Finally, we discuss the current challenges and future perspectives to integrate multi-omics analysis for improving biomarker implementation. The practical integration of bioinformatics analysis and multi-omics datasets under complementary computational analysis is having a great impact on the search for predictive and prognostic biomarkers and may lead to an important revolution in treatment.
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Affiliation(s)
- Tasuku Matsuoka
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan;
- Institute of Medical Genetics, Osaka Metropolitan University, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan;
- Institute of Medical Genetics, Osaka Metropolitan University, 1-4-3 Asahi-machi, Abeno-ku, Osaka 5458585, Japan
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2
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Inamo J, Suzuki A, Ueda MT, Yamaguchi K, Nishida H, Suzuki K, Kaneko Y, Takeuchi T, Hatano H, Ishigaki K, Ishihama Y, Yamamoto K, Kochi Y. Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms. Nat Commun 2024; 15:4285. [PMID: 38806455 PMCID: PMC11133395 DOI: 10.1038/s41467-024-48615-4] [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: 12/04/2022] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Alternative splicing events are a major causal mechanism for complex traits, but they have been understudied due to the limitation of short-read sequencing. Here, we generate a full-length isoform annotation of human immune cells from an individual by long-read sequencing for 29 cell subsets. This contains a number of unannotated transcripts and isoforms such as a read-through transcript of TOMM40-APOE in the Alzheimer's disease locus. We profile characteristics of isoforms and show that repetitive elements significantly explain the diversity of unannotated isoforms, providing insight into the human genome evolution. In addition, some of the isoforms are expressed in a cell-type specific manner, whose alternative 3'-UTRs usage contributes to their specificity. Further, we identify disease-associated isoforms by isoform switch analysis and by integration of several quantitative trait loci analyses with genome-wide association study data. Our findings will promote the elucidation of the mechanism of complex diseases via alternative splicing.
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Affiliation(s)
- Jun Inamo
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Kensuke Yamaguchi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Biomedical Engineering Research Innovation Center, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Hiroshi Nishida
- Department of Molecular Systems Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Katsuya Suzuki
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yuko Kaneko
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
- Saitama Medical University, 38 Morohongo, Moroyama, Iruma, Saitama, 350-0495, Japan
| | - Hiroaki Hatano
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yasushi Ishihama
- Department of Molecular Systems Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
- Laboratory of Proteomics for Drug Discovery, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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3
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Wang S, Han Z, Strick TR. Single-molecule characterization of Sen1 translocation properties provides insights into eukaryotic factor-dependent transcription termination. Nucleic Acids Res 2024; 52:3249-3261. [PMID: 38261990 PMCID: PMC11013386 DOI: 10.1093/nar/gkae026] [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: 08/09/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
Sen1 is an essential helicase for factor-dependent transcription termination in Saccharomyces cerevisiae, whose molecular-motor mechanism has not been well addressed. Here, we use single-molecule experimentation to better understand the molecular-motor determinants of its action on RNA polymerase II (Pol II) complex. We quantify Sen1 translocation activity on single-stranded DNA (ssDNA), finding elevated translocation rates, high levels of processivity and ATP affinities. Upon deleting the N- and C-terminal domains, or further deleting different parts of the prong subdomain, which is an essential element for transcription termination, Sen1 displays changes in its translocation properties, such as slightly reduced translocation processivities, enhanced translocation rates and statistically identical ATP affinities. Although these parameters fulfil the requirements for Sen1 translocating along the RNA transcript to catch up with a stalled Pol II complex, we observe significant reductions in the termination efficiencies as well as the factions of the formation of the previously described topological intermediate prior to termination, suggesting that the prong may preserve an interaction with Pol II complex during factor-dependent termination. Our results underscore a more detailed rho-like mechanism of Sen1 and a critical interaction between Sen1 and Pol II complex for factor-dependent transcription termination in eukaryotes.
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Affiliation(s)
- Shuang Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190 Beijing, China
- Songshan Lake Materials Laboratory, 523808 Dongguan, Guangdong, China
- Molecular Motors and Machines group, Ecole normale supérieure, Institut de Biologie de l’Ecole normale supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Zhong Han
- Metabolism and Function of RNA in the Nucleus, Institut Jacques Monod, CNRS, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Terence R Strick
- Molecular Motors and Machines group, Ecole normale supérieure, Institut de Biologie de l’Ecole normale supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France
- Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
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4
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Chorostecki U, Saus E, Gabaldón T. Probing RNA structural landscapes across Candida yeast genomes. Front Microbiol 2024; 15:1362067. [PMID: 38468856 PMCID: PMC10926079 DOI: 10.3389/fmicb.2024.1362067] [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: 12/27/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of the Candida genus, which are the leading cause of hospital-acquired fungal infections. Our work addresses the gap between RNA structure and their biology by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four major Candida pathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5' untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species. Additionally, we provide the first experimental characterization of lncRNA structures in Candida species. Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs across Candida species, humans, and Arabidopsis thaliana, suggesting a conserved role for these structures. In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function in Candida pathogens, with implications for gene expression regulation and potential therapeutic strategies against Candida infections.
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Affiliation(s)
- Uciel Chorostecki
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- ICREA, Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
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5
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Grandchamp A, Czuppon P, Bornberg-Bauer E. Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster. Nucleic Acids Res 2024; 52:274-287. [PMID: 38000384 PMCID: PMC10783523 DOI: 10.1093/nar/gkad1079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/13/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
Most of the transcribed eukaryotic genomes are composed of non-coding transcripts. Among these transcripts, some are newly transcribed when compared to outgroups and are referred to as de novo transcripts. De novo transcripts have been shown to play a major role in genomic innovations. However, little is known about the rates at which de novo transcripts are gained and lost in individuals of the same species. Here, we address this gap and estimate the de novo transcript turnover rate with an evolutionary model. We use DNA long reads and RNA short reads from seven geographically remote samples of inbred individuals of Drosophila melanogaster to detect de novo transcripts that are gained on a short evolutionary time scale. Overall, each sampled individual contains around 2500 unspliced de novo transcripts, with most of them being sample specific. We estimate that around 0.15 transcripts are gained per year, and that each gained transcript is lost at a rate around 5× 10-5 per year. This high turnover of transcripts suggests frequent exploration of new genomic sequences within species. These rate estimates are essential to comprehend the process and timescale of de novo gene birth.
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Affiliation(s)
- Anna Grandchamp
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Peter Czuppon
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
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6
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Liang P, Wu Y, Qu S, Younis M, Wang W, Wu Z, Huang X. Exploring the biomarkers and potential therapeutic drugs for sepsis via integrated bioinformatic analysis. BMC Infect Dis 2024; 24:32. [PMID: 38166628 PMCID: PMC10763157 DOI: 10.1186/s12879-023-08883-9] [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: 06/01/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Sepsis is a life-threatening condition caused by an excessive inflammatory response to an infection, associated with high mortality. However, the regulatory mechanism of sepsis remains unclear. RESULTS In this study, bioinformatics analysis revealed the novel key biomarkers associated with sepsis and potential regulators. Three public datasets (GSE28750, GSE57065 and GSE95233) were employed to recognize the differentially expressed genes (DEGs). Taking the intersection of DEGs from these three datasets, GO and KEGG pathway enrichment analysis revealed 537 shared DEGs and their biological functions and pathways. These genes were mainly enriched in T cell activation, differentiation, lymphocyte differentiation, mononuclear cell differentiation, and regulation of T cell activation based on GO analysis. Further, pathway enrichment analysis revealed that these DEGs were significantly enriched in Th1, Th2 and Th17 cell differentiation. Additionally, five hub immune-related genes (CD3E, HLA-DRA, IL2RB, ITK and LAT) were identified from the protein-protein interaction network, and sepsis patients with higher expression of hub genes had a better prognosis. Besides, 14 drugs targeting these five hub related genes were revealed on the basis of the DrugBank database, which proved advantageous for treating immune-related diseases. CONCLUSIONS These results strengthen the new understanding of sepsis development and provide a fresh perspective into discriminating the candidate biomarkers for predicting sepsis as well as identifying new drugs for treating sepsis.
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Affiliation(s)
- Pingping Liang
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China
| | - Yongjian Wu
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China
| | - Siying Qu
- Department of Clinical Laboratory, Zhuhai Hospital of Integrated Traditional Chinese and Western Medicine, The Second People's Hospital of Zhuhai, Guangdong Province, Zhuhai, 519020, China
| | - Muhammad Younis
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China
| | - Wei Wang
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China
| | - Zhilong Wu
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China.
| | - Xi Huang
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China.
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China.
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7
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Bian LH, Wang SQ, Li WJ, Li J, Yin Y, Ye FF, Guo JY. Cryptotanshinone regulates gut microbiota and PI3K-AKT pathway in rats to alleviate CUMS induced depressive symptoms. Biomed Pharmacother 2023; 169:115921. [PMID: 38011787 DOI: 10.1016/j.biopha.2023.115921] [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: 09/19/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
Cryptotanshinone (CPT), a bioactive compound derived from the traditional Chinese herb Salvia miltiorrhiza, exhibits promising antidepressant properties. Employing a rat model subjected to Chronic Unpredictable Mild Stress (CUMS), behavioral analyses (open field experiment, elevated cross maze experiment, sugar water preference experiment, forced swimming experiment) and inflammatory factor assessments were conducted to assess the efficacy of CPT in alleviating depressive symptoms and inflammatory responses induced by CUMS. Moreover, 16 S rDNA analysis revealed alterations in the gut microbiota of rats exposed to both CUMS and CPT administration. Notably, CPT administration was found to mitigate harmful bacterial shifts associated with depression. Preliminary exploration of the molecular mechanism underlying CPT's antidepressant effects via transcriptomics analysis and molecular docking indicated that CPT might exert its influence by regulating the PI3K-AKT pathway. This study sheds light on the potential therapeutic role of CPT in managing depressive disorders, offering a comprehensive understanding of its impact on behavior, inflammation, gut microbiota, and molecular pathways.
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Affiliation(s)
- Li-Hua Bian
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Qi Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 4A DatunRoad, Chaoyang District, Beijing 100101, China
| | - Wen-Jing Li
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 4A DatunRoad, Chaoyang District, Beijing 100101, China
| | - Jie Li
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 4A DatunRoad, Chaoyang District, Beijing 100101, China
| | - Yi Yin
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 4A DatunRoad, Chaoyang District, Beijing 100101, China
| | - Fang-Fu Ye
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-You Guo
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 4A DatunRoad, Chaoyang District, Beijing 100101, China.
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8
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Garrido-Godino AI, Gupta I, Pelechano V, Navarro F. RNA Pol II Assembly Affects ncRNA Expression. Int J Mol Sci 2023; 25:507. [PMID: 38203678 PMCID: PMC10778713 DOI: 10.3390/ijms25010507] [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: 11/30/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
RNA pol II assembly occurs in the cytoplasm before translocation of the enzyme to the nucleus. Affecting this assembly influences mRNA transcription in the nucleus and mRNA decay in the cytoplasm. However, very little is known about the consequences on ncRNA synthesis. In this work, we show that impairment of RNA pol II assembly leads to a decrease in cryptic non-coding RNAs (preferentially CUTs and SUTs). This alteration is partially restored upon overcoming the assembly defect. Notably, this drop in ncRNAs is only partially dependent on the nuclear exosome, which suggests a major specific effect of enzyme assembly. Our data also point out a defect in transcription termination, which leads us to propose that CTD phosphatase Rtr1 could be involved in this process.
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Affiliation(s)
- Ana I. Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain;
| | - Ishaan Gupta
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany;
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain;
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva (INUO), Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
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9
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Wang Z, Zhou K, Yuan Q, Chen D, Hu X, Xie F, Liu Y, Xing J. A High-Efficiency Capture-Based NGS Approach for Comprehensive Analysis of Mitochondrial Transcriptome. Anal Chem 2023; 95:17046-17053. [PMID: 37937716 DOI: 10.1021/acs.analchem.3c03741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
The transcription of the mitochondrial genome is pivotal for maintenance of mitochondrial functions, and the deregulated mitochondrial transcriptome contributes to various pathological changes. Despite substantial progress having been achieved in uncovering the transcriptional complexity of the nuclear transcriptome, many unknowns and controversies remain for the mitochondrial transcriptome, partially owing to the lack of a highly efficient mitochondrial RNA (mtRNA) sequencing and analysis approach. Here, we first comprehensively evaluated the influence of essential experimental protocols, including strand-specific library construction, two RNA enrichment strategies, and optimal rRNA depletion, on accurately profiling mitochondrial transcriptome in whole-transcriptome sequencing (WTS) data. Based on these insights, we developed a highly efficient approach specifically suitable for targeted sequencing of whole mitochondrial transcriptome, termed capture-based mtRNA seq (CAP), in which strand-specific library construction and optimal rRNA depletion were applied. Compared with WTS, CAP has a great decrease of required data volume without affecting the sensitivity and accuracy of detection. In addition, CAP also characterized the unannotated mt-tRNA transcripts whose expression levels are below the detection limits of conventional WTS. As a proof-of-concept characterization of mtRNAs, the transcription initiation sites and mtRNA cleavage ratio were accurately identified in CAP data. Moreover, CAP had very reliable performance in plasma and single-cell samples, highlighting its wide application. Altogether, the present study has established a highly efficient pipeline for targeted sequencing of mtRNAs, which may pave the way toward functional annotation of mtRNAs and mtRNA-based diagnostic and therapeutic strategies in various diseases.
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Affiliation(s)
- Zhenni Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an710032, China
| | - Kaixiang Zhou
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an710032, China
| | - Qing Yuan
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an710072, China
| | - Dongbo Chen
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an710072, China
| | - Xi'e Hu
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an710038, China
| | - Fanfan Xie
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an710032, China
| | - Yang Liu
- Department of Clinical Diagnosis, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Jinliang Xing
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an710032, China
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10
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Liao J, Chen B, Zhu Z, Du C, Gao S, Zhao G, Zhao P, Wang Y, Wang A, Schwartz Z, Song L, Hong J, Wagstaff W, Haydon RC, Luu HH, Fan J, Reid RR, He TC, Shi L, Hu N, Huang W. Long noncoding RNA (lncRNA) H19: An essential developmental regulator with expanding roles in cancer, stem cell differentiation, and metabolic diseases. Genes Dis 2023; 10:1351-1366. [PMID: 37397543 PMCID: PMC10311118 DOI: 10.1016/j.gendis.2023.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/07/2023] [Accepted: 02/08/2023] [Indexed: 07/04/2023] Open
Abstract
Recent advances in deep sequencing technologies have revealed that, while less than 2% of the human genome is transcribed into mRNA for protein synthesis, over 80% of the genome is transcribed, leading to the production of large amounts of noncoding RNAs (ncRNAs). It has been shown that ncRNAs, especially long non-coding RNAs (lncRNAs), may play crucial regulatory roles in gene expression. As one of the first isolated and reported lncRNAs, H19 has gained much attention due to its essential roles in regulating many physiological and/or pathological processes including embryogenesis, development, tumorigenesis, osteogenesis, and metabolism. Mechanistically, H19 mediates diverse regulatory functions by serving as competing endogenous RNAs (CeRNAs), Igf2/H19 imprinted tandem gene, modular scaffold, cooperating with H19 antisense, and acting directly with other mRNAs or lncRNAs. Here, we summarized the current understanding of H19 in embryogenesis and development, cancer development and progression, mesenchymal stem cell lineage-specific differentiation, and metabolic diseases. We discussed the potential regulatory mechanisms underlying H19's functions in those processes although more in-depth studies are warranted to delineate the exact molecular, cellular, epigenetic, and genomic regulatory mechanisms underlying the physiological and pathological roles of H19. Ultimately, these lines of investigation may lead to the development of novel therapeutics for human diseases by exploiting H19 functions.
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Affiliation(s)
- Junyi Liao
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Bowen Chen
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Zhenglin Zhu
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Chengcheng Du
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Shengqiang Gao
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Guozhi Zhao
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Piao Zhao
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Yonghui Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Clinical Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
| | - Annie Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Zander Schwartz
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- School of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Lily Song
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jeffrey Hong
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- The Medical Scientist Training Program, The University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jiaming Fan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, Department of Clinical Biochemistry, The School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Russell R. Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Laboratory of Craniofacial Suture Biology and Development, Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Laboratory of Craniofacial Suture Biology and Development, Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Lewis Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Ning Hu
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Wei Huang
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
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11
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Zhao Z, Chen Y, Cheng X, Huang L, Wen H, Xu Q, Zhou X, Zhang X, Chen J, Ni T. The landscape of cryptic antisense transcription in human cancers reveals an oncogenic noncoding RNA in lung cancer. SCIENCE ADVANCES 2023; 9:eadf3264. [PMID: 37018400 PMCID: PMC10075970 DOI: 10.1126/sciadv.adf3264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Cryptic transcription initiation has been previously linked to activation of oncogenic transcripts. However, the prevalence and impact of cryptic antisense transcription from the opposite strand of protein-coding genes were mostly unknown in cancer. Applying a robust computational pipeline to publicly available transcriptome and epigenome datasets, we identified hundreds of previously unannotated cryptic antisense polyadenylated transcripts (CAPTs) that were enriched in tumor samples. We showed that the activation of cryptic antisense transcription was associated with increased chromatin accessibility and active histone marks. Accordingly, we found that many of the antisense transcripts were inducible by treatment of epigenetic drugs. Moreover, CRISPR-mediated epigenetic editing assays revealed that transcription of a noncoding RNA LRRK1-CAPT promoted LUSC cell proliferation, suggesting its oncogenic role. Our findings largely expand our understanding of cancer-associated transcription events, which may facilitate the development of novel strategies for cancer diagnosis and treatment.
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Affiliation(s)
- Zhaozhao Zhao
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu Chen
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaomeng Cheng
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Leihuan Huang
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haimei Wen
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiushi Xu
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaolan Zhou
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoyang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jing Chen
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
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12
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Chen F, Li X, Feng X, Gao T, Zhang W, Cheng Z, Zhao X, Chen R, Lu X. Long Noncoding RNA Lx8-SINE B2 Interacts with Eno1 to Regulate Self-Renewal and Metabolism of Embryonic Stem Cells. Stem Cells 2022; 40:1094-1106. [PMID: 36087098 DOI: 10.1093/stmcls/sxac067] [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: 04/06/2022] [Accepted: 08/30/2022] [Indexed: 01/04/2023]
Abstract
Long noncoding RNAs (lncRNAs) emerge as important orchestrators of biological processes in embryonic stem cells (ESCs). LncRNA Lx8-SINE B2 was recently identified as an ESC-specific lncRNA that marks pluripotency. Here, we studied the function of lncRNA Lx8-SINE B2 in ESCs. Depletion of Lx8-SINE B2 disrupted ESC proliferation, repressed the expression of pluripotency genes, activated differentiation genes, and inhibited reprogramming to induced pluripotent stem cells. The reduction of the colony formation ability of ESCs upon Lx8-SINE B2 knockdown was accompanied by the elongation of the G1 phase and the shortening of the S phase. Transcriptome analysis revealed that Lx8-SINE B2 deficiency affected multiple metabolic pathways, particularly glycolysis. Mechanistically, Lx8-SINE B2 functions as a cytoplasmic lncRNA and interacts with the glycolytic enzyme Eno1 as shown by RNA pull-down and RNA localization analysis. Lx8-SINE B2 and Eno1 interact with and regulate each other's expression, hence promoting the expression of metabolic genes and influencing glycolysis. In conclusion, we have identified lncRNA Lx8-SINE B2 as a novel regulator of ESC proliferation, cell cycle, and metabolism through working with Eno1.
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Affiliation(s)
- Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Xiaomin Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Xiao Feng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Tingting Gao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Zhi Cheng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Xuan Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Ruiqing Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China
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13
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Temporal regulation of head-on transcription at replication initiation sites. iScience 2022; 26:105791. [PMID: 36594032 PMCID: PMC9803852 DOI: 10.1016/j.isci.2022.105791] [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: 04/28/2022] [Revised: 09/14/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022] Open
Abstract
Head-on (HO) collisions between the DNA replication machinery and RNA polymerase over R-loop forming sequences (RLFS) are genotoxic, leading to replication fork blockage and DNA breaks. Current models suggest that HO collisions are avoided through replication initiation site (RIS) positioning upstream of active genes, ensuring co-orientation of replication fork movement and genic transcription. However, this model does not account for pervasive transcription, or intragenic RIS. Moreover, pervasive transcription initiation and CG-rich DNA is a feature of RIS, suggesting that HO transcription units (HO TUs) capable of forming R-loops might occur. Through mining phased GRO-seq data, and developing an informatics strategy to stringently identify RIS, we demonstrate that HO TUs containing RLFS occur at RIS in MCF-7 cells, and are downregulated at the G1/S phase boundary. Our analysis reveals a novel spatiotemporal relationship between transcription and replication, and supports the idea that HO collisions are avoided through transcriptional regulatory mechanisms.
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14
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Multi-Omics Approaches in Colorectal Cancer Screening and Diagnosis, Recent Updates and Future Perspectives. Cancers (Basel) 2022; 14:cancers14225545. [PMID: 36428637 PMCID: PMC9688479 DOI: 10.3390/cancers14225545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/15/2022] Open
Abstract
Colorectal cancer (CRC) is common Cancer as well as the third leading cause of mortality around the world; its exact molecular mechanism remains elusive. Although CRC risk is significantly correlated with genetic factors, the pathophysiology of CRC is also influenced by external and internal exposures and their interactions with genetic factors. The field of CRC research has recently benefited from significant advances through Omics technologies for screening biomarkers, including genes, transcripts, proteins, metabolites, microbiome, and lipidome unbiasedly. A promising application of omics technologies could enable new biomarkers to be found for the screening and diagnosis of CRC. Single-omics technologies cannot fully understand the molecular mechanisms of CRC. Therefore, this review article aims to summarize the multi-omics studies of Colorectal cancer, including genomics, transcriptomics, proteomics, microbiomics, metabolomics, and lipidomics that may shed new light on the discovery of novel biomarkers. It can contribute to identifying and validating new CRC biomarkers and better understanding colorectal carcinogenesis. Discovering biomarkers through multi-omics technologies could be difficult but valuable for disease genotyping and phenotyping. That can provide a better knowledge of CRC prognosis, diagnosis, and treatments.
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15
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Wu AC, Vivori C, Patel H, Sideri T, Moretto F, van Werven FJ. RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription. Life Sci Alliance 2022; 5:e202201394. [PMID: 36114005 PMCID: PMC9481977 DOI: 10.26508/lsa.202201394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
The directionality of gene promoters-the ratio of protein-coding over divergent noncoding transcription-is highly variable. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription relative to protein-coding transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus to a decrease in promoter directionality. We find that RSC has a modest effect on nucleosome positioning upstream in promoters at the sites of divergent transcription. These promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 DNA-binding protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription relative to coding direction transcription. We propose that any DNA-binding factor, when stably associated with cryptic transcription start sites, forms a barrier which represses divergent transcription, thereby promoting promoter directionality.
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Affiliation(s)
- Andrew Ck Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Vivori
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Theodora Sideri
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
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Construction and analysis of a ceRNA network and patterns of immune infiltration in chronic rhinosinusitis with nasal polyps: based on data mining and experimental verification. Sci Rep 2022; 12:9735. [PMID: 35697826 PMCID: PMC9192587 DOI: 10.1038/s41598-022-13818-6] [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: 01/19/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
Recent studies have revealed the significant role of the competing endogenous RNA (ceRNA) network in human diseases. However, systematic analysis of the ceRNA mechanism in chronic rhinosinusitis with nasal polyps (CRSwNP) is limited. In this study, we constructed a competitive endogenous RNA (ceRNA) network and identified a potential regulatory axis in CRSwNP based on bioinformatics analysis and experimental verification. We obtained lncRNA, miRNA, and mRNA expression profiles from the Gene Expression Omnibus. After analysis of CRSwNP patients and the control groups, we identified 565 DE-lncRNAs, 23 DE-miRNAs, and 1799 DE-mRNAs by the DESeq2 R package or limma R package. Enrichment analysis of 1799 DE-mRNAs showed that CRSwNP was associated with inflammation and immunity. Moreover, we identified 21 lncRNAs, 8 miRNAs and 8 mRNAs to construct the lncRNA-miRNA-mRNA ceRNA network. A potential MIAT/miR-125a/IRF4 axis was determined according to the degree and positive correlation between a lncRNA and its competitive endogenous mRNAs. The GSEA results suggested that IRF4 may be involved in immune cell infiltration. The validation of another dataset confirmed that MIAT and IRF4 were differentially expressed between the CRSwNP and control groups. The area under the ROC curve (AUC) of MIAT and IRF4 was 0.944. The CIBERSORT analysis revealed that eosinophils and M2 macrophages may be involved in the CRSwNP process. MIAT was correlated with dendritic cells and M2 macrophages, and IRF4 was correlated with dendritic cells. Finally, to validate the key genes, we performed in-silico validation using another dataset and experimental validation using immunohistochemistry, immunofluorescence, and Western blot. In summary, the constructed novel MIAT/miR-125a/IRF4 axis may play a critical role in the development and progression of CRSwNP. We believe that the ceRNA network and immune cell infiltration could offer further insight into novel molecular therapeutic targets for CRSwNP.
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17
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Guintini L, Paillé A, Graf M, Luke B, Wellinger RJ, Conconi A. Transcription of ncRNAs promotes repair of UV induced DNA lesions in Saccharomyces cerevisiae subtelomeres. PLoS Genet 2022; 18:e1010167. [PMID: 35486666 PMCID: PMC9106180 DOI: 10.1371/journal.pgen.1010167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 05/13/2022] [Accepted: 03/25/2022] [Indexed: 11/19/2022] Open
Abstract
Ultraviolet light causes DNA lesions that are removed by nucleotide excision repair (NER). The efficiency of NER is conditional to transcription and chromatin structure. UV induced photoproducts are repaired faster in the gene transcribed strands than in the non-transcribed strands or in transcriptionally inactive regions of the genome. This specificity of NER is known as transcription-coupled repair (TCR). The discovery of pervasive non-coding RNA transcription (ncRNA) advocates for ubiquitous contribution of TCR to the repair of UV photoproducts, beyond the repair of active gene-transcribed strands. Chromatin rules transcription, and telomeres form a complex structure of proteins that silences nearby engineered ectopic genes. The essential protective function of telomeres also includes preventing unwanted repair of double-strand breaks. Thus, telomeres were thought to be transcriptionally inert, but more recently, ncRNA transcription was found to initiate in subtelomeric regions. On the other hand, induced DNA lesions like the UV photoproducts must be recognized and repaired also at the ends of chromosomes. In this study, repair of UV induced DNA lesions was analyzed in the subtelomeric regions of budding yeast. The T4-endonuclease V nicking-activity at cyclobutene pyrimidine dimer (CPD) sites was exploited to monitor CPD formation and repair. The presence of two photoproducts, CPDs and pyrimidine (6,4)-pyrimidones (6-4PPs), was verified by the effective and precise blockage of Taq DNA polymerase at these sites. The results indicate that UV photoproducts in silenced heterochromatin are slowly repaired, but that ncRNA transcription enhances NER throughout one subtelomeric element, called Y’, and in distinct short segments of the second, more conserved element, called X. Therefore, ncRNA-transcription dependent TCR assists global genome repair to remove CPDs and 6-4PPs from subtelomeric DNA. Our skin is constantly exposed to sunlight and the ultraviolet component of it can severely damage the DNA of our chromosomes. If that damage is not efficiently repaired, the cells’ physiology becomes deregulated and very often cancer ensues. The specific molecular mechanism that will remove this damage is called nucleotide excision repair or NER. NER is conserved from humans to yeast, and it is much more efficient on DNA that is transcribed into RNA. Here we report how NER acts at the very ends of the chromosomes, the telomeres. In particular, the results show that in this area of the chromosomes with very few genes and where transcription is kept very low, the remaining transcription of non-coding RNAs such as TERRAs still stimulates NER and therefore helps guarding the integrity of DNA. These findings therefore suggest that the spurious transcription of subtelomeric DNA has a very positive impact on DNA repair efficiency. Hence, in addition to the known functions of TERRA and other ncRNAs in telomere maintenance, their transcription per se can be viewed as a genome stabilizing function.
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Affiliation(s)
- Laetitia Guintini
- Department of Microbiology and Infectious Diseases at the Université de Sherbrooke, Sherbrooke, Canada
| | - Audrey Paillé
- Department of Microbiology and Infectious Diseases at the Université de Sherbrooke, Sherbrooke, Canada
| | - Marco Graf
- Institute for Developmental and Neurobiology (IDN) at the Johannes-Gutenberg-University, Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases at the Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (RJW); (AC)
| | - Antonio Conconi
- Department of Microbiology and Infectious Diseases at the Université de Sherbrooke, Sherbrooke, Canada
- * E-mail: (RJW); (AC)
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Shi ZE, Zhang MY, Liu JY, Zhang WD, Hu DM, Wang QX, Ji XL, Jiang YY, Qu YQ. Autophagy Induced by BCL2-Related ceRNA Network Participates in the Occurrence of COPD. Int J Chron Obstruct Pulmon Dis 2022; 17:791-808. [PMID: 35431545 PMCID: PMC9005473 DOI: 10.2147/copd.s347733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/28/2022] [Indexed: 12/13/2022] Open
Abstract
Purpose Chronic obstructive pulmonary disease (COPD) is a predominant cause of mortality worldwide. Autophagy, which depends on a lysosomal degradation pathway, plays an essential role in the occurrence of COPD. The aim of our study was to identify the potential function of autophagy and construct a BCL2-related competing endogenous RNA (ceRNA) network that induces autophagy in COPD. Methods Blood sample data from GSE31568, GSE24709, and GSE61741 were collected from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs in COPD and controls were identified via GEO2R. Transcription factors were obtained from FunRich. DIANA, miRDB, miRTarBase, and TargetScan were used to predict target genes of miRNAs. Autophagy genes were collected from the Human Autophagy Database (HADb). The GSE151052 dataset was used to identify autophagy-related differentially expressed genes in tissues. Functional enrichment and protein–protein interaction (PPI) network analyses were conducted via Metascape and the STRING network. Spearman correlation analysis was used to analyze the relationship between autophagy-related differentially expressed genes and lung function. The BCL2-related ceRNA network was modeled by Cytoscape. Results We obtained 41 differentially expressed miRNAs and 10 significantly different transcription factors. We identified 19 autophagy-related differentially expressed genes that were significantly different (P<0.05) in tissue samples. The most significant enrichment in Metascape was an autophagy item, which further confirmed autophagy participation in the occurrence of COPD. PPI network analysis found four genes (BCL2, BECN1, MAPK8, and ITPR1), among which BCL2 was correlated with both FEV1/FVC and FEV1 prediction. Finally, the BCL2-related ceRNA network was constructed to clarify the interaction of RNAs and occurrence of autophagy, including 18 miRNAs and 65 lncRNAs. Conclusion We identified 19 autophagy-related differentially expressed genes that participated in COPD; among them, BCL2 was correlated with lung function, and a BCL2-related ceRNA network was constructed, which further revealed the potential mechanism of autophagy involvement in COPD.
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Affiliation(s)
- Zhuang-E Shi
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Meng-Yu Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Jian-Yu Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Wen-Di Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Dong-Mei Hu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Qing-Xiang Wang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Jinan Traditional Chinese Medicine Hospital, Jinan, People’s Republic of China
| | - Yuan-Yuan Jiang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China
- Correspondence: Yi-Qing Qu, Department of pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People’s Republic of China, Tel +86 531 8216 9335, Fax +86 531 8296 7544, Email
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19
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Liu X, Guo Z, Han J, Peng B, Zhang B, Li H, Hu X, David CJ, Chen M. The PAF1 complex promotes 3' processing of pervasive transcripts. Cell Rep 2022; 38:110519. [PMID: 35294889 DOI: 10.1016/j.celrep.2022.110519] [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] [Received: 08/24/2021] [Revised: 01/06/2022] [Accepted: 02/18/2022] [Indexed: 11/03/2022] Open
Abstract
The PAF1 complex (PAF1C) functions in multiple transcriptional processes involving RNA polymerase II (RNA Pol II). Enhancer RNAs (eRNAs) and promoter upstream transcripts (PROMPTs) are pervasive transcripts transcribed by RNA Pol II and degraded rapidly by the nuclear exosome complex after 3' endonucleolytic cleavage by the Integrator complex (Integrator). Here we show that PAF1C has a role in termination of eRNAs and PROMPTs that are cleaved 1-3 kb downstream of the transcription start site. Mechanistically, PAF1C facilitates recruitment of Integrator to sites of pervasive transcript cleavage, promoting timely cleavage and transcription termination. We also show that PAF1C recruits Integrator to coding genes, where PAF1C then dissociates from Integrator upon entry into processive elongation. Our results demonstrate a function of PAF1C in limiting the length and accumulation of pervasive transcripts that result from non-productive transcription.
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Affiliation(s)
- Xinhong Liu
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Ziwei Guo
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Jing Han
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Bo Peng
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Bin Zhang
- Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China; Institute for Immunology, Tsinghua University School of Medicine, Beijing 100084, China
| | - Haitao Li
- Tsinghua University School of Medicine, Beijing 100084, China; Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China; MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Xiaoyu Hu
- Tsinghua University School of Medicine, Beijing 100084, China; Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China; Institute for Immunology, Tsinghua University School of Medicine, Beijing 100084, China
| | - Charles J David
- Tsinghua University School of Medicine, Beijing 100084, China; Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China
| | - Mo Chen
- Tsinghua University School of Medicine, Beijing 100084, China.
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20
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Li J, Singh U, Bhandary P, Campbell J, Arendsee Z, Seetharam AS, Wurtele ES. Foster thy young: enhanced prediction of orphan genes in assembled genomes. Nucleic Acids Res 2021; 50:e37. [PMID: 34928390 PMCID: PMC9023268 DOI: 10.1093/nar/gkab1238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023] Open
Abstract
Proteins encoded by newly-emerged genes ('orphan genes') share no sequence similarity with proteins in any other species. They provide organisms with a reservoir of genetic elements to quickly respond to changing selection pressures. Here, we systematically assess the ability of five gene prediction pipelines to accurately predict genes in genomes according to phylostratal origin. BRAKER and MAKER are existing, popular ab initio tools that infer gene structures by machine learning. Direct Inference is an evidence-based pipeline we developed to predict gene structures from alignments of RNA-Seq data. The BIND pipeline integrates ab initio predictions of BRAKER and Direct inference; MIND combines Direct Inference and MAKER predictions. We use highly-curated Arabidopsis and yeast annotations as gold-standard benchmarks, and cross-validate in rice. Each pipeline under-predicts orphan genes (as few as 11 percent, under one prediction scenario). Increasing RNA-Seq diversity greatly improves prediction efficacy. The combined methods (BIND and MIND) yield best predictions overall, BIND identifying 68% of annotated orphan genes, 99% of ancient genes, and give the highest sensitivity score regardless dataset in Arabidopsis. We provide a light weight, flexible, reproducible, and well-documented solution to improve gene prediction.
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Affiliation(s)
- Jing Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA
| | - Urminder Singh
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Priyanka Bhandary
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Jacqueline Campbell
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agriculture Research Service, Ames, IA 50014, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA 50014, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
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21
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Choudhary C, Meghwanshi KK, Shukla N, Shukla JN. Innate and adaptive resistance to RNAi: a major challenge and hurdle to the development of double stranded RNA-based pesticides. 3 Biotech 2021; 11:498. [PMID: 34881161 PMCID: PMC8595431 DOI: 10.1007/s13205-021-03049-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/31/2021] [Indexed: 10/19/2022] Open
Abstract
RNA interference (RNAi) is a post-transcriptional gene silencing process where short interfering RNAs degrade targeted mRNA. Exploration of gene function through reverse genetics is the major achievement of RNAi discovery. Besides, RNAi can be used as a potential strategy for the control of insect pests. This has led to the idea of developing RNAi-based pesticides. Differential RNAi efficiency in the different insect orders is the biggest biological obstacle in developing RNAi-based pesticides. dsRNA stability, the sensitivity of core RNAi machinery, uptake of dsRNA and amplification and spreading of the RNAi signal are the key factors responsible for RNAi efficiency in insects. This review discusses the physiological and adaptive factors responsible for reduced RNAi in insects that pose a major challenge in developing dsRNA- based pesticides.
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Affiliation(s)
- Chhavi Choudhary
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Distt. Ajmer, Kishangarh, Rajasthan 305817 India
| | - Keshav Kumar Meghwanshi
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Distt. Ajmer, Kishangarh, Rajasthan 305817 India
| | - Nidhi Shukla
- Birla Institute of Scientific Research, Statue Circle, Prithviraj Rd, C-Scheme, Jaipur, Rajasthan 302001 India
| | - Jayendra Nath Shukla
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Distt. Ajmer, Kishangarh, Rajasthan 305817 India
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22
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Kugelberg U, Nätt D, Skog S, Kutter C, Öst A. 5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA. RNA Biol 2021; 18:1588-1599. [PMID: 33382953 PMCID: PMC8594926 DOI: 10.1080/15476286.2020.1861770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 12/21/2022] Open
Abstract
Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5´ nucleotide modifications, make many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that captures a more complete picture of sRNA. By tagging 5´P sRNA during library preparation, 5XP-seq combines an open approach that includes all types of 5'-terminal modifications (5´X), with a selective approach for 5-phosphorylated sRNA (5´P). We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to insect translation of several tRNA (tRFs) and rRNA (rRFs) fragments. By combining 5´ insensitive library strategies with 5´ sensitive tagging, we have successfully tackled an intrinsic bias in modern sRNA sequencing that will help us reveal the true complexity and the evolutionary significance of the sRNA world.
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Affiliation(s)
- Unn Kugelberg
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Daniel Nätt
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Signe Skog
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm
| | - Anita Öst
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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23
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Zhou J, Flores-Bellver M, Pan J, Benito-Martin A, Shi C, Onwumere O, Mighty J, Qian J, Zhong X, Hogue T, Amponsah-Antwi B, Einbond L, Gharbaran R, Wu H, Chen BJ, Zheng Z, Tchaikovskaya T, Zhang X, Peinado H, Canto-Soler MV, Redenti S. Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitor cells. Sci Rep 2021; 11:21128. [PMID: 34702879 PMCID: PMC8548301 DOI: 10.1038/s41598-021-00542-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/07/2021] [Indexed: 01/23/2023] Open
Abstract
The mechanisms underlying retinal development have not been completely elucidated. Extracellular vesicles (EVs) are novel essential mediators of cell-to-cell communication with emerging roles in developmental processes. Nevertheless, the identification of EVs in human retinal tissue, characterization of their cargo, and analysis of their potential role in retina development has not been accomplished. Three-dimensional retinal tissue derived from human induced pluripotent stem cells (hiPSC) provide an ideal developmental system to achieve this goal. Here we report that hiPSC-derived retinal organoids release exosomes and microvesicles with small noncoding RNA cargo. EV miRNA cargo-predicted targetome correlates with Gene Ontology (GO) pathways involved in mechanisms of retinogenesis relevant to specific developmental stages corresponding to hallmarks of native human retina development. Furthermore, uptake of EVs by human retinal progenitor cells leads to changes in gene expression correlated with EV miRNA cargo predicted gene targets, and mechanisms involved in retinal development, ganglion cell and photoreceptor differentiation and function.
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Affiliation(s)
- Jing Zhou
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Miguel Flores-Bellver
- CellSight Ocular Stem Cell and Regeneration Program, Department of Ophthalmology, Sue Anschutz- Rodgers Eye Center, University of Colorado, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Jianbo Pan
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Alberto Benito-Martin
- Departments of Pediatrics, Hematology/Oncology Division, Weill Medical College of Cornell University, 413 E. 69th St., New York, NY, 10021, USA
| | - Cui Shi
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | | | - Jason Mighty
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Xiufeng Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tasmim Hogue
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | | | - Linda Einbond
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | | | - Hao Wu
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Bo-Juen Chen
- New York Genome Center, New York, NY, 10013, USA
| | - Zhiliang Zheng
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | - Tatyana Tchaikovskaya
- Department of Medicine, Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xusheng Zhang
- Department of Medicine, Computational Genomics Core in Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hector Peinado
- Microenvironment and Metastasis Laboratory, Department of Molecular Oncology, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Maria Valeria Canto-Soler
- CellSight Ocular Stem Cell and Regeneration Program, Department of Ophthalmology, Sue Anschutz- Rodgers Eye Center, University of Colorado, 12800 East 19th Avenue, Aurora, CO, 80045, USA.
| | - Stephen Redenti
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA.
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA.
- Biochemistry Doctoral Program, The Graduate School, City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.
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24
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Naftaly AS, Pau S, White MA. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish. Genome Res 2021; 31:1486-1497. [PMID: 34131005 PMCID: PMC8327910 DOI: 10.1101/gr.274282.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
Alternate isoforms are important contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five organs in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly in which gene annotations are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq-predicted transcription start sites were more accurate and verified through ATAC-seq. We also detected many alternative splicing events between sexes and across organs. We found a substantial number of genes in both somatic and gonadal samples that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.
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Affiliation(s)
- Alice S Naftaly
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Shana Pau
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Biology, University of Texas Arlington, Arlington, Texas 76019, USA
| | - Michael A White
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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25
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Gu X, Ke S, Wang Q, Zhuang T, Xia C, Xu Y, Yang L, Zhou M. Energy metabolism in major depressive disorder: Recent advances from omics technologies and imaging. Biomed Pharmacother 2021; 141:111869. [PMID: 34225015 DOI: 10.1016/j.biopha.2021.111869] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/06/2021] [Accepted: 06/28/2021] [Indexed: 02/08/2023] Open
Abstract
Major depressive disorder (MDD) is a serious psychiatric disorder that associated with high rate of disability and increasing suicide rate, and the pathogenesis is still unclear. Many researches showed that the energy metabolism of patients with depression is impaired, which may be the direction of depression treatment. In this review, we focus on the "omics" technologies such as genomics, proteomics, transcriptomics and metabolomics, as well as imaging, and the progress on energy metabolism of MDD. These findings indicate that abnormal energy metabolism is one of the important mechanisms for the occurrence and development of depression. Although the research on various mechanisms of depression is still ongoing, the rapid development of new technologies and the joint use of various technologies will help to clarify the pathogenesis of depression and explore efficient diagnosis and treatment methods.
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Affiliation(s)
- Xinyi Gu
- Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shuang Ke
- Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qixue Wang
- Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Tongxi Zhuang
- Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Chenyi Xia
- Department of Physiology, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ying Xu
- Department of Physiology, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Li Yang
- Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mingmei Zhou
- Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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26
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Li J, Liu X, Yin Z, Hu Z, Zhang KQ. An Overview on Identification and Regulatory Mechanisms of Long Non-coding RNAs in Fungi. Front Microbiol 2021; 12:638617. [PMID: 33995298 PMCID: PMC8113380 DOI: 10.3389/fmicb.2021.638617] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
For decades, more and more long non-coding RNAs (lncRNAs) have been confirmed to play important functions in key biological processes of different organisms. At present, most identified lncRNAs and those with known functional roles are from mammalian systems. However, lncRNAs have also been found in primitive eukaryotic fungi, and they have different functions in fungal development, metabolism, and pathogenicity. In this review, we highlight some recent researches on lncRNAs in the primitive eukaryotic fungi, particularly focusing on the identification of lncRNAs and their regulatory roles in diverse biological processes.
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Affiliation(s)
- Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xiaoying Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ziyu Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zhihong Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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27
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Agostini F, Zagalak J, Attig J, Ule J, Luscombe NM. Intergenic RNA mainly derives from nascent transcripts of known genes. Genome Biol 2021; 22:136. [PMID: 33952325 PMCID: PMC8097831 DOI: 10.1186/s13059-021-02350-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Eukaryotic genomes undergo pervasive transcription, leading to the production of many types of stable and unstable RNAs. Transcription is not restricted to regions with annotated gene features but includes almost any genomic context. Currently, the source and function of most RNAs originating from intergenic regions in the human genome remain unclear. RESULTS We hypothesize that many intergenic RNAs can be ascribed to the presence of as-yet unannotated genes or the "fuzzy" transcription of known genes that extends beyond the annotated boundaries. To elucidate the contributions of these two sources, we assemble a dataset of more than 2.5 billion publicly available RNA-seq reads across 5 human cell lines and multiple cellular compartments to annotate transcriptional units in the human genome. About 80% of transcripts from unannotated intergenic regions can be attributed to the fuzzy transcription of existing genes; the remaining transcripts originate mainly from putative long non-coding RNA loci that are rarely spliced. We validate the transcriptional activity of these intergenic RNAs using independent measurements, including transcriptional start sites, chromatin signatures, and genomic occupancies of RNA polymerase II in various phosphorylation states. We also analyze the nuclear localization and sensitivities of intergenic transcripts to nucleases to illustrate that they tend to be rapidly degraded either on-chromatin by XRN2 or off-chromatin by the exosome. CONCLUSIONS We provide a curated atlas of intergenic RNAs that distinguishes between alternative processing of well-annotated genes from independent transcriptional units based on the combined analysis of chromatin signatures, nuclear RNA localization, and degradation pathways.
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Affiliation(s)
| | - Julian Zagalak
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Jan Attig
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, Gower Street, London, WC1E 6BT, UK
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
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28
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Wang S, Liang H, Xu Y, Li L, Wang H, Sahu DN, Petersen M, Melkonian M, Sahu SK, Liu H. Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes. Commun Biol 2021; 4:412. [PMID: 33767367 PMCID: PMC7994812 DOI: 10.1038/s42003-021-01933-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/24/2021] [Indexed: 11/09/2022] Open
Abstract
Small RNAs play a major role in the post-transcriptional regulation of gene expression in eukaryotes. Despite the evolutionary importance of streptophyte algae, knowledge on small RNAs in this group of green algae is almost non-existent. We used genome and transcriptome data of 34 algal and plant species, and performed genome-wide analyses of small RNA (miRNA & siRNA) biosynthetic and degradation pathways. The results suggest that Viridiplantae started to evolve plant-like miRNA biogenesis and degradation after the divergence of the Mesostigmatophyceae in the streptophyte algae. We identified two major evolutionary transitions in small RNA metabolism in streptophyte algae; during the first transition, the origin of DCL-New, DCL1, AGO1/5/10 and AGO4/6/9 in the last common ancestor of Klebsormidiophyceae and all other streptophytes could be linked to abiotic stress responses and evolution of multicellularity in streptophytes. During the second transition, the evolution of DCL 2,3,4, and AGO 2,3,7 as well as DRB1 in the last common ancestor of Zygnematophyceae and embryophytes, suggests their possible contribution to pathogen defense and antibacterial immunity. Overall, the origin and diversification of DICER and AGO along with several other small RNA pathway-related genes among streptophyte algae suggested progressive adaptations of streptophyte algae during evolution to a subaerial environment. Wang, Liang et al. conduct a genome-wide investigation into the origin of small RNA pathway-related genes in Viridiplantae. Their findings suggest that streptophyte algae progressively adapted to a subaerial environment through generation of these pathways.
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Affiliation(s)
- Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hongping Liang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Yan Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | | | - Morten Petersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael Melkonian
- Integrative Bioinformatics, Department Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. .,Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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29
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Supplitt S, Karpinski P, Sasiadek M, Laczmanska I. Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine. Int J Mol Sci 2021; 22:1422. [PMID: 33572595 PMCID: PMC7866970 DOI: 10.3390/ijms22031422] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Over the last decades, transcriptome profiling emerged as one of the most powerful approaches in oncology, providing prognostic and predictive utility for cancer management. The development of novel technologies, such as revolutionary next-generation sequencing, enables the identification of cancer biomarkers, gene signatures, and their aberrant expression affecting oncogenesis, as well as the discovery of molecular targets for anticancer therapies. Transcriptomics contribute to a change in the holistic understanding of cancer, from histopathological and organic to molecular classifications, opening a more personalized perspective for tumor diagnostics and therapy. The further advancement on transcriptome profiling may allow standardization and cost reduction of its analysis, which will be the next step for transcriptomics to become a canon of contemporary cancer medicine.
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Affiliation(s)
- Stanislaw Supplitt
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
| | - Pawel Karpinski
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
- Laboratory of Genomics and Bioinformatics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Maria Sasiadek
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
| | - Izabela Laczmanska
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
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30
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Laneuville O, Rocheleau L, Chan Chun Kong D, Pelchat M, Trudel G. Effect of rehabilitation on biologic and transcriptomic responses after hospital-acquired deconditioning: a prospective longitudinal feasibility study. Disabil Rehabil 2021; 44:3623-3631. [PMID: 33478276 DOI: 10.1080/09638288.2021.1875507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE The objective of this study is to explore the transcriptomic and biologic variables characterizing the longitudinal rehabilitation intervention of patients with hospital-acquired deconditioning (HAD). METHODS This prospective clinical trial recruited HAD patients (n = 10) who spent ≥3 weeks hospitalized and then received inpatient rehabilitation. Functional improvement was measured using the Functional Independence Measure (FIM). Transcriptomic and biological variables were recorded at rehabilitation admission and 1, 2, 4, and 6 weeks post-admission. RNA sequencing studied the temporal changes of gene expression in leukocytes. Between-subject transcriptome comparisons were performed using principle component analysis. Within-subject changes in gene expression were analyzed using a gene ontology hierarchical clustering to identify common biological terms. Heart rate, weight, albumin, creatinine, and complete blood counts were analyzed. RESULTS Patients average age was 50.6 ± 7.2, FIM increased during inpatient rehabilitation (p = 0.01), weight increased (p = 0.01), lymphocytes decreased (p = 0.05), neutrophil increased (0.03) and red cell distribution width decreased (p = 0.05). The temporal profiles of gene expression revealed within-patient homogeneity and between-patients heterogeneity. The biological terms "bone morphogenesis" and "muscle cell development" were the most significantly enriched differentially expressed genes. CONCLUSION Transcriptomic and biologic markers paralleled the functional improvements of HAD patients during inpatient rehabilitation. Transcriptomic analyses were consistent with the cohort heterogeneity. Enrichment of the biological pathways bone morphogenesis and muscle cell development constituted evidence at the gene expression level of the effect of rehabilitation. Larger studies of various rehabilitation patient groups may increase gene expression profile homogeneity. Objective transcriptomic and biologic markers have the potential to improve the rehabilitation of HAD patients.IMPLICATIONS FOR REHABILITATIONNovel gene expression methods are increasingly being integrated into clinical practice and may apply to rehabilitation.Patients with hospital-acquired deconditioning (HAD) enriched gene expression of pathways targeted by inpatient rehabilitation such as bone morphogenesis and muscle cell development.The gene expression paralleled functional improvement of HAD patients.These data demonstrated the feasibility of molecular methods to identify markers of rehabilitation success in HAD patients.
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Affiliation(s)
- Odette Laneuville
- Bone and Joint Research Laboratory, University of Ottawa, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Lynda Rocheleau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | | | - Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Guy Trudel
- Bone and Joint Research Laboratory, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Division of Physical Medicine and Rehabilitation, Department of Medicine, The Ottawa Hospital Research Institute, Ottawa, ON, Canada
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31
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Brex D, Barbagallo C, Mirabella F, Caponnetto A, Battaglia R, Barbagallo D, Caltabiano R, Broggi G, Memeo L, Di Pietro C, Purrello M, Ragusa M. LINC00483 Has a Potential Tumor-Suppressor Role in Colorectal Cancer Through Multiple Molecular Axes. Front Oncol 2021; 10:614455. [PMID: 33552987 PMCID: PMC7855711 DOI: 10.3389/fonc.2020.614455] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/04/2020] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are the most heterogeneous class of non-protein-coding RNAs involved in a broad spectrum of molecular mechanisms controlling genome function, including the generation of complex networks of RNA-RNA competitive interactions. Accordingly, their dysregulation contributes to the onset of many tumors, including colorectal cancer (CRC). Through a combination of in silico approaches (statistical screening of expression datasets) and in vitro analyses (enforced expression, artificial inhibition, or activation of pathways), we identified LINC00483 as a potential tumor suppressor lncRNA in CRC. LINC00483 was downregulated in CRC biopsies and metastases and its decreased levels were associated with severe clinical features. Inhibition of the MAPK pathway and cell cycle arrest by starvation induced an upregulation of LINC00483, while the epithelial to mesenchymal transition activation by TGFβ-1 and IL-6 caused its down-modulation. Moreover, enforced expression of LINC00483 provoked a slowing down of cell migration rate without affecting cell proliferation. Since LINC00483 was predominantly cytoplasmic, we hypothesized a “miRNA sponge” role for it. Accordingly, we computationally reconstructed the LINC00483/miRNA/mRNA axes and evaluated the expression of mRNAs in different experimental conditions inducing LINC00483 alteration. By this approach, we identified a set of mRNAs sharing the miRNA response elements with LINC00483 and modulated in accordance with it. Moreover, we found that LINC00483 is potentially under negative control of transcription factor HNF4α. In conclusion, we propose that LINC00483 is a tumor suppressor in CRC that, through an RNA-RNA network, may control cell migration and participate in proliferation signaling.
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Affiliation(s)
- Duilia Brex
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Federica Mirabella
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Rosario Caltabiano
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, Catania, Italy
| | - Giuseppe Broggi
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, Catania, Italy
| | - Lorenzo Memeo
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), Catania, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences - Section of Biology and Genetics "Giovanni Sichel," University of Catania, Catania, Italy
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Abstract
The discovery of new classes of non-coding RNAs has always been preceded or accompanied by technological breakthroughs, and these outstanding progresses in transcriptomics approaches enabled to regularly add new members to the list. From the first detection of tRNAs, through the revolution of miRNAs discovery, to the recent identification of eRNAs or the identification of new functions for already known ncRNAs, this introductive review provides a very concise historical and functional overview of most prominent small regulatory non-coding RNA families.
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Affiliation(s)
| | - Yoann Abel
- IGMM, CNRS, Université de Montpellier, Montpellier, France
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Wang S, Zhu W, Qiu J, Chen F. lncRNA SNHG4 promotes cell proliferation, migration, invasion and the epithelial-mesenchymal transition process via sponging miR-204-5p in gastric cancer. Mol Med Rep 2020; 23:85. [PMID: 33236157 PMCID: PMC7716413 DOI: 10.3892/mmr.2020.11724] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Long non-coding (lnc)RNAs and microRNAs (miRNAs/miRs) have physiological and pathological functions in various diseases, including gastric cancer (GC). The current study explored the association between lncRNA small nucleolar RNA host gene 4 (SNHG4) and miR-148a-3p, and their functions in GC cells. SNHG4 expression and overall survival data were analyzed using bioinformatics, and the interaction of SNHG4 and miR-148a-3p was predicted using starBase and confirmed via a dual-luciferase reporter assay. Cell viability, colony formation ability and apoptosis rate were detected using Cell Counting Kit-8, colony formation and flow cytometry assays, respectively. Cell migration and invasion were determined via wound-healing and Transwell assays. mRNA and protein expression levels were determined via reverse transcription-quantitative PCR and western blotting. The results demonstrated that in GC tissues and cell lines, SNHG4 was highly expressed, while miR-204-5p expression was decreased, and that the expression levels of SNHG4 and miR-204-5p were negatively correlated. The downregulated expression of SNHG4 decreased the effects of miR-204-5p inhibitor on promoting cell proliferation, migration, invasion and epithelial-mesenchymal transition, but enhanced the inhibitory effect of miR-204-5p on GC cell apoptosis. The findings of the current study revealed the potential mechanism of the SNHG4-miR-204-5p pathway in GC, which may be conducive to the development of novel drugs against GC growth.
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Affiliation(s)
- Shimei Wang
- Department of Gastroenterology, Zhuji People's Hospital of Zhejiang Province, Shaoxing, Zhejiang 311800, P.R. China
| | - Wei Zhu
- Department of General Surgery, Zhuji Central Hospital, Shaoxing, Zhejiang 311800, P.R. China
| | - Ji Qiu
- Department of Gastroenterology, Zhuji People's Hospital of Zhejiang Province, Shaoxing, Zhejiang 311800, P.R. China
| | - Fei Chen
- Department of Gastroenterology, Zhuji People's Hospital of Zhejiang Province, Shaoxing, Zhejiang 311800, P.R. China
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Liu W, Liu Y, Pan Z, Zhang X, Qin Y, Chen X, Li M, Chen X, Zheng Q, Liu X, Li D. Systematic Analysis of tRNA-Derived Small RNAs Discloses New Therapeutic Targets of Caloric Restriction in Myocardial Ischemic Rats. Front Cell Dev Biol 2020; 8:568116. [PMID: 33224944 PMCID: PMC7670042 DOI: 10.3389/fcell.2020.568116] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
Caloric restriction (CR) is a novel dietary therapy that has a protective effect on myocardial ischemia. However, the mechanisms underlying the therapeutic effect of CR remain unclear. Transfer RNA-derived small RNAs (tsRNAs) are a novel type of short non-coding RNAs that have potential regulatory functions in various physiological and pathological processes. In this study, we explored new therapeutic targets of CR through tsRNA sequencing. Rats were randomly divided into three groups: a normal control group (norm group), isoproterenol (ISO)-induced myocardial ischemic group (MI group), and CR pretreatment plus ISO-induced myocardial ischemic group (CR + MI group). Triphenyl tetrazolium chloride staining, terminal deoxynucleotidyl transferase dUTP nick-end labeling staining, serum creatine kinase (CK) and lactic acid dehydrogenase activity detection kits, and creatine kinase isoenzyme 1 levels were used to measure the degree of myocardial ischemic injury. These indicators of myocardial ischemia were significantly improved in the CR + MI group compared with those in the MI group. In the ischemic myocardial tissue of the MI group, a total of 708 precisely matched tsRNAs were identified, and 302 tsRNAs (fold change >1.5, P < 0.05) were significantly changed when compared with those in the norm group. Furthermore, 55 tsRNAs were significantly regulated by CR pretreatment, among which five tsRNAs (tiRNA-His-GTG-004, tRF-Gly-TCC-018, tRF-Cys-GCA-022, tRF-Lys-CTT-026, tRF-Met-CAT-008) were randomly selected and verified by quantitative real-time polymerase chain reaction. In addition, predictions of target genes and bioinformatics analysis indicated that these tsRNAs may play a therapeutic role through the regulation of macromolecular metabolism. In conclusion, our findings reveal that tsRNAs are potential therapeutic targets for CR pre-pretreatment to improve myocardial ischemic injury. This study provides new ideas for future research on elucidating the mechanisms of CR pretreatment in ameliorating myocardial ischemic injury.
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Affiliation(s)
- Wenjing Liu
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Yang Liu
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhaohai Pan
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Xin Zhang
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Yao Qin
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Xiaojie Chen
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Minjing Li
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Xiaoyu Chen
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Qiusheng Zheng
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China.,Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Ministry of Education, School of Pharmacy, Shihezi University, Shihezi, China
| | - Xiaona Liu
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Defang Li
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
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35
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The Multi-Omics Architecture of Juvenile Idiopathic Arthritis. Cells 2020; 9:cells9102301. [PMID: 33076506 PMCID: PMC7602566 DOI: 10.3390/cells9102301] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/30/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
Juvenile idiopathic arthritis (JIA) is highly heterogeneous in terms of etiology and clinical presentation with ambiguity in JIA classification. The advance of high-throughput omics technologies in recent years has gained us significant knowledge about the molecular mechanisms of JIA. Besides a minor proportion of JIA cases as monogenic, most JIA cases are polygenic disease caused by autoimmune mechanisms. A number of HLA alleles (including both HLA class I and class II genes), and 23 non-HLA genetic loci have been identified of association with different JIA subtypes. Omics technologies, i.e., transcriptome profiling and epigenomic analysis, contributed significant knowledge on the molecular mechanisms of JIA in addition to the genetic approach. New molecular knowledge on different JIA subtypes enables us to reconsider the JIA classification, but also highlights novel therapeutic targets to develop a cure for the devastating JIA.
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36
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Villagra C, Frías-Lasserre D. Epigenetic Molecular Mechanisms in Insects. NEOTROPICAL ENTOMOLOGY 2020; 49:615-642. [PMID: 32514997 DOI: 10.1007/s13744-020-00777-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.
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Affiliation(s)
- C Villagra
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile.
| | - D Frías-Lasserre
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile
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37
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Ni WJ, Xie F, Leng XM. Terminus-Associated Non-coding RNAs: Trash or Treasure? Front Genet 2020; 11:552444. [PMID: 33101379 PMCID: PMC7522407 DOI: 10.3389/fgene.2020.552444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
3′ untranslated regions (3′ UTRs) of protein-coding genes are well known for their important roles in determining the fate of mRNAs in diverse processes, including trafficking, stabilization, translation, and RNA–protein interactions. However, non-coding RNAs (ncRNAs) scattered around 3′ termini of the protein-coding genes, here referred to as terminus-associated non-coding RNAs (TANRs), have not attracted wide attention in RNA research. Indeed, whether TANRs are transcriptional noise, degraded mRNA products, alternative 3′ UTRs, or functional molecules has remained unclear for a long time. As a new category of ncRNAs, TANRs are widespread, abundant, and conserved in diverse eukaryotes. The biogenesis of TANRs mainly follows the same promoter model, the RNA-dependent RNA polymerase activity-dependent model, or the independent promoter model. Functional studies of TANRs suggested that they are significantly involved in the versatile regulation of gene expression. For instance, at the transcriptional level, they can lead to transcriptional interference, induce the formation of gene loops, and participate in transcriptional termination. Furthermore, at the posttranscriptional level, they can act as microRNA sponges, and guide cleavage or modification of target RNAs. Here, we review current knowledge of the potential role of TANRs in the modulation of gene expression. In this review, we comprehensively summarize the current state of knowledge about TANRs, and discuss TANR nomenclature, relation to ncRNAs, cross-talk biogenesis pathways and potential functions. We further outline directions of future studies of TANRs, to promote investigations of this emerging and enigmatic category of RNA.
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Affiliation(s)
- Wen-Juan Ni
- School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Fuhua Xie
- School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Xiao-Min Leng
- School of Basic Medicine, Gannan Medical University, Ganzhou, China
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38
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Razgonova MP, Zakharenko AM, Golokhvast KS, Thanasoula M, Sarandi E, Nikolouzakis K, Fragkiadaki P, Tsoukalas D, Spandidos DA, Tsatsakis A. Telomerase and telomeres in aging theory and chronographic aging theory (Review). Mol Med Rep 2020; 22:1679-1694. [PMID: 32705188 PMCID: PMC7411297 DOI: 10.3892/mmr.2020.11274] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/24/2020] [Indexed: 01/03/2023] Open
Abstract
The current review focuses on the connection of telomerase and telomeres with aging. In this review, we describe the changes in telomerase and telomere length (TEL) during development, their role in carcinogenesis processes, and the consequences of reduced telomerase activity. More specifically, the connection of TEL in peripheral blood cells with the development of aging‑associated diseases is discussed. The review provides systematic data on the role of telomerase in mitochondria, the biology of telomeres in stem cells, as well as the consequences of the forced expression of telomerase (telomerization) in human cells. Additionally, it presents the effects of chronic stress exposure on telomerase activity, the effect of TEL on fertility, and the effect of nutraceutical supplements on TEL. Finally, a comparative review of the chronographic theory of aging, presented by Olovnikov is provided based on currently available scientific research on telomere, telomerase activity, and the nature of aging by multicellular organisms.
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Affiliation(s)
- Mayya P. Razgonova
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 Saint-Petersburg, Russia
- Far Eastern Federal University, 690950 Vladivostok, Russia
| | - Alexander M. Zakharenko
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 Saint-Petersburg, Russia
- Far Eastern Federal University, 690950 Vladivostok, Russia
| | - Kirill S. Golokhvast
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 Saint-Petersburg, Russia
- Far Eastern Federal University, 690950 Vladivostok, Russia
- Pacific Geographical Institute, Far Eastern Branch of The Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Maria Thanasoula
- Metabolomic Μedicine, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece
| | - Evangelia Sarandi
- Metabolomic Μedicine, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece
| | | | - Persefoni Fragkiadaki
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece
- Spin-Off Toxplus S.A., 71601 Heraklion, Greece
| | - Dimitris Tsoukalas
- Metabolomic Μedicine, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion 71003, Greece
| | - Aristidis Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece
- Spin-Off Toxplus S.A., 71601 Heraklion, Greece
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LncRNA RP11-86H7.1 promotes airway inflammation induced by TRAPM2.5 by acting as a ceRNA of miRNA-9-5p to regulate NFKB1 in HBECS. Sci Rep 2020; 10:11587. [PMID: 32665564 PMCID: PMC7360621 DOI: 10.1038/s41598-020-68327-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/19/2020] [Indexed: 01/21/2023] Open
Abstract
Traffic-related air pollution particulate matter 2.5 (TRAPM2.5), is involved in chronic obstructive pulmonary disease (COPD), which is characterized by airway inflammation. Specifically, these harmful particles or gases can increase chronic airway inflammation. Some recent studies have shown that lncRNAs are closely related to COPD and participate in the regulation of airway inflammation. However, the precise mechanisms remain unknown. In the present study, we investigated the effect of TRAPM2.5 on airway inflammation in human bronchial epithelial cells (HBECs) and the underlying mechanisms mediated by a lncRNA. After exposure to TRAPM2.5, the novel lncRNA RP11-86H7.1 was markedly upregulated in HBECs. Functional assays indicated that the lncRNA RP11-86H7.1 was required for the TRAPM2.5-induced expression of inflammatory factors in HBECs. A mechanistic study demonstrated that lncRNA RP11-86H7.1 might participate in TRAPM2.5-induced inflammatory responses by activating the NF-κB signaling pathway. Moreover, the lncRNA RP11-86H7.1 can promote the inflammatory response by acting as a competing endogenous RNA of miR-9-5p, reversing the inhibitory effect of its target gene NFKB1, and sustaining NF-κB activation. In summary, our study elucidates the pro-inflammatory roles of the lncRNA RP11-86H7.1–miR-9-5p–NFKB1 regulatory network in airway inflammation induced by TRAPM2.5 and indicates that the components of this network might serve as novel diagnostic biomarkers and potential therapeutic targets.
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Small Interfering RNAs and RNA Therapeutics in Cardiovascular Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:369-381. [PMID: 32285425 DOI: 10.1007/978-981-15-1671-9_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribonucleic acid (RNA) is being exploited and understood in its many aspects of function and structure for development of valuable tools in the therapeutics of various diseases such as cardiovascular etc. The expanded knowledge regarding function of RNA in the genomics and inside the cell has dramatically changed the therapeutic strategies in the past few years. RNA has become a spotlight of attention for developing novel therapeutic schemes and hence variety of therapeutic strategies is being coming into the picture that includes RNA interference, use of aptamers, role of microRNA (miRNA) that can alter the complex gene expression patterns. It is due to the fact that RNA offers various advantages in disease management as it can be edited and modified in its various forms such as secondary and tertiary structures. Although scientists are in process of manufacturing RNA-targeting therapies using variety of endogenous gene silencing regulators, Small interfering RNAs (Si RNAs), aptamers and microRNA for cardiovascular diseases yet the development of a novel, risk free therapeutic strategy is a major challenge and need of the hour in cardiovascular medicine. In this regard these agents are required to overcome pleothra of barriers such as stability of drug targets, immunogenicity, adequate binding, targeted delivery etc. to become effective drugs. Recent years have witnessed the progress of RNA therapeutic strategies in cardiovascular diseases that are likely to significantly expand the cardiovascular therapeutic repertoire within the next decade. The present manuscript has been compiled to summarize various approaches of siRNA based therapies in cardiovascular diseases along with the advantages, outcomes and limitations if any in this regard. In addition, the future prospects of RNA therapeutic modalities in cardiovascular diseases are summarized.
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Pollak AJ, Hickman JH, Liang XH, Crooke ST. Gapmer Antisense Oligonucleotides Targeting 5S Ribosomal RNA Can Reduce Mature 5S Ribosomal RNA by Two Mechanisms. Nucleic Acid Ther 2020; 30:312-324. [PMID: 32589504 DOI: 10.1089/nat.2020.0864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this study, we demonstrate that 5S ribosomal RNA (rRNA), a highly structured and protein-bound RNA, is quite difficult to reduce with antisense oligonucleotides (ASOs). However, we found a single accessible site that was targetable with a high-affinity complementary ASO. The ASO appeared to bind to the site, recruit RNaseH1, and cause degradation of the 5S RNA. Intriguingly, we also observed that the same ASO induced an accumulation of pre-5S RNA, which may contribute to reduced levels of mature 5S rRNA. As expected, ASO mediated reduction of 5S RNA, and modest inhibition of processing of pre-5S RNA resulted in nucleolar toxicity. However, the toxicity induced was minimal compared with actinomycin D, consistent with its modest effects on pre-5S rRNA. Mechanistically, we show that the accumulation of pre-5S rRNA required ASO hybridization to the cognate rRNA sequence but was independent of RNaseH1 activity. We found that Ro60 and La, proteins known to bind misprocessed RNAs, likely sequester the ASO-pre-5S rRNA species and block RNaseH1 activity, thus identifying another example of competitive mechanisms mediated by proteins that compete with RNaseH1 for binding to ASO-RNA heteroduplexes.
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Affiliation(s)
- Adam J Pollak
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Justin H Hickman
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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Chen C, Huang Z, Mo X, Song Y, Li X, Li X, Zhang M. The circular RNA 001971/miR-29c-3p axis modulates colorectal cancer growth, metastasis, and angiogenesis through VEGFA. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:91. [PMID: 32430042 PMCID: PMC7236474 DOI: 10.1186/s13046-020-01594-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/08/2020] [Indexed: 02/06/2023]
Abstract
Background Colorectal cancer (CRC) is one of the most common malignant tumors globally. Angiogenesis is a key event maintaining tumor cell survival and aggressiveness. The expression of vascular endothelial growth factor A (VEGFA), one of the most significant tumor cell-secreted proangiogenic factors, is frequently upregulated in CRC. Methods The MTT assay was used to detect the viability of CRC cells. Transwell assays were performed to detect the invasion capacity of target cells. Relative protein levels were determined by immunoblotting. Pathological characteristics of tissues were detected by H&E staining and immunohistochemical (IHC) staining. A RIP assay was conducted to validate the predicted binding between genes. Results We observed that circ-001971 expression was dramatically increased in CRC tissue samples and cells. Circ-001971 knockdown suppressed the capacity of CRC cells to proliferate and invade and HUVEC tube formation in vitro, as well as tumor growth in mice bearing SW620 cell-derived tumors in vivo. The expression of circ-001971 and VEGFA was dramatically increased whereas the expression of miR-29c-3p was reduced in tumor tissue samples. Circ-001971 relieved miR-29c-3p-induced inhibition of VEGFA by acting as a ceRNA, thereby aggravating the proliferation, invasion and angiogenesis of CRC. Consistent with the above findings, the expression of VEGFA was increased, whereas the expression of miR-29c-3p was decreased in tumor tissue samples. miR-29c-3p had a negative correlation with both circ-001971 and VEGFA, while circ-001971 was positively correlated with VEGFA. Conclusions In conclusion, the circ-001971/miR-29c-3p axis modulated CRC cell proliferation, invasion, and angiogenesis by targeting VEGFA.
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Affiliation(s)
- Chen Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhiguo Huang
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Xiaoye Mo
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Yanmin Song
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Xiangmin Li
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Xiaogang Li
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Mu Zhang
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.
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Lucero L, Fonouni-Farde C, Crespi M, Ariel F. Long noncoding RNAs shape transcription in plants. Transcription 2020; 11:160-171. [PMID: 32406332 DOI: 10.1080/21541264.2020.1764312] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The advent of novel high-throughput sequencing techniques has revealed that eukaryotic genomes are massively transcribed although only a small fraction of RNAs exhibits protein-coding capacity. In the last years, long noncoding RNAs (lncRNAs) have emerged as regulators of eukaryotic gene expression in a wide range of molecular mechanisms. Plant lncRNAs can be transcribed by alternative RNA polymerases, acting directly as long transcripts or can be processed into active small RNAs. Several lncRNAs have been recently shown to interact with chromatin, DNA or nuclear proteins to condition the epigenetic environment of target genes or modulate the activity of transcriptional complexes. In this review, we will summarize the recent discoveries about the actions of plant lncRNAs in the regulation of gene expression at the transcriptional level.
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Affiliation(s)
- Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Centro Científico Tecnológico CONICET Santa Fe , Santa Fe, Argentina
| | - Camille Fonouni-Farde
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Centro Científico Tecnológico CONICET Santa Fe , Santa Fe, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Batiment 630 , Gif Sur Yvette, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Centro Científico Tecnológico CONICET Santa Fe , Santa Fe, Argentina
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Phenolic Compounds Exerting Lipid-Regulatory, Anti-Inflammatory and Epigenetic Effects as Complementary Treatments in Cardiovascular Diseases. Biomolecules 2020; 10:biom10040641. [PMID: 32326376 PMCID: PMC7226566 DOI: 10.3390/biom10040641] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022] Open
Abstract
Atherosclerosis is the main process behind cardiovascular diseases (CVD), maladies which continue to be responsible for up to 70% of death worldwide. Despite the ongoing development of new and potent drugs, their incomplete efficacy, partial intolerance and numerous side effects make the search for new alternatives worthwhile. The focus of the scientific world turned to the potential of natural active compounds to prevent and treat CVD. Essential for effective prevention or treatment based on phytochemicals is to know their mechanisms of action according to their bioavailability and dosage. The present review is focused on the latest data about phenolic compounds and aims to collect and correlate the reliable existing knowledge concerning their molecular mechanisms of action to counteract important risk factors that contribute to the initiation and development of atherosclerosis: dyslipidemia, and oxidative and inflammatory-stress. The selection of phenolic compounds was made to prove their multiple benefic effects and endorse them as CVD remedies, complementary to allopathic drugs. The review also highlights some aspects that still need clear scientific explanations and draws up some new molecular approaches to validate phenolic compounds for CVD complementary therapy in the near future.
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45
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Brain Cytoplasmic RNAs in Neurons: From Biosynthesis to Function. Biomolecules 2020; 10:biom10020313. [PMID: 32079202 PMCID: PMC7072442 DOI: 10.3390/biom10020313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 01/10/2023] Open
Abstract
Flexibility in signal transmission is essential for high-level brain function. This flexibility is achieved through strict spatial and temporal control of gene expression in neurons. Given the key regulatory roles of a variety of noncoding RNAs (ncRNAs) in neurons, studying neuron-specific ncRNAs provides an important basis for understanding molecular principles of brain function. This approach will have wide use in understanding the pathogenesis of brain diseases and in the development of therapeutic agents in the future. Brain cytoplasmic RNAs (BC RNAs) are a leading paradigm for research on neuronal ncRNAs. Since the first confirmation of brain-specific expression of BC RNAs in 1982, their investigation has been an area of active research. In this review, we summarize key studies on the characteristics and functions of BC RNAs in neurons.
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46
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Mok L, Park T. HisCoM-PAGE: software for hierarchical structural component models for pathway analysis of gene expression data. Genomics Inform 2019; 17:e45. [PMID: 31896245 PMCID: PMC6944051 DOI: 10.5808/gi.2019.17.4.e45] [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: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 12/04/2022] Open
Abstract
To identify pathways associated with survival phenotypes using gene expression data, we recently proposed the hierarchical structural component model for pathway analysis of gene expression data (HisCoM-PAGE) method. The HisCoM-PAGE software can consider hierarchical structural relationships between genes and pathways and analyze multiple pathways simultaneously. It can be applied to various types of gene expression data, such as microarray data or RNA sequencing data. We expect that the HisCoM-PAGE software will make our method more easily accessible to researchers who want to perform pathway analysis for survival times.
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Affiliation(s)
- Lydia Mok
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
- Department of Statistics, Seoul National University, Seoul 08826, Korea
- Corresponding author: E-mail:
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Zhang Z, Liu J, Zeng Z, Fan J, Huang S, Zhang L, Zhang B, Wang X, Feng Y, Ye Z, Zhao L, Cao D, Yang L, Pakvasa M, Liu B, Wagstaff W, Wu X, Luo H, Zhang J, Zhang M, He F, Mao Y, Ding H, Zhang Y, Niu C, Haydon RC, Luu HH, Lee MJ, Wolf JM, Shao Z, He TC. lncRNA Rmst acts as an important mediator of BMP9-induced osteogenic differentiation of mesenchymal stem cells (MSCs) by antagonizing Notch-targeting microRNAs. Aging (Albany NY) 2019; 11:12476-12496. [PMID: 31825894 PMCID: PMC6949095 DOI: 10.18632/aging.102583] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/26/2019] [Indexed: 02/05/2023]
Abstract
Understanding the bone and musculoskeletal system is essential to maintain the health and quality of life of our aging society. Mesenchymal stem cells (MSCs) can undergo self-renewal and differentiate into multiple tissue types including bone. We demonstrated that BMP9 is the most potent osteogenic factors although molecular mechanism underlying BMP9 action is not fully understood. Long noncoding RNAs (lncRNAs) play important regulatory roles in many physiological and/or pathologic processes. Here, we investigated the role of lncRNA Rmst in BMP9-induced osteogenic differentiation of MSCs. We found that Rmst was induced by BMP9 through Smad signaling in MSCs. Rmst knockdown diminished BMP9-induced osteogenic, chondrogenic and adipogenic differentiation in vitro, and attenuated BMP9-induced ectopic bone formation. Silencing Rmst decreased the expression of Notch receptors and ligands. Bioinformatic analysis predicted Rmst could directly bind to eight Notch-targeting miRNAs, six of which were downregulated by BMP9. Silencing Rmst restored the expression of four microRNAs (miRNAs). Furthermore, an activating Notch mutant NICD1 effectively rescued the decreased ALP activity caused by Rmst silencing. Collectively, our results strongly suggest that the Rmst-miRNA-Notch regulatory axis may play an important role in mediating BMP9-induced osteogenic differentiation of MSCs.
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Affiliation(s)
- Zhicai Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jianxiang Liu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Zongyue Zeng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Jiaming Fan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Shifeng Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Linghuan Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Bo Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Key Laboratory of Orthopaedic Surgery of Gansu Province, and the Departments of Orthopaedic Surgery and Obstetrics and Gynecology, The First and Second Hospitals of Lanzhou University, Lanzhou 730030, China
| | - Xi Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Yixiao Feng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Zhenyu Ye
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Ling Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Daigui Cao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
- Departments of Orthopaedic Surgery and Laboratory Medicine, Chongqing General Hospital, Chongqing 400013, China
| | - Lijuan Yang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Key Laboratory of Orthopaedic Surgery of Gansu Province, and the Departments of Orthopaedic Surgery and Obstetrics and Gynecology, The First and Second Hospitals of Lanzhou University, Lanzhou 730030, China
| | - Mikhail Pakvasa
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Bin Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- School of Life Sciences, Southwest University, Chongqing 400715, China
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Xiaoxing Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Huaxiu Luo
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jing Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Meng Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine and the School of Laboratory Medicine; and the Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China
| | - Yukun Mao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, The Affiliated Zhongnan Hospital of Wuhan University, Wuhan 430072, China
| | - Huimin Ding
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, BenQ Medical Center Affiliated with Nanjing Medical University, Nanjing 210000, China
| | - Yongtao Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266061, China
| | - Changchun Niu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Departments of Orthopaedic Surgery and Laboratory Medicine, Chongqing General Hospital, Chongqing 400013, China
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Michael J. Lee
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jennifer Moriatis Wolf
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Zengwu Shao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
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Liu H, Cai Y. Pervasive Transcription Represses Coding Gene Expression by Closing Their Nucleosome-Depleted Regions. Bioessays 2019; 41:e1900159. [PMID: 31577040 DOI: 10.1002/bies.201900159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yiran Cai
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
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Luo S, He F, Luo J, Dou S, Wang Y, Guo A, Lu J. Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response. Nucleic Acids Res 2019; 46:5250-5268. [PMID: 29548011 PMCID: PMC6007262 DOI: 10.1093/nar/gky189] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/03/2018] [Indexed: 12/11/2022] Open
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of small RNAs, yet their regulatory roles have not been well understood. Here we studied the molecular mechanisms and consequences of tsRNA-mediated regulation in Drosophila. By analyzing 495 public small RNA libraries, we demonstrate that most tsRNAs are conserved, prevalent and abundant in Drosophila. By carrying out mRNA sequencing and ribosome profiling of S2 cells transfected with single-stranded tsRNA mimics and mocks, we show that tsRNAs recognize target mRNAs through conserved complementary sequence matching and suppress target genes by translational inhibition. The target prediction suggests that tsRNAs preferentially suppress translation of the key components of the general translation machinery, which explains how tsRNAs inhibit the global mRNA translation. Serum starvation experiments confirm tsRNAs participate in cellular starvation responses by preferential targeting the ribosomal proteins and translational initiation or elongation factors. Knock-down of AGO2 in S2 cells under normal and starved conditions reveals a dependence of the tsRNA-mediated regulation on AGO2. We also validated the repressive effects of representative tsRNAs on cellular global translation and specific targets with luciferase reporter assays. Our study suggests the tsRNA-mediated regulation might be crucial for the energy homeostasis and the metabolic adaptation in the cellular systems.
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Affiliation(s)
- Shiqi Luo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Feng He
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junjie Luo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shengqian Dou
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yirong Wang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Annan Guo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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50
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Navarro FCP, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB. TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput Biol 2019; 15:e1007293. [PMID: 31425522 PMCID: PMC6715295 DOI: 10.1371/journal.pcbi.1007293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/29/2019] [Accepted: 07/26/2019] [Indexed: 11/19/2022] Open
Abstract
The Long interspersed nuclear element 1 (LINE-1) is a primary source of genetic variation in humans and other mammals. Despite its importance, LINE-1 activity remains difficult to study because of its highly repetitive nature. Here, we developed and validated a method called TeXP to gauge LINE-1 activity accurately. TeXP builds mappability signatures from LINE-1 subfamilies to deconvolve the effect of pervasive transcription from autonomous LINE-1 activity. In particular, it apportions the multiple reads aligned to the many LINE-1 instances in the genome into these two categories. Using our method, we evaluated well-established cell lines, cell-line compartments and healthy tissues and found that the vast majority (91.7%) of transcriptome reads overlapping LINE-1 derive from pervasive transcription. We validated TeXP by independently estimating the levels of LINE-1 autonomous transcription using ddPCR, finding high concordance. Next, we applied our method to comprehensively measure LINE-1 activity across healthy somatic cells, while backing out the effect of pervasive transcription. Unexpectedly, we found that LINE-1 activity is present in many normal somatic cells. This finding contrasts with earlier studies showing that LINE-1 has limited activity in healthy somatic tissues, except for neuroprogenitor cells. Interestingly, we found that the amount of LINE-1 activity was associated with the with the amount of cell turnover, with tissues with low cell turnover rates (e.g. the adult central nervous system) showing lower LINE-1 activity. Altogether, our results show how accounting for pervasive transcription is critical to accurately quantify the activity of highly repetitive regions of the human genome. Repetitive sequences, such as LINEs, comprise more than half of the human genome. Due to their repetitive nature, LINEs are hard to grasp. In particular, we find that pervasive transcription is a major confounding factor in transcriptome data. We observe that, on average, more than 90% of LINE signal derives from pervasive transcription. To investigate this issue, we developed and validated a new method called TeXP. TeXP accounts and removes the effects of pervasive transcription when quantifying LINE activity. Our method uses the broad distribution of LINEs to estimate the effects of pervasive transcription. Using TeXP, we processed thousands of transcriptome datasets to uniformly, and unbiasedly measure LINE-1 activity across healthy somatic cells. By removing the pervasive transcription component, we find that (1) LINE-1 is broadly expressed in healthy somatic tissues; (2) Adult brain show small levels of LINE transcription and; (3) LINE-1 transcription level is correlated with tissue cell turnover. Our method thus offers insights into how repetitive sequences and influenced by pervasive transcription. Moreover, we uncover the activity of LINE-1 in somatic tissues at an unmatched scale.
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Affiliation(s)
- Fabio CP Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jacob Hoops
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Lauren Bellfy
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
- Department of Life Sciences, Ewha Womans University, Seoul, Korea
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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