201
|
Huang Z, Lei W, Hu H, Zhang H, Zhu Y. H19 promotes non‐small‐cell lung cancer (NSCLC) development through STAT3 signaling via sponging miR‐17. J Cell Physiol 2018; 233:6768-6776. [PMID: 29693721 DOI: 10.1002/jcp.26530] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/31/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Zhiwen Huang
- Department of Respiratory Medicine The First Affiliated Hospital of Soochow University Suzhou Jiangsu China
- Department of Respiratory Medicine Affiliated Renhe Hospital of China Three Gorges University Yichang Hubei China
| | - Wei Lei
- Department of Respiratory Medicine The First Affiliated Hospital of Soochow University Suzhou Jiangsu China
| | - Hai‐Bo Hu
- Department of Respiratory Medicine Affiliated Renhe Hospital of China Three Gorges University Yichang Hubei China
| | - Hongyan Zhang
- Department of Respiratory Medicine Affiliated Renhe Hospital of China Three Gorges University Yichang Hubei China
| | - Yehan Zhu
- Department of Respiratory Medicine The First Affiliated Hospital of Soochow University Suzhou Jiangsu China
| |
Collapse
|
202
|
Plakos K, DeRose VJ. Mapping platinum adducts on yeast ribosomal RNA using high-throughput sequencing. Chem Commun (Camb) 2018; 53:12746-12749. [PMID: 29099140 DOI: 10.1039/c7cc06708a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Methods to map small-molecule binding sites on cellular RNAs are important for understanding interactions with both endogenous and exogenous compounds. Pt(ii) reagents are well-known DNA and RNA crosslinking agents, but sequence-specific and genome-wide identification of Pt targets following in-cell treatment is challenging. Here we describe application of high-throughput 'Pt-Seq' to identify Pt-rRNA adducts following treatment of S. cerevisiae with cisplatin.
Collapse
Affiliation(s)
- Kory Plakos
- Department of Chemistry and Biochemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
| | | |
Collapse
|
203
|
Identification and functional characterization of bacterial small non-coding RNAs and their target: A review. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
204
|
Early Detection of Preeclampsia Using Circulating Small non-coding RNA. Sci Rep 2018; 8:3401. [PMID: 29467498 PMCID: PMC5821867 DOI: 10.1038/s41598-018-21604-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/30/2018] [Indexed: 12/17/2022] Open
Abstract
Preeclampsia is one of the most dangerous pregnancy complications, and the leading cause of maternal and perinatal mortality and morbidity. Although the clinical symptoms appear late, its origin is early, and hence detection is feasible already at the first trimester. In the current study, we investigated the abundance of circulating small non-coding RNAs in the plasma of pregnant women in their first trimester, seeking transcripts that best separate the preeclampsia samples from those of healthy pregnant women. To this end, we performed small non-coding RNAs sequencing of 75 preeclampsia and control samples, and identified 25 transcripts that were differentially expressed between preeclampsia and the control groups. Furthermore, we utilized those transcripts and created a pipeline for a supervised classification of preeclampsia. Our pipeline generates a logistic regression model using a 5-fold cross validation on numerous random partitions into training and blind test sets. Using this classification procedure, we achieved an average AUC value of 0.86. These findings suggest the predictive value of circulating small non-coding RNA in the first trimester, warranting further examination, and lay the foundation for producing a novel early non-invasive diagnostic tool for preeclampsia, which could reduce the life-threatening risk for both the mother and fetus.
Collapse
|
205
|
Deregulation of linc-PINT in acute lymphoblastic leukemia is implicated in abnormal proliferation of leukemic cells. Oncotarget 2018; 9:12842-12852. [PMID: 29560114 PMCID: PMC5849178 DOI: 10.18632/oncotarget.24401] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 01/19/2018] [Indexed: 11/25/2022] Open
Abstract
Long Non-Coding RNAs (lncRNAs) are functional RNAs longer than 200 nucleotides in length. Several lncRNAs are involved in cell proliferation and are deregulated in several human tumors. Few lncRNAs have been described to play a role in Acute Lymphoblastic Leukemia (ALL). In this study, we carried out a genome wide lncRNA expression profiling in ALL samples and peripheral blood samples obtained from healthy donors. We detected 43 lncRNAs that were aberrantly expressed in ALL. Interestingly, among them, linc-PINT showed a significant downregulation in T and B-ALL. Re-expression of linc-PINT in ALL cells induced inhibition of leukemic cell growth that was associated with apoptosis induction and cell cycle arrest in G2/M phase. linc-PINT induced the transcription of HMOX1 which reduced the viability of ALL cells. Intriguingly, we observed that treatment with anti-tumoral epigenetic drugs like LBH-589 (Panobinostat) and Curcumin induced the expression of linc-PINT and HMOX1 in ALL. These results indicate that the downregulation of linc-PINT plays a relevant role in the pathogenesis of ALL, and linc-PINT re-expression may be one of the mechanisms exerted by epigenetic drugs to reduce cell proliferation in ALL.
Collapse
|
206
|
Ahmadzada T, Reid G, McKenzie DR. Fundamentals of siRNA and miRNA therapeutics and a review of targeted nanoparticle delivery systems in breast cancer. Biophys Rev 2018; 10:69-86. [PMID: 29327101 PMCID: PMC5803180 DOI: 10.1007/s12551-017-0392-1] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/15/2017] [Indexed: 12/11/2022] Open
Abstract
Gene silencing via RNA interference (RNAi) is rapidly evolving as a personalized approach to cancer treatment. The effector molecules-small interfering RNAs (siRNAs) and microRNAs (miRNAs)-can be used to silence or "switch off" specific cancer genes. Currently, the main barrier to implementing siRNA- and miRNA-based therapies in clinical practice is the lack of an effective delivery system that can protect the RNA molecules from nuclease degradation, deliver to them to tumor tissue, and release them into the cytoplasm of the target cancer cells, all without inducing adverse effects. Here, we review the fundamentals of RNAi, cell membrane transport pathways, and factors that affect intracellular delivery. We discuss the advantages and disadvantages of the various types of nanoparticle delivery systems, with a focus on those that have been investigated in breast cancer in vivo.
Collapse
Affiliation(s)
- Tamkin Ahmadzada
- Sydney Medical School, The University of Sydney, Sydney, Australia.
| | - Glen Reid
- Sydney Medical School, The University of Sydney, Sydney, Australia
- Asbestos Diseases Research Institute (ADRI), Sydney, Australia
| | | |
Collapse
|
207
|
Antunes D, Jorge NAN, Caffarena ER, Passetti F. Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools. Front Genet 2018; 8:231. [PMID: 29403526 PMCID: PMC5780412 DOI: 10.3389/fgene.2017.00231] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022] Open
Abstract
RNA molecules are essential players in many fundamental biological processes. Prokaryotes and eukaryotes have distinct RNA classes with specific structural features and functional roles. Computational prediction of protein structures is a research field in which high confidence three-dimensional protein models can be proposed based on the sequence alignment between target and templates. However, to date, only a few approaches have been developed for the computational prediction of RNA structures. Similar to proteins, RNA structures may be altered due to the interaction with various ligands, including proteins, other RNAs, and metabolites. A riboswitch is a molecular mechanism, found in the three kingdoms of life, in which the RNA structure is modified by the binding of a metabolite. It can regulate multiple gene expression mechanisms, such as transcription, translation initiation, and mRNA splicing and processing. Due to their nature, these entities also act on the regulation of gene expression and detection of small metabolites and have the potential to helping in the discovery of new classes of antimicrobial agents. In this review, we describe software and web servers currently available for riboswitch aptamer identification and secondary and tertiary structure prediction, including applications.
Collapse
Affiliation(s)
- Deborah Antunes
- Scientific Computing Program (PROCC), Computational Biophysics and Molecular Modeling Group, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Natasha A N Jorge
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz, Curitiba, Brazil
| | - Ernesto R Caffarena
- Scientific Computing Program (PROCC), Computational Biophysics and Molecular Modeling Group, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fabio Passetti
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz, Curitiba, Brazil
| |
Collapse
|
208
|
Involvement of Noncoding RNAs in Stress-Related Neuropsychiatric Diseases Caused by DOHaD Theory : ncRNAs and DOHaD-Induced Neuropsychiatric Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1012:49-59. [PMID: 29956194 DOI: 10.1007/978-981-10-5526-3_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
According to the DOHaD theory, low birth weight is a risk factor for various noncommunicable chronic diseases that develop later in life. Noncoding RNAs (ncRNAs), including miRNAs, siRNAs, piRNAs, and lncRNAs, are functional RNA molecules that are transcribed from DNA but that are not translated into proteins. In general, miRNAs, siRNAs, and piRNAs function to regulate gene expression at the transcriptional and posttranscriptional levels. Studying ncRNAs has provided opportunities for new diagnosis and therapeutic knowledge in the endocrinological and metabolic fields as well as cancer biology. In this review, we focus on the roles of miRNAs and lncRNAs in the pathophysiology of stress-related neuropsychiatric diseases, which show abnormal blood hormone levels due to loss of feedback control and/or decreased sensitivity. Numerous recent studies have begun to unveil the importance of ncRNAs in regulation of stress-related hormone levels and functions. We summarize the involvement of abnormal ncRNA expression in the development of stress-related neuropsychiatric diseases based on the DOHaD theory.
Collapse
|
209
|
Jiang Z, Jiang C, Fang J. Up-regulated lnc-SNHG1 contributes to osteosarcoma progression through sequestration of miR-577 and activation of WNT2B/Wnt/β-catenin pathway. Biochem Biophys Res Commun 2018; 495:238-245. [DOI: 10.1016/j.bbrc.2017.11.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 12/31/2022]
|
210
|
Noncoding RNAs in Retrovirus Replication. RETROVIRUS-CELL INTERACTIONS 2018. [PMCID: PMC7173536 DOI: 10.1016/b978-0-12-811185-7.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although a limited percentage of the genome produces proteins, approximately 90% is transcribed, indicating important roles for noncoding RNA (ncRNA). It is now known that these ncRNAs have a multitude of cellular functions ranging from the regulation of gene expression to roles as structural elements in ribonucleoprotein complexes. ncRNA is also represented at nearly every step of viral life cycles. This chapter will focus on ncRNAs of both host and viral origin and their roles in retroviral life cycles. Cellular ncRNA represents a significant portion of material packaged into retroviral virions and includes transfer RNAs, 7SL RNA, U RNA, and vault RNA. Initially thought to be random packaging events, these host RNAs are now proposed to contribute to viral assembly and infectivity. Within the cell, long ncRNA and endogenous retroviruses have been found to regulate aspects of the retroviral life cycle in diverse ways. Additionally, the HIV-1 transactivating response element RNA is thought to impact viral infection beyond the well-characterized role as a transcription activator. RNA interference, thought to be an early version of the innate immune response to viral infection, can still be observed in plants and invertebrates today. The ability of retroviral infection to manipulate the host RNAi pathway is described here. Finally, RNA-based therapies, including gene editing approaches, are being explored as antiretroviral treatments and are discussed.
Collapse
|
211
|
Frías-Lasserre D, Villagra CA. The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution. Front Microbiol 2017; 8:2483. [PMID: 29312192 PMCID: PMC5744636 DOI: 10.3389/fmicb.2017.02483] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022] Open
Abstract
Neo-Darwinian explanations of organic evolution have settled on mutation as the principal factor in producing evolutionary novelty. Mechanistic characterizations have been also biased by the classic dogma of molecular biology, where only proteins regulate gene expression. This together with the rearrangement of genetic information, in terms of genes and chromosomes, was considered the cornerstone of evolution at the level of natural populations. This predominant view excluded both alternative explanations and phenomenologies that did not fit its paradigm. With the discovery of non-coding RNAs (ncRNAs) and their role in the control of genetic expression, new mechanisms arose providing heuristic power to complementary explanations to evolutionary processes overwhelmed by mainstream genocentric views. Viruses, epimutation, paramutation, splicing, and RNA editing have been revealed as paramount functions in genetic variations, phenotypic plasticity, and diversity. This article discusses how current epigenetic advances on ncRNAs have changed the vision of the mechanisms that generate variation, how organism-environment interaction can no longer be underestimated as a driver of organic evolution, and how it is now part of the transgenerational inheritance and evolution of species.
Collapse
Affiliation(s)
- Daniel Frías-Lasserre
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
| | | |
Collapse
|
212
|
Abstract
The majority of the human genome encodes RNAs that do not code for proteins. These non-coding RNAs (ncRNAs) affect normal expression of the genes, including oncogenes and tumour suppressive genes, which make them a new class of targets for drug development in cancer. Although microRNAs (miRNAs) are the most studied regulatory ncRNAs to date, and miRNA-targeted therapeutics have already reached clinical development, including the mimics of the tumour suppressive miRNAs miR-34 and miR-16, which reached phase I clinical trials for the treatment of liver cancer and mesothelioma, the importance of long non-coding RNAs (lncRNAs) is increasingly being recognised. Here, we describe obstacles and advances in the development of ncRNA therapeutics and provide the comprehensive overview of the ncRNA chemistry and delivery technologies. Furthermore, we summarise recent knowledge on the biological functions of miRNAs and their involvement in carcinogenesis, and discuss the strategies of their therapeutic manipulation in cancer. We review also the emerging insights into the role of lncRNAs and their potential as targets for novel treatment paradigms. Finally, we provide the up-to-date summary of clinical trials involving miRNAs and future directions in the development of ncRNA therapeutics.
Collapse
Affiliation(s)
- Ondrej Slaby
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Richard Laga
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Sedlacek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
213
|
Leggio L, Vivarelli S, L'Episcopo F, Tirolo C, Caniglia S, Testa N, Marchetti B, Iraci N. microRNAs in Parkinson's Disease: From Pathogenesis to Novel Diagnostic and Therapeutic Approaches. Int J Mol Sci 2017; 18:ijms18122698. [PMID: 29236052 PMCID: PMC5751299 DOI: 10.3390/ijms18122698] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 01/09/2023] Open
Abstract
Parkinson’s disease (PD) is the most prevalent central nervous system (CNS) movement disorder and the second most common neurodegenerative disease overall. PD is characterized by the progressive loss of dopaminergic (DAergic) neurons in the substantia nigra pars compacta (SNpc) within the midbrain, accumulation of alpha-synuclein (α-SYN) in Lewy bodies and neurites and excessive neuroinflammation. The neurodegenerative processes typically begin decades before the appearance of clinical symptoms. Therefore, the diagnosis is achievable only when the majority of the relevant DAergic neurons have already died and for that reason available treatments are only palliative at best. The causes and mechanism(s) of this devastating disease are ill-defined but complex interactions between genetic susceptibility and environmental factors are considered major contributors to the etiology of PD. In addition to the role of classical gene mutations in PD, the importance of regulatory elements modulating gene expression has been increasingly recognized. One example is the critical role played by microRNAs (miRNAs) in the development and homeostasis of distinct populations of neurons within the CNS and, in particular, in the context of PD. Recent reports demonstrate how distinct miRNAs are involved in the regulation of PD genes, whereas profiling approaches are unveiling variations in the abundance of certain miRNAs possibly relevant either to the onset or to the progression of the disease. In this review, we provide an overview of the miRNAs recently found to be implicated in PD etiology, with particular focus on their potential relevance as PD biomarkers, as well as their possible use in PD targeted therapy.
Collapse
Affiliation(s)
- Loredana Leggio
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Torre Biologica, Via S. Sofia 97, 95125 Catania, Italy.
| | - Silvia Vivarelli
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Torre Biologica, Via S. Sofia 97, 95125 Catania, Italy.
| | - Francesca L'Episcopo
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Cataldo Tirolo
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Salvo Caniglia
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Nunzio Testa
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Bianca Marchetti
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Torre Biologica, Via S. Sofia 97, 95125 Catania, Italy.
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Nunzio Iraci
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Torre Biologica, Via S. Sofia 97, 95125 Catania, Italy.
| |
Collapse
|
214
|
Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
Collapse
Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
| |
Collapse
|
215
|
Jain S, Schlick T. F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly. J Mol Biol 2017; 429:3587-3605. [PMID: 28988954 PMCID: PMC5693719 DOI: 10.1016/j.jmb.2017.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/12/2017] [Accepted: 09/22/2017] [Indexed: 10/18/2022]
Abstract
Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce candidate graphs. However, for a more detailed study and analysis, construction of atomic from coarse-grained models is required. Here we present our graph-based fragment assembly algorithm (F-RAG) to convert candidate three-dimensional (3D) tree graph models, produced by RAGTOP into atomic structures. We use our related RAG-3D utilities to partition graphs into subgraphs and search for structurally similar atomic fragments in a data set of RNA 3D structures. The fragments are edited and superimposed using common residues, full atomic models are scored using RAGTOP's knowledge-based potential, and geometries of top scoring models is optimized. To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of residue interactions) with respect to experimentally solved structures and compare our results to other fragment assembly programs. For a set of 50 RNA structures, we obtain atomic models with reasonable geometries and interactions, particularly good for RNAs containing junctions. Additional improvements to our protocol and databases are outlined. These results provide a good foundation for further work on RNA structure prediction and design applications.
Collapse
Affiliation(s)
- Swati Jain
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA; New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, North Zhongshan Road, 3663 Shanghai, China.
| |
Collapse
|
216
|
Zinad HS, Natasya I, Werner A. Natural Antisense Transcripts at the Interface between Host Genome and Mobile Genetic Elements. Front Microbiol 2017; 8:2292. [PMID: 29209299 PMCID: PMC5701935 DOI: 10.3389/fmicb.2017.02292] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/06/2017] [Indexed: 12/26/2022] Open
Abstract
Non-coding RNAs are involved in epigenetic processes, playing a role in the regulation of gene expression at the transcriptional and post-transcriptional levels. A particular group of ncRNA are natural antisense transcripts (NATs); these are transcribed in the opposite direction to protein coding transcripts and are widespread in eukaryotes. Their abundance, evidence of phylogenetic conservation and an increasing number of well-characterized examples of antisense-mediated gene regulation are indicative of essential biological roles of NATs. There is evidence to suggest that they interfere with their corresponding sense transcript to elicit concordant and discordant regulation. The main mechanisms involved include transcriptional interference as well as dsRNA formation. Sense–antisense hybrid formation can trigger RNA interference, RNA editing or protein kinase R. However, the exact molecular mechanisms elicited by NATs in the context of these regulatory roles are currently poorly understood. Several examples confirm that ectopic expression of antisense transcripts trigger epigenetic silencing of the related sense transcript. Genomic approaches suggest that the antisense transcriptome carries a broader biological significance which goes beyond the physiological regulation of the directly related sense transcripts. Because NATs show evidence of conservation we speculate that they played a role in evolution, with early eukaryotes gaining selective advantage through the regulatory effects. With the surge of genome and transcriptome sequencing projects, there is promise of a more comprehensive understanding of the biological role of NATs and the regulatory mechanisms involved.
Collapse
Affiliation(s)
- Hany S Zinad
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Inas Natasya
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andreas Werner
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
217
|
Ratnu VS, Emami MR, Bredy TW. Genetic and epigenetic factors underlying sex differences in the regulation of gene expression in the brain. J Neurosci Res 2017; 95:301-310. [PMID: 27870402 DOI: 10.1002/jnr.23886] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/14/2022]
Abstract
There are inherent biological differences between males and females that contribute to sex differences in brain function and to many sex-specific illnesses and disorders. Traditionally, it has been thought that such differences are due largely to hormonal regulation; however, there are also genetic and epigenetic effects caused by the inheritance and unequal dosage of genes located on the X and Y chromosomes. Here we discuss the evidence in favor of a genetic and epigenetic basis for sexually dimorphic behavior, as a consequence of underlying differences in the regulation of genes that drive brain function. A better understanding of sex-specific molecular processes in the brain will provide further insight for the development of novel therapeutic approaches for the treatment of neuropsychiatric disorders characterized by sex differences. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Vikram S Ratnu
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael R Emami
- Department of Neurobiology and Behavior, University of California, Irvine, California
| | - Timothy W Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Department of Neurobiology and Behavior, University of California, Irvine, California
| |
Collapse
|
218
|
Wu H, Wu R, Chen M, Li D, Dai J, Zhang Y, Gao K, Yu J, Hu G, Guo Y, Lin C, Li X. Comprehensive analysis of differentially expressed profiles of lncRNAs and construction of miR-133b mediated ceRNA network in colorectal cancer. Oncotarget 2017; 8:21095-21105. [PMID: 28177879 PMCID: PMC5400568 DOI: 10.18632/oncotarget.15045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/09/2017] [Indexed: 01/15/2023] Open
Abstract
Background Growing evidence suggests that long non-coding RNAs (lncRNAs) play a key role in tumorigenesis. However, the mechanism remains largely unknown. Results Thousands of significantly dysregulated lncRNAs and mRNAs were identified by microarray. Furthermore, a miR-133b-meditated lncRNA-mRNA ceRNA network was revealed, a subset of which was validated in 14 paired CRC patient tumor/non-tumor samples. Gene set enrichment analysis (GSEA) results demonstrated that lncRNAs ENST00000520055 and ENST00000535511 shared KEGG pathways with miR-133b target genes. Materials and Methods We used microarrays to survey the lncRNA and mRNA expression profiles of colorectal cancer and para-cancer tissues. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed to explore the functions of the significantly dysregulated genes. An innovate method was employed that combined analyses of two microarray data sets to construct a miR-133b-mediated lncRNA-mRNA competing endogenous RNAs (ceRNA) network. Quantitative RT-PCR analysis was used to validate part of this network. GSEA was used to predict the potential functions of these lncRNAs. Conclusions This study identifies and validates a new method to investigate the miR-133b-mediated lncRNA-mRNA ceRNA network and lays the foundation for future investigation into the role of lncRNAs in colorectal cancer.
Collapse
Affiliation(s)
- Hao Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Runliu Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Miao Chen
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Daojiang Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Jing Dai
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Yi Zhang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Kai Gao
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Jun Yu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Gui Hu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Yihang Guo
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| |
Collapse
|
219
|
How prokaryotes 'encode' their environment: Systemic tools for organizing the information flow. Biosystems 2017; 164:26-38. [PMID: 28987781 DOI: 10.1016/j.biosystems.2017.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 01/04/2023]
Abstract
An important issue related to code biology concerns the cell's informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows. The analysis here of the simplest cells will involve two basic aspects. On the one side, the molecular apparatuses of the prokaryotic signaling system, with all its variety of environmental signals and component pathways (which have been called 1-2-3 Component Systems), including the role of a few second messengers which have been pointed out in bacteria too. And in the other side, the gene transcription system as depending not only on signaling inputs but also on a diversity of factors. Amidst the continuum of energy, matter, and information flows, there seems to be evidence for signaling codes, mostly established around the arrangement of life-cycle stages, in large metabolic changes, or in the relationships with conspecifics (quorum sensing) and within microbial ecosystems. Additionally, and considering the complexity growth of signaling systems from prokaryotes to eukaryotes, four avenues or "roots" for the advancement of such complexity would come out. A comparative will be established in between the signaling strategies and organization of both kinds of cellular systems. Finally, a new characterization of "informational architectures" will be proposed in order to explain the coding spectrum of both prokaryotic and eukaryotic signaling systems. Among other evolutionary aspects, cellular strategies for the construction of novel functional codes via the intermixing of informational architectures could be related to the persistence of retro-elements with obvious viral ancestry.
Collapse
|
220
|
Yang Y, Yang YCT, Yuan J, Lu ZJ, Li JJ. Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states. Nucleic Acids Res 2017; 45:1657-1672. [PMID: 27980097 PMCID: PMC5389511 DOI: 10.1093/nar/gkw1256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 12/01/2016] [Indexed: 12/30/2022] Open
Abstract
Distinguishing cell states based only on gene expression data remains a challenging task. This is true even for analyses within a species. In cross-species comparisons, the results obtained by different groups have varied widely. Here, we integrate RNA-seq data from more than 40 cell and tissue types of four mammalian species to identify sets of associated genes as indicators for specific cell states in each species. We employ a statistical method, TROM, to identify both protein-coding and non-coding indicators. Next, we map the cell states within each species and also between species using these indicator genes. We recapitulate known phenotypic similarity between related cell and tissue types and reveal molecular basis for their similarity. We also report novel associations between several tissues and cell types with functional support. Moreover, our identified conserved associated genes are found to be a good resource for studying cell differentiation and reprogramming. Lastly, long non-coding RNAs can serve well as associated genes to indicate cell states. We further infer the biological functions of those non-coding associated genes based on their co-expressed protein-coding genes. This study demonstrates that combining statistical modeling with public RNA-seq data can be powerful for improving our understanding of cell identity control.
Collapse
Affiliation(s)
- Yang Yang
- PKU-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China.,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu-Cheng T Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiapei Yuan
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA 90095-1554, USA.,Department of Human Genetics, University of California, Los Angeles, CA 90095-7088, USA
| |
Collapse
|
221
|
Yu Y, Nangia-Makker P, Farhana L, Majumdar APN. A novel mechanism of lncRNA and miRNA interaction: CCAT2 regulates miR-145 expression by suppressing its maturation process in colon cancer cells. Mol Cancer 2017; 16:155. [PMID: 28964256 PMCID: PMC5622467 DOI: 10.1186/s12943-017-0725-5] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/20/2017] [Indexed: 11/10/2022] Open
Abstract
Background Although both long and micro RNAs are emerging as important functional components in colorectal cancer (CRC) progression and metastasis, the mechanism of their interaction remains poorly understood. CCAT2 (Colon cancer-associated transcript-2), a long noncoding RNA (lncRNA), has been reported to be over-expressed in CRC and is found to promote tumor growth. miRNAs, a class of naturally occurring short RNAs negatively control the expression of target genes by cleaving mRNA or through translation repression. Recently, we reported that miR-145 and miR-21 cooperate to regulate colon cancer stem cell (CSC) proliferation and differentiation. Considering that CCAT2 is mainly located in the nucleus and miRNA maturation process begins in the nucleus, we hypothesize that CCAT2 selectively blocks miR-145 maturation process, resulting in decreased mature miR-145 affecting colon CSC proliferation and differentiation. Methods The levels of CCAT2 were manipulated by transfection of CCAT2 expression plasmid or knockdown by siRNA or by CRISPR/Cas9. Quantitative RT-PCR was performed to examine the expression of CCAT2 and pri-, pre- and mature miR-145/21. Fluorescence in situ hybridization (FISH) was used to visualize CCAT2 in the cells. In vitro processing of pri-miRNA-145 was performed using T7 RNA polymerase and recombinant human Dicer. Results We have observed that modulated expression of CCAT2 regulates the expression of miR-145 in colon cancer HCT-116 and HT-29 cells. Knockout of CCAT2 increases miR-145 and negatively regulates miR-21 in HCT-116 cells, impairs proliferation and differentiation. In contrast, stable up-regulation of CCAT2 decreases mature miR-145 and increases the expression of several CSC markers in colon cancer cells. We have also observed that CCAT2 is enriched in the nucleus and correlates with the expression of pre-miR-145 but not pre-miR-21 in HCT-116 cells. These results indicate CCAT2 selectively blocks miR-145 maturation by inhibiting pre-miR-145 export to cytoplasm. Further, we revealed that CCAT2 blocks cleavage of pre-miR-145 by Dicer in vitro. Conclusions Our results identify CCAT2 as a negative regulator of miRNA-145 biogenesis, and expose a novel mechanism of lncRNA-miRNA crosstalk. Electronic supplementary material The online version of this article (10.1186/s12943-017-0725-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yingjie Yu
- Department of Veterans Affairs Medical Center, 4646 John R, Detroit, MI, 48201, USA. .,Departments of Internal Medicine, Wayne State University, Detroit, MI, 48201, USA.
| | - Pratima Nangia-Makker
- Department of Veterans Affairs Medical Center, 4646 John R, Detroit, MI, 48201, USA.,Karmanos Cancer Institute, Detroit, MI, 48201, USA.,Departments of Internal Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Lulu Farhana
- Department of Veterans Affairs Medical Center, 4646 John R, Detroit, MI, 48201, USA.,Departments of Internal Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Adhip P N Majumdar
- Department of Veterans Affairs Medical Center, 4646 John R, Detroit, MI, 48201, USA. .,Karmanos Cancer Institute, Detroit, MI, 48201, USA. .,Departments of Internal Medicine, Wayne State University, Detroit, MI, 48201, USA.
| |
Collapse
|
222
|
Hubé F, Ulveling D, Sureau A, Forveille S, Francastel C. Short intron-derived ncRNAs. Nucleic Acids Res 2017; 45:4768-4781. [PMID: 28053119 PMCID: PMC5416886 DOI: 10.1093/nar/gkw1341] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/21/2016] [Indexed: 01/02/2023] Open
Abstract
Introns represent almost half of the human genome, although they are eliminated from transcripts through RNA splicing. Yet, different classes of non-canonical miRNAs have been proposed to originate directly from intron splicing. Here, we considered the alternative splicing of introns as an interesting source of miRNAs, compatible with a developmental switch. We report computational prediction of new Short Intron-Derived ncRNAs (SID), defined as precursors of smaller ncRNAs like miRNAs and snoRNAs produced directly by splicing, and tested their dependence on each key factor in canonical or alternative miRNAs biogenesis (Drosha, DGCR8, DBR1, snRNP70, U2AF65, PRP8, Dicer, Ago2). We found that about half of predicted SID rely on debranching of the excised intron-lariat by the enzyme DBR1, as proposed for mirtrons. However, we identified new classes of SID for which miRNAs biogenesis may rely on intermingling between canonical and alternative pathways. We validated selected SID as putative miRNAs precursors and identified new endogenous miRNAs produced by non-canonical pathways, including one hosted in the first intron of SRA (Steroid Receptor RNA activator). Consistent with increased SRA intron retention during myogenic differentiation, release of SRA intron and its associated mature miRNA decreased in cells from healthy subjects but not from myotonic dystrophy patients with splicing defects.
Collapse
Affiliation(s)
- Florent Hubé
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
| | - Damien Ulveling
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
| | - Alain Sureau
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
| | - Sabrina Forveille
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
| | - Claire Francastel
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
| |
Collapse
|
223
|
Sugihara Y, Nakata Y, Yamayoshi A, Murakami A, Kobori A. Inhibition Effect of Photoresponsive α-Haloaldehyde-conjugated Oligonucleotides on the Gene Expression in HeLa Cells Stably Expressing GFP. CHEM LETT 2017. [DOI: 10.1246/cl.170298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yuta Sugihara
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
| | - Yuki Nakata
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
| | - Asako Yamayoshi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
- The Hakubi Center for Advanced Research, Kyoto University, Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501
| | - Akira Murakami
- Kyoto Pharmaceutical University, 1 Misasagi-Shichonocho, Yamashina-ku, Kyoto 607-8412
| | - Akio Kobori
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
| |
Collapse
|
224
|
Bidnenko V, Nicolas P, Grylak-Mielnicka A, Delumeau O, Auger S, Aucouturier A, Guerin C, Repoila F, Bardowski J, Aymerich S, Bidnenko E. Termination factor Rho: From the control of pervasive transcription to cell fate determination in Bacillus subtilis. PLoS Genet 2017; 13:e1006909. [PMID: 28723971 PMCID: PMC5540618 DOI: 10.1371/journal.pgen.1006909] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/02/2017] [Accepted: 07/06/2017] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis. Rho inactivation strongly affected gene expression in B. subtilis, as assessed by transcriptome and proteome analysis of a rho-null mutant during exponential growth in rich medium. Subsequent physiological analyses demonstrated that a considerable part of Rho-controlled transcription is connected to balanced regulation of three mutually exclusive differentiation programs: cell motility, biofilm formation, and sporulation. In the absence of Rho, several up-regulated sense and antisense transcripts affect key structural and regulatory elements of these differentiation programs, thereby suppressing motility and biofilm formation and stimulating sporulation. We dissected how Rho is involved in the activity of the cell fate decision-making network, centered on the master regulator Spo0A. We also revealed a novel regulatory mechanism of Spo0A activation through Rho-dependent intragenic transcription termination of the protein kinase kinB gene. Altogether, our findings indicate that distinct Rho-controlled transcripts are functional and constitute a previously unknown built-in module for the control of cell differentiation in B. subtilis. In a broader context, our results highlight the recruitment of the termination factor Rho, for which the conserved biological role is probably to repress pervasive transcription, in highly integrated, bacterium-specific, regulatory networks.
Collapse
Affiliation(s)
- Vladimir Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Pierre Nicolas
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Aleksandra Grylak-Mielnicka
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Olivier Delumeau
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sandrine Auger
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Anne Aucouturier
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cyprien Guerin
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Francis Repoila
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jacek Bardowski
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Stéphane Aymerich
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Elena Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
| |
Collapse
|
225
|
Kaneko H, Terasaki H. Biological Involvement of MicroRNAs in Proliferative Vitreoretinopathy. Transl Vis Sci Technol 2017; 6:5. [PMID: 28706757 PMCID: PMC5505124 DOI: 10.1167/tvst.6.4.5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/25/2017] [Indexed: 12/20/2022] Open
Abstract
Even with a high surgical success rate for retinal detachment and proliferative vitreoretinopathy (PVR) supported by the robust improvement in vitrectomy surgery and its related devices, certain questions still remain for the pathogenesis and treatment of PVR. One of the important biological events in PVR is epithelial–mesenchymal transition (EMT) of the retinal pigment epithelial (RPE) cells. MicroRNAs are noncoding, small, single-strand RNAs that posttranscriptionally regulate gene expression and have essential roles in homeostasis and pathogenesis in many diseases. Recently, microRNAs also had a critical role in EMT in many tissues and cells. One main purpose of this brief review is to describe the knowledge obtained from microRNA research, especially concerning vitreoretinal diseases. In addition, the potential role of microRNAs in prevention of PVR by regulating EMT in RPE cells is described. Understanding microRNA involvement in PVR could be helpful for developing new biological markers or therapeutic targets and reducing the rate of visual disability due to PVR.
Collapse
Affiliation(s)
- Hiroki Kaneko
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya Japan
| |
Collapse
|
226
|
Epigenetic aspects of rheumatoid arthritis: contribution of non-coding RNAs. Semin Arthritis Rheum 2017; 46:724-731. [DOI: 10.1016/j.semarthrit.2017.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/20/2016] [Accepted: 01/13/2017] [Indexed: 01/07/2023]
|
227
|
Abstract
Long noncoding RNAs (lncRNAs) are a relatively well-characterized class of noncoding RNA (ncRNA) molecules, involved in the regulation of various cell processes, including transcription, intracellular trafficking, and chromosome remodeling. Their deregulation has been associated with the development and progression of various cancer types, the fact which makes them suitable as biomarkers for cancer diagnosis and prognosis. In recent years, detection of cancer-associated lncRNAs in body fluids of cancer patients has proven itself as an especially valuable method to effectively diagnose cancer. Cancer diagnosis and prognosis employing circulating lncRNAs are preferential when compared to classical biopsies of tumor tissues, especially due to their noninvasiveness, and have great potential for routine usage in clinical practice. Thus, this review focuses on summarizing the perspectives of lncRNAs as biomarkers in cancer, based on evaluating their expression profiles determined in body fluids of cancer patients.
Collapse
|
228
|
Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
|
229
|
Chen Y, Zhou J. LncRNAs: macromolecules with big roles in neurobiology and neurological diseases. Metab Brain Dis 2017; 32:281-291. [PMID: 28161776 DOI: 10.1007/s11011-017-9965-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 01/31/2017] [Indexed: 01/05/2023]
Abstract
Long noncoding RNAs (lncRNAs) are recently defined as thousands of RNA molecules longer than 200 nucleotides and lacking an appreciable open reading frame in mammals. Although lncRNAs lack protein-coding function, they play critical roles in the regulation of almost all the protein-coding genes in a cell at various stages including chromatin modification, transcription and post-transcriptional processing. It is thus not surprising that lncRNAs may be the crucial regulators in the normal development, physiology and pathology. LncRNAs in neuroscience is a novel research field. Interestingly, recent studies have demonstrated that many lncRNAs are highly expressed in brain and their dysregulations occur in neurological disorders. In this review, we describe the current understanding of lncRNAs in neurobiology and neurological diseases including cerebral injury. LncRNAs could be novel biomarkers and could be potential new targets for new drugs for many neurological diseases in the future, although the related studies are still at in the early stages.
Collapse
Affiliation(s)
- Ye Chen
- Department of Traditional Chinese Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Jun Zhou
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, No.25 Taiping Street, Luzhou, Sichuan Province, 646000, People's Republic of China.
| |
Collapse
|
230
|
Gumienny R, Jedlinski DJ, Schmidt A, Gypas F, Martin G, Vina-Vilaseca A, Zavolan M. High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Res 2017; 45:2341-2353. [PMID: 28031372 PMCID: PMC5389715 DOI: 10.1093/nar/gkw1321] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/08/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023] Open
Abstract
High-throughput sequencing has greatly facilitated the discovery of long and short non-coding RNAs (ncRNAs), which frequently guide ribonucleoprotein complexes to RNA targets, to modulate their metabolism and expression. However, for many ncRNAs, the targets remain to be discovered. In this study, we developed computational methods to map C/D box snoRNA target sites using data from core small nucleolar ribonucleoprotein crosslinking and immunoprecipitation and from transcriptome-wide mapping of 2΄-O-ribose methylation sites. We thereby assigned the snoRNA guide to a known methylation site in the 18S rRNA, we uncovered a novel partially methylated site in the 28S ribosomal RNA, and we captured a site in the 28S rRNA in interaction with multiple snoRNAs. Although we also captured mRNAs in interaction with snoRNAs, we did not detect 2΄-O-methylation of these targets. Our study provides an integrated approach to the comprehensive characterization of 2΄-O-methylation targets of snoRNAs in species beyond those in which these interactions have been traditionally studied and contributes to the rapidly developing field of 'epitranscriptomics'.
Collapse
MESH Headings
- Algorithms
- Base Sequence
- Cross-Linking Reagents/chemistry
- Databases, Genetic
- High-Throughput Nucleotide Sequencing/methods
- Immunoprecipitation
- Methylation
- Protein Binding
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Ribose/metabolism
- Software
- Transcriptome
- RNA, Guide, CRISPR-Cas Systems
Collapse
Affiliation(s)
- Rafal Gumienny
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
| | | | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Switzerland
| | - Foivos Gypas
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
| | - Arnau Vina-Vilaseca
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
| |
Collapse
|
231
|
Shaikh MH, Clarke DTW, Johnson NW, McMillan NAJ. Can gene editing and silencing technologies play a role in the treatment of head and neck cancer? Oral Oncol 2017; 68:9-19. [PMID: 28438299 DOI: 10.1016/j.oraloncology.2017.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 01/25/2017] [Accepted: 02/19/2017] [Indexed: 01/04/2023]
Abstract
Conventional treatment strategies have done little to improve the prognosis or disease-free survival in head and neck cancer (HNC) patients. Recent progress in our understanding of molecular aspects of head and neck squamous cell carcinoma (HNSCC) has provided insights into the potential use of molecular targeted therapies in combination with current treatment strategies. Here we review the current understanding of treatment modalities for both HPV-positive and HPV-negative HNSCCs with the potential to use gene editing and silencing technologies therapeutically. The development of sequence-specific RNA interference (RNAi) with its strong gene-specific silencing ability, high target specificity, greater potency and reduced side effects, has shown it to be a promising therapeutic candidate for treating cancers. CRISPR/Cas gene editing is the newest technology with the ability to delete, mutate or replace genes of interest and has great potential for treating HNSCCs. We also discuss the major challenge in using these approaches in HNSCC; that being the choice of target and the ability to deliver the payload. Finally, we highlight the potential combination of RNAi or CRIPSR/Cas with current treatment strategies and outline the possible path to the clinic.
Collapse
Affiliation(s)
- Mushfiq H Shaikh
- School of Dentistry and Oral Health, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; School of Medical Science, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Australia.
| | - Daniel T W Clarke
- School of Medical Science, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Australia.
| | - Newell W Johnson
- School of Dentistry and Oral Health, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Australia.
| | - Nigel A J McMillan
- School of Medical Science, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Australia.
| |
Collapse
|
232
|
Adams BD, Parsons C, Walker L, Zhang WC, Slack FJ. Targeting noncoding RNAs in disease. J Clin Invest 2017; 127:761-771. [PMID: 28248199 DOI: 10.1172/jci84424] [Citation(s) in RCA: 488] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Many RNA species have been identified as important players in the development of chronic diseases, including cancer. Over the past decade, numerous studies have highlighted how regulatory RNAs such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) play crucial roles in the development of a disease state. It is clear that the aberrant expression of miRNAs promotes tumor initiation and progression, is linked with cardiac dysfunction, allows for the improper physiological response in maintaining glucose and insulin levels, and can prevent the appropriate integration of neuronal networks, resulting in neurodegenerative disorders. Because of this, there has been a major effort to therapeutically target these noncoding RNAs. In just the past 5 years, over 100 antisense oligonucleotide-based therapies have been tested in phase I clinical trials, a quarter of which have reached phase II/III. Most notable are fomivirsen and mipomersen, which have received FDA approval to treat cytomegalovirus retinitis and high blood cholesterol, respectively. The continued improvement of innovative RNA modifications and delivery entities, such as nanoparticles, will aid in the development of future RNA-based therapeutics for a broader range of chronic diseases. Here we summarize the latest promises and challenges of targeting noncoding RNAs in disease.
Collapse
MESH Headings
- Clinical Trials, Phase I as Topic
- Clinical Trials, Phase II as Topic
- Cytomegalovirus Retinitis/drug therapy
- Cytomegalovirus Retinitis/genetics
- Cytomegalovirus Retinitis/metabolism
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- MicroRNAs/antagonists & inhibitors
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplasms/drug therapy
- Neoplasms/genetics
- Neoplasms/metabolism
- Neurodegenerative Diseases/drug therapy
- Neurodegenerative Diseases/genetics
- Neurodegenerative Diseases/metabolism
- Oligodeoxyribonucleotides, Antisense/genetics
- Oligodeoxyribonucleotides, Antisense/therapeutic use
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Neoplasm/antagonists & inhibitors
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
Collapse
|
233
|
Abstract
Protein-coding RNAs represent only a small fraction of the transcriptional output in higher eukaryotes. The remaining RNA species encompass a broad range of molecular functions and regulatory roles, a consequence of the structural polyvalence of RNA polymers. Albeit several classes of small noncoding RNAs are relatively well characterized, the accessibility of affordable high-throughput sequencing is generating a wealth of novel, unannotated transcripts, especially long noncoding RNAs (lncRNAs) that are derived from genomic regions that are antisense, intronic, intergenic, and overlapping protein-coding loci. Parsing and characterizing the functions of noncoding RNAs-lncRNAs in particular-is one of the great challenges of modern genome biology. Here we discuss concepts and computational methods for the identification of structural domains in lncRNAs from genomic and transcriptomic data. In the first part, we briefly review how to identify RNA structural motifs in individual lncRNAs. In the second part, we describe how to leverage the evolutionary dynamics of structured RNAs in a computationally efficient screen to detect putative functional lncRNA motifs using comparative genomics.
Collapse
Affiliation(s)
- Martin A Smith
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia. .,St-Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, NSW, 2052, Australia.
| | - John S Mattick
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia.,St-Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, NSW, 2052, Australia
| |
Collapse
|
234
|
Jarroux J, Morillon A, Pinskaya M. History, Discovery, and Classification of lncRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:1-46. [PMID: 28815535 DOI: 10.1007/978-981-10-5203-3_1] [Citation(s) in RCA: 558] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s. Thirty years later, the first regulatory non-coding RNAs (ncRNAs) were initially identified in bacteria and then in most eukaryotic organisms. A few long ncRNAs (lncRNAs) such as H19 and Xist were characterized in the pre-genomic era but remained exceptions until the early 2000s. Indeed, when the sequence of the human genome was published in 2001, studies showed that only about 1.2% encodes proteins, the rest being deemed "non-coding." It was later shown that the genome is pervasively transcribed into many ncRNAs, but their functionality remained controversial. Since then, regulatory lncRNAs have been characterized in many species and were shown to be involved in processes such as development and pathologies, revealing a new layer of regulation in eukaryotic cells. This newly found focus on lncRNAs, together with the advent of high-throughput sequencing, was accompanied by the rapid discovery of many novel transcripts which were further characterized and classified according to specific transcript traits.In this review, we will discuss the many discoveries that led to the study of lncRNAs, from Friedrich Miescher's "nuclein" in 1869 to the elucidation of the human genome and transcriptome in the early 2000s. We will then focus on the biological relevance during lncRNA evolution and describe their basic features as genes and transcripts. Finally, we will present a non-exhaustive catalogue of lncRNA classes, thus illustrating the vast complexity of eukaryotic transcriptomes.
Collapse
Affiliation(s)
- Julien Jarroux
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France.
| | - Marina Pinskaya
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France
| |
Collapse
|
235
|
Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, de Silva N, Kasukurthi MV, Jha VK, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M. The development of non-coding RNA ontology. INT J DATA MIN BIOIN 2016; 15:214-232. [PMID: 27990175 DOI: 10.1504/ijdmb.2016.077072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data.
Collapse
Affiliation(s)
- Jingshan Huang
- School of Computing, University of South Alabama, Shelby Hall, Room 1123, 150 Jaguar Drive Mobile, AL 36688, USA,
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA,
| | - Barry Smith
- University at Buffalo - SUNY, Buffalo, New York 14260, USA,
| | | | - Dejing Dou
- Computer and Information Science Department, University of Oregon, Eugene, Oregon 97403, USA,
| | - Weili Huang
- Miracle Query, Inc., Eugene, Oregon 97405, USA,
| | - Darren A Natale
- Georgetown University Medical Center, Washington DC 20007, USA,
| | | | - Jun Huan
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, Kansas 66045, USA,
| | - Michael T Zimmermann
- Division of Biomedical Statistics and Informatics, College of Medicine at Mayo Clinic, Rochester, Minnesota 55905, USA,
| | - Guoqian Jiang
- Division of Biomedical Statistics and Informatics, College of Medicine at Mayo Clinic, Rochester, Minnesota 55905, USA,
| | - Yu Lin
- Data Coordination and Integration Center, University of Miami, Miami, Florida 33146, USA,
| | - Bin Wu
- Endocrinology Department, Kunming Medical University, Kunming, Yunnan, 650032 China,
| | - Harrison J Strachan
- School of Computing, University of South Alabama, Mobile, Alabama 36688, USA,
| | - Nisansa de Silva
- Computer and Information Science, University of Oregon, Eugene, Oregon 97403, USA,
| | | | - Vikash Kumar Jha
- School of Computing, University of South Alabama, Mobile, Alabama 36688, USA,
| | - Yongqun He
- Lab Animal Medicine, Microbiology, Immunology and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA,
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, Florida 32816, USA,
| | - Xiaowei Wang
- Cancer Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA,
| | - Zixing Liu
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604, USA,
| | - Glen M Borchert
- Department of Biology, University of South Alabama, Mobile, Alabama 36688, USA,
| | - Ming Tan
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604, USA,
| |
Collapse
|
236
|
A Review of Computational Methods for Finding Non-Coding RNA Genes. Genes (Basel) 2016; 7:genes7120113. [PMID: 27918472 PMCID: PMC5192489 DOI: 10.3390/genes7120113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/04/2016] [Accepted: 11/17/2016] [Indexed: 12/19/2022] Open
Abstract
Finding non-coding RNA (ncRNA) genes has emerged over the past few years as a cutting-edge trend in bioinformatics. There are numerous computational intelligence (CI) challenges in the annotation and interpretation of ncRNAs because it requires a domain-related expert knowledge in CI techniques. Moreover, there are many classes predicted yet not experimentally verified by researchers. Recently, researchers have applied many CI methods to predict the classes of ncRNAs. However, the diverse CI approaches lack a definitive classification framework to take advantage of past studies. A few review papers have attempted to summarize CI approaches, but focused on the particular methodological viewpoints. Accordingly, in this article, we summarize in greater detail than previously available, the CI techniques for finding ncRNAs genes. We differentiate from the existing bodies of research and discuss concisely the technical merits of various techniques. Lastly, we review the limitations of ncRNA gene-finding CI methods with a point-of-view towards the development of new computational tools.
Collapse
|
237
|
Iguchi E, Safgren SL, Marks DL, Olson RL, Fernandez-Zapico ME. Pancreatic Cancer, A Mis-interpreter of the Epigenetic Language. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:575-590. [PMID: 28018146 PMCID: PMC5168833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pancreatic cancer is the third leading cause of cancer mortality in the U.S. with close to 40,000 deaths per year. Pancreatic ductal adenocarcinoma (PDAC) represents approximately 90 percent of all pancreatic cancer cases and is the most lethal form of the disease. Current therapies for PDAC are ineffective and most patients cannot be treated by surgical resection. Most research efforts have primarily focused on how genetic alterations cause, alter progression, contribute to diagnosis, and influence PDAC management. Over the past two decades, a model has been advanced of PDAC initiation and progression as a multi-step process driven by the acquisition of mutations leading to loss of tumor suppressors and activation of oncogenes. The recognition of the essential roles of these genetic alterations in the development of PDAC has revolutionized our knowledge of this disease. However, none of these findings have turned into effective treatment for this dismal malignancy. In recent years, studies in the areas of chromatin modifications, and non-coding RNAs have uncovered mechanisms for regulating gene expression which occur independently of genetic alterations. Chromatin-based mechanisms are interwoven with microRNA-driven regulation of protein translation to create an integrated epigenetic language, which is grossly dysregulated in PDAC. Thus in PDAC, key tumor suppressors that are well established to play a role in PDAC may be repressed, and oncogenes can be upregulated secondary to epigenetic alterations. Unlike mutations, epigenetic changes are potentially reversible. Given this feature of epigenetic mechanisms, it is conceivable that targeting epigenetic-based events promoting and maintaining PDAC could serve as foundation for the development of new therapeutic and diagnostic approaches for this disease.
Collapse
Affiliation(s)
- Eriko Iguchi
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | - David L. Marks
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Rachel L. Olson
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | |
Collapse
|
238
|
Gokoolparsadh A, Sutton GJ, Charamko A, Green NFO, Pardy CJ, Voineagu I. Searching for convergent pathways in autism spectrum disorders: insights from human brain transcriptome studies. Cell Mol Life Sci 2016; 73:4517-4530. [PMID: 27405608 PMCID: PMC11108267 DOI: 10.1007/s00018-016-2304-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/16/2016] [Accepted: 07/05/2016] [Indexed: 01/07/2023]
Abstract
Autism spectrum disorder (ASD) is one of the most heritable neuropsychiatric conditions. The complex genetic landscape of the disorder includes both common and rare variants at hundreds of genetic loci. This marked heterogeneity has thus far hampered efforts to develop genetic diagnostic panels and targeted pharmacological therapies. Here, we give an overview of the current literature on the genetic basis of ASD, and review recent human brain transcriptome studies and their role in identifying convergent pathways downstream of the heterogeneous genetic variants. We also discuss emerging evidence on the involvement of non-coding genomic regions and non-coding RNAs in ASD.
Collapse
Affiliation(s)
- Akira Gokoolparsadh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Gavin J Sutton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Alexiy Charamko
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Nicole F Oldham Green
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Christopher J Pardy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia.
| |
Collapse
|
239
|
ALS and FTD: an epigenetic perspective. Acta Neuropathol 2016; 132:487-502. [PMID: 27282474 DOI: 10.1007/s00401-016-1587-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/17/2016] [Accepted: 06/02/2016] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two fatal neurodegenerative diseases seen in comorbidity in up to 50 % of cases. Despite tremendous efforts over the last two decades, no biomarkers or effective therapeutics have been identified to prevent, decelerate, or stop neuronal death in patients. While the identification of multiple mutations in more than two dozen genes elucidated the involvement of several mechanisms in the pathogenesis of both diseases, identifying the hexanucleotide repeat expansion in C9orf72, the most common genetic abnormality in ALS and FTD, opened the door to the discovery of several novel pathogenic biological routes, including chromatin remodeling and transcriptome alteration. Epigenetic processes regulate DNA replication and repair, RNA transcription, and chromatin conformation, which in turn further dictate transcriptional regulation and protein translation. Transcriptional and post-transcriptional epigenetic regulation is mediated by enzymes and chromatin-modifying complexes that control DNA methylation, histone modifications, and RNA editing. While the alteration of DNA methylation and histone modification has recently been reported in ALS and FTD, the assessment of epigenetic involvement in both diseases is still at an early stage, and the involvement of multiple epigenetic players still needs to be evaluated. As the epigenome serves as a way to alter genetic information not only during aging, but also following environmental signals, epigenetic mechanisms might play a central role in initiating ALS and FTD, especially for sporadic cases. Here, we provide a review of what is currently known about altered epigenetic processes in both ALS and FTD and discuss potential therapeutic strategies targeting epigenetic mechanisms. As approximately 85 % of ALS and FTD cases are still genetically unexplained, epigenetic therapeutics explored for other diseases might represent a profitable direction for the field.
Collapse
|
240
|
Munkácsy G, Sztupinszki Z, Herman P, Bán B, Pénzváltó Z, Szarvas N, Győrffy B. Validation of RNAi Silencing Efficiency Using Gene Array Data shows 18.5% Failure Rate across 429 Independent Experiments. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e366. [PMID: 27673562 PMCID: PMC5056990 DOI: 10.1038/mtna.2016.66] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 01/31/2023]
Abstract
No independent cross-validation of success rate for studies utilizing small interfering RNA (siRNA) for gene silencing has been completed before. To assess the influence of experimental parameters like cell line, transfection technique, validation method, and type of control, we have to validate these in a large set of studies. We utilized gene chip data published for siRNA experiments to assess success rate and to compare methods used in these experiments. We searched NCBI GEO for samples with whole transcriptome analysis before and after gene silencing and evaluated the efficiency for the target and off-target genes using the array-based expression data. Wilcoxon signed-rank test was used to assess silencing efficacy and Kruskal–Wallis tests and Spearman rank correlation were used to evaluate study parameters. All together 1,643 samples representing 429 experiments published in 207 studies were evaluated. The fold change (FC) of down-regulation of the target gene was above 0.7 in 18.5% and was above 0.5 in 38.7% of experiments. Silencing efficiency was lowest in MCF7 and highest in SW480 cells (FC = 0.59 and FC = 0.30, respectively, P = 9.3E−06). Studies utilizing Western blot for validation performed better than those with quantitative polymerase chain reaction (qPCR) or microarray (FC = 0.43, FC = 0.47, and FC = 0.55, respectively, P = 2.8E−04). There was no correlation between type of control, transfection method, publication year, and silencing efficiency. Although gene silencing is a robust feature successfully cross-validated in the majority of experiments, efficiency remained insufficient in a significant proportion of studies. Selection of cell line model and validation method had the highest influence on silencing proficiency.
Collapse
Affiliation(s)
- Gyöngyi Munkácsy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary.,MTA-SE Pediatrics and Nephrology Research Group, Budapest, Hungary
| | - Zsófia Sztupinszki
- Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Péter Herman
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary
| | - Bence Bán
- Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Zsófia Pénzváltó
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary
| | - Nóra Szarvas
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary.,Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| |
Collapse
|
241
|
Zhai N, Xia Y, Yin R, Liu J, Gao F. A negative regulation loop of long noncoding RNA HOTAIR and p53 in non-small-cell lung cancer. Onco Targets Ther 2016; 9:5713-5720. [PMID: 27695348 PMCID: PMC5033503 DOI: 10.2147/ott.s110219] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) is one of the leading causes of cancer-related death worldwide, and the 5-year survival rate is still low despite advances in diagnosis and therapeutics. A long noncoding RNA (lncRNA) HOX antisense intergenic RNA (HOTAIR) has been revealed to play important roles in NSCLC carcinogenesis but the detailed mechanisms are still unclear. In the current study, we aimed to investigate the regulation between the lncRNA HOTAIR and p53 in the NSCLC patient samples and cell lines. Our results showed that HOTAIR expression was significantly higher in the cancer tissues than that in the adjacent normal tissue, and was negatively correlated with p53 functionality rather than expression. When p53 was overexpressed in A549 cells, the lncRNA HOTAIR expression was downregulated, and the cell proliferation rate and cell invasion capacity decreased as a consequence. We identified two binding sites of p53 on the promoter region of HOTAIR, where the p53 protein would bind to and suppress the HOTAIR mRNA transcription. Inversely, overexpression of lncRNA HOTAIR inhibited the expression of p53 in A549 cells. Mechanistic studies revealed that HOTAIR modified the promoter of p53 and enhanced histone H3 lysine 27 trimethylation (H3K27me3). These studies identified a specific negative regulation loop of lncRNA HOTAIR and p53 in NSCLC cells, which revealed a new understanding of tumorigenesis in p53 dysfunction NSCLC cells.
Collapse
Affiliation(s)
- Nailiang Zhai
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University
| | - Yongfu Xia
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University
| | - Rui Yin
- Department of Respiratory Medicine, People's Hospital of Binzhou City
| | - Jinping Liu
- Department of Pharmacology, Binzhou Medical University, Binzhou, Shandong, People's Republic of China
| | - Fuquan Gao
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University
| |
Collapse
|
242
|
Gao YF, Wang ZB, Zhu T, Mao CX, Mao XY, Li L, Yin JY, Zhou HH, Liu ZQ. A critical overview of long non-coding RNA in glioma etiology 2016: an update. Tumour Biol 2016; 37:14403-14413. [DOI: 10.1007/s13277-016-5307-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/05/2016] [Indexed: 12/31/2022] Open
|
243
|
Qu J, Zhao M, Hsiang T, Feng X, Zhang J, Huang C. Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2503023. [PMID: 27703969 PMCID: PMC5040776 DOI: 10.1155/2016/2503023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/21/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022]
Abstract
Noncoding RNAs (ncRNAs) have been identified in many fungi. However, no genome-scale identification of ncRNAs has been inventoried for basidiomycetes. In this research, we detected 254 small noncoding RNAs (sncRNAs) in a genome assembly of an isolate (CCEF00389) of Pleurotus ostreatus, which is a widely cultivated edible basidiomycetous fungus worldwide. The identified sncRNAs include snRNAs, snoRNAs, tRNAs, and miRNAs. SnRNA U1 was not found in CCEF00389 genome assembly and some other basidiomycetous genomes by BLASTn. This implies that if snRNA U1 of basidiomycetes exists, it has a sequence that varies significantly from other organisms. By analyzing the distribution of sncRNA loci, we found that snRNAs and most tRNAs (88.6%) were located in pseudo-UTR regions, while miRNAs are commonly found in introns. To analyze the evolutionary conservation of the sncRNAs in P. ostreatus, we aligned all 254 sncRNAs to the genome assemblies of some other Agaricomycotina fungi. The results suggest that most sncRNAs (77.56%) were highly conserved in P. ostreatus, and 20% were conserved in Agaricomycotina fungi. These findings indicate that most sncRNAs of P. ostreatus were not conserved across Agaricomycotina fungi.
Collapse
Affiliation(s)
- Jibin Qu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Mengran Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Xiaoxing Feng
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Micro & Nano Research Institute of IC and System Applications, Shenzhen, Guangdong, China
| | - Jinxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| |
Collapse
|
244
|
Shapiro JA. Exploring the read-write genome: mobile DNA and mammalian adaptation. Crit Rev Biochem Mol Biol 2016; 52:1-17. [DOI: 10.1080/10409238.2016.1226748] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| |
Collapse
|
245
|
Veneziano D, Di Bella S, Nigita G, Laganà A, Ferro A, Croce CM. Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges. Hum Mutat 2016; 37:1283-1298. [PMID: 27516218 DOI: 10.1002/humu.23066] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/09/2016] [Indexed: 02/06/2023]
Abstract
One of the most significant biological discoveries of the last decade is represented by the reality that the vast majority of the transcribed genomic output comprises diverse classes of noncoding RNAs (ncRNAs) that may play key roles and/or be affected by many biochemical cellular processes (i.e., RNA editing), with implications in human health and disease. With 90% of the human genome being transcribed and novel classes of ncRNA emerging (tRNA-derived small RNAs and circular RNAs among others), the great majority of the human transcriptome suggests that many important ncRNA functions/processes are yet to be discovered. An approach to filling such vast void of knowledge has been recently provided by the increasing application of next-generation sequencing (NGS), offering the unprecedented opportunity to obtain a more accurate profiling with higher resolution, increased throughput, sequencing depth, and low experimental complexity, concurrently posing an increasing challenge in terms of efficiency, accuracy, and usability of data analysis software. This review provides an overview of ncRNAs, NGS technology, and the most recent/popular computational approaches and the challenges they attempt to solve, which are essential to a more sensitive and comprehensive ncRNA annotation capable of furthering our understanding of this still vastly uncharted genomic territory.
Collapse
Affiliation(s)
- Dario Veneziano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210
| | | | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210
| | - Alessandro Laganà
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, 10029
| | - Afredo Ferro
- Department of Clinical and Molecular Biomedicine, University of Catania, Catania, 95125, Italy
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210
| |
Collapse
|
246
|
Motterle A, Sanchez-Parra C, Regazzi R. Role of long non-coding RNAs in the determination of β-cell identity. Diabetes Obes Metab 2016; 18 Suppl 1:41-50. [PMID: 27615130 DOI: 10.1111/dom.12714] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/04/2016] [Indexed: 12/22/2022]
Abstract
Pancreatic β-cells are highly specialized cells committed to secrete insulin in response to changes in the level of nutrients, hormones and neurotransmitters. Chronic exposure to elevated concentrations of glucose, fatty acids or inflammatory mediators can result in modifications in β-cell gene expression that alter their functional properties. This can lead to the release of insufficient amount of insulin to cover the organism's needs, and thus to the development of diabetes mellitus. Although most of the studies carried out in the last decades to elucidate the causes of β-cell dysfunction under disease conditions have focused on protein-coding genes, we now know that insulin-secreting cells also contain thousands of molecules of RNA that do not encode polypeptides but play key roles in the acquisition and maintenance of a highly differentiated state. In this review, we will highlight the involvement of long non-coding RNAs (lncRNAs), a particular class of non-coding transcripts, in the differentiation of β-cells and in the regulation of their specialized tasks. We will also discuss the crosstalk between the activities of lncRNAs and microRNAs and present the emerging evidence of a potential contribution of particular lncRNAs to the development of both type 1 and type 2 diabetes.
Collapse
Affiliation(s)
- A Motterle
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.
| | - C Sanchez-Parra
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - R Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
247
|
Biomarkers of genome instability and cancer epigenetics. Tumour Biol 2016; 37:13029-13038. [DOI: 10.1007/s13277-016-5278-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/15/2016] [Indexed: 02/06/2023] Open
|
248
|
Shang D, Zheng T, Zhang J, Tian Y, Liu Y. Profiling of mRNA and long non-coding RNA of urothelial cancer in recipients after renal transplantation. Tumour Biol 2016; 37:12673-12684. [PMID: 27448299 DOI: 10.1007/s13277-016-5148-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/11/2016] [Indexed: 12/14/2022] Open
Abstract
The molecular mechanism and signal transduction pathways involved in urothelial cancer (UC) after renal transplantation (RTx) remain unknown. In this study, we investigated the profiling of messenger RNA (mRNA) and long non-coding RNA (lncRNA) in RTx recipients with UC. The mRNA and lncRNA of six pairs of UC and corresponding normal urothelial tissues in RTx recipients were profiled using Arraystar Human lncRNA Microarray V3.0, which is designed for the global profiling of 26,109 coding transcripts and 30,586 lncRNAs. Quantitative real-time PCR (qRT-PCR) was used to validate the differentially expressed mRNAs and lncRNAs. Molecular function classification and biological process classification for the differentially expressed mRNAs were analyzed with Gene Ontology. The key pathways that were associated with UC after RTx were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Compared to normal urothelial tissues, 1597 mRNAs were upregulated and 1032 mRNAs were downregulated in UC; 2107 lncRNAs were upregulated and 1794 lncRNAs were downregulated (greater than twofold). Further qRT-PCR analysis of mRNA and lncRNA expression showed well consistency with the data of microarray analysis. The expression of matrix metalloprotease (MMP)-3, MMP-10, MMP-12, and MMP-13 was significantly increased, while the expression of CD36 was decreased in UC after RTx. Co-expression analysis of lncRNAs and their nearby coding genes showed that lncRNAs may play critical roles in regulating nearby genes in the carcinogenesis of UC. Our results also suggest that peroxisome proliferator-activated receptor (PPAR) signaling may be involved in UC after RTx. Moreover, several cytokines and their receptors were also significantly upregulated in UC after RTx, suggesting that cytokines might be modulated and participated in the carcinogenesis of UC after RTx. We analyzed the potential molecular mechanism and pathways involved in the UC of RTx recipients. Our results revealed that several key regulatory pathways and lncRNAs play critical roles in the carcinogenesis of UC, and suggest that UC in RTx recipients may be more likely to invade and metastasis. However, the detailed functional analysis of these mechanisms should be further performed in the future.
Collapse
Affiliation(s)
- Donghao Shang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Tie Zheng
- Department of Cardiovascular Surgery, Beijing Aortic Disease Center, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Engineering Research Center for Vascular Prostheses, Beijing, 100029, China
| | - Jian Zhang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Ye Tian
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Yuting Liu
- Department of Pathology, Capital Medical University, Beijing, 100069, China.
| |
Collapse
|
249
|
Arnes L, Akerman I, Balderes DA, Ferrer J, Sussel L. βlinc1 encodes a long noncoding RNA that regulates islet β-cell formation and function. Genes Dev 2016; 30:502-7. [PMID: 26944677 PMCID: PMC4782045 DOI: 10.1101/gad.273821.115] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Pancreatic β cells are responsible for maintaining glucose homeostasis; their absence or malfunction results in diabetes mellitus. Although there is evidence that long noncoding RNAs (lncRNAs) play important roles in development and disease, none have been investigated in vivo in the context of pancreas development. In this study, we demonstrate that βlinc1 (β-cell long intergenic noncoding RNA 1), a conserved lncRNA, is necessary for the specification and function of insulin-producing β cells through the coordinated regulation of a number of islet-specific transcription factors located in the genomic vicinity of βlinc1. Furthermore, deletion of βlinc1 results in defective islet development and disruption of glucose homeostasis in adult mice.
Collapse
Affiliation(s)
- Luis Arnes
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
| | - Ildem Akerman
- Genomic Programming of Β-Cells Laboratory, Institut d'Investigacions August Pi I Sunyer (IDIBAPS), Barcelona 08036, Spain; Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Dina A Balderes
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
| | - Jorge Ferrer
- Genomic Programming of Β-Cells Laboratory, Institut d'Investigacions August Pi I Sunyer (IDIBAPS), Barcelona 08036, Spain; Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Lori Sussel
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
| |
Collapse
|
250
|
Luan Y, Li D, Gao L, Xie S, Pei L. A single nucleotide polymorphism in hsa‑miR‑146a is responsible for the development of bronchial hyperresponsiveness in response to intubation during general anesthesia. Mol Med Rep 2016; 14:2297-304. [PMID: 27431205 DOI: 10.3892/mmr.2016.5499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 04/27/2016] [Indexed: 11/06/2022] Open
Abstract
Bronchial hyperresponsiveness (BHR) is the most common clinical manifestation identified in asthmatic patients, and intubation is the major factor that stimulates the airway of patients receiving general anesthetic. In the present study, nitric oxide synthase 1 (NOS1) was identified as a target gene of micro (mi)R‑146a using in silico analysis and luciferase assay. Furthermore, the regulatory role of miR‑146a was demonstrated by the observation that the NOS1 expression level in pulmonary artery smooth muscle cells (PASMCs) transfected with miR‑146a mimics was significantly downregulated and the NOS1 expression level in PASMCs transfected with miR‑146a inhibitors was significantly upregulated. Additionally, it was identified that a polymorphism in pri‑miR‑146 interfered with mature processing and reduced the quantity of mature miRNA. To assess the association between the polymorphism and the development of BHR, 563 patients with basic pulmonary diseases, such as asthma, emphysema or bronchitis were enrolled in the present study. Each participant received a general anesthetic and the development of BHR was evaluated. The miR‑146a rs2910164 polymorphism CC genotype was identified to be significantly associated with a decreased risk of BHR in response to intubation when compared with the GG or GC genotype (odds ratio, 0.38; confidence interval, 0.18‑0.78). These findings indicate that the miR‑146a rs2910164 polymorphism is associated with a decrease risk of BHR, and the CC genotype increased the level of NOS1 expression, which was physiologically inhibited by wild‑type miR‑146a.
Collapse
Affiliation(s)
- Yong Luan
- Department of Anesthesiology, The First Hospital of China Medical University, Dalian, Liaoning 110000, P.R. China
| | - Dongjiang Li
- Department of Anesthesiology, The First Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
| | - Lulu Gao
- Department of Anesthesiology, The First Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
| | - Sha Xie
- Department of Anesthesiology, The First Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
| | - Ling Pei
- Department of Anesthesiology, The First Hospital of China Medical University, Dalian, Liaoning 110000, P.R. China
| |
Collapse
|