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Etebari K, Furlong MJ, Asgari S. Genome wide discovery of long intergenic non-coding RNAs in Diamondback moth (Plutella xylostella) and their expression in insecticide resistant strains. Sci Rep 2015; 5:14642. [PMID: 26411386 PMCID: PMC4585956 DOI: 10.1038/srep14642] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/02/2015] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in genomic imprinting, cancer, differentiation and regulation of gene expression. Here, we identified 3844 long intergenic ncRNAs (lincRNA) in Plutella xylostella, which is a notorious pest of cruciferous plants that has developed field resistance to all classes of insecticides, including Bacillus thuringiensis (Bt) endotoxins. Further, we found that some of those lincRNAs may potentially serve as precursors for the production of small ncRNAs. We found 280 and 350 lincRNAs that are differentially expressed in Chlorpyrifos and Fipronil resistant larvae. A survey on P. xylostella midgut transcriptome data from Bt-resistant populations revealed 59 altered lincRNA in two resistant strains compared with the susceptible population. We validated the transcript levels of a number of putative lincRNAs in deltamethrin-resistant larvae that were exposed to deltamethrin, which indicated that this group of lincRNAs might be involved in the response to xenobiotics in this insect. To functionally characterize DBM lincRNAs, gene ontology (GO) enrichment of their associated protein-coding genes was extracted and showed over representation of protein, DNA and RNA binding GO terms. The data presented here will facilitate future studies to unravel the function of lincRNAs in insecticide resistance or the response to xenobiotics of eukaryotic cells.
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Affiliation(s)
- Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
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52
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Kang M, Sang Y, Gu H, Zheng L, Wang L, Liu C, Shi Y, Shao A, Ding G, Chen S, Tang W, Yin J. Long noncoding RNAs POLR2E rs3787016 C/T and HULC rs7763881 A/C polymorphisms are associated with decreased risk of esophageal cancer. Tumour Biol 2015; 36:6401-8. [PMID: 25874495 DOI: 10.1007/s13277-015-3328-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/12/2015] [Indexed: 11/28/2022] Open
Abstract
Worldwide, rates of esophageal cancer have been keeping highly in recent decades. Genetic variants in multiple cellular pathways might play an important role in altering risk of esophageal carcinoma. In this study, long noncoding RNAs (lncRNAs) functional single nucleotide polymorphisms (SNPs) were investigated in Chinese Han populations. We have genotyped the ANRIL rs2151280 T/C, POLR2E rs3787016 C/T, and HULC rs7763881 A/C SNPs in 380 esophageal squamous cell carcinoma (ESCC) cases and 380 cancer-free controls. POLR2E rs3787016 C/T was associated with a significantly decreased risk for ESCC (CT vs. CC: OR 0.62, 95 % CI 0.44-0.87, P = 0.005; adjusted OR 0.62, 95 % CI 0.44-0.87, P = 0.005). The other SNP, HULC rs7763881, also showed a suggestive association (AC vs. AA: OR 0.70, 95 % CI 0.50-0.98, P = 0.037; adjusted OR 0.69, 95 % CI 0.49-0.97, P = 0.031). ANRIL rs2151280 T/C SNP was not associated with risk of ESCC. In the future, larger studies with other ethnic populations, tissue-specific biological characterization, and detailed individual information should be undertaken to validate current findings.
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Affiliation(s)
- Mingqiang Kang
- Department of Thoracic Surgery, Affiliated Union Hospital, Fujian Medical University, Fuzhou, 350001, Fujian Province, China,
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Dynamics of hnRNPs and omega speckles in normal and heat shocked live cell nuclei of Drosophila melanogaster. Chromosoma 2015; 124:367-83. [PMID: 25663367 DOI: 10.1007/s00412-015-0506-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/27/2014] [Accepted: 01/20/2015] [Indexed: 01/14/2023]
Abstract
The nucleus limited long-noncoding hsrω-n transcripts, hnRNPs, and some other RNA processing proteins organize nucleoplasmic omega speckles in Drosophila. Unlike other nuclear speckles, omega speckles rapidly disappear following cell stress, while hnRNPs and other associated proteins move away from chromosome sites, nucleoplasm, and the disappearing speckles to get uniquely sequestered at hsrω locus. Omega speckles reappear and hnRNPs get redistributed to normal locations during recovery from stress. With a view to understand the dynamics of omega speckles and their associated proteins, we used live imaging of GFP tagged hnRNPs (Hrb87F, Hrb98DE, or Squid) in unstressed and stressed Drosophila cells. Omega speckles display size-dependent mobility in nucleoplasmic domains with significant colocalization with nuclear matrix Tpr/Megator and SAFB proteins, which also accumulate at hsrω gene site after stress. Instead of moving towards the nuclear periphery located hsrω locus following heat shock or colchicine treatment, omega speckles rapidly disappear within nucleoplasm while chromosomal and nucleoplasmic hnRNPs move, stochastically or, more likely, by nuclear matrix-mediated transport to hsrω locus in non-particulate form. Continuing transcription of hsrω during cell stress is essential for sequestering incoming hnRNPs at the site. While recovering from stress, the sequestered hnRNPs are released as omega speckles in ISWI-dependent manner. Photobleaching studies reveal hnRNPs to freely move between nucleoplasm, omega speckles, chromosome regions, and hsrω gene site although their residence periods at chromosomes and hsrω locus are longer. A model for regulation of exchange of hnRNPs between nuclear compartments by hsrω-n transcripts is presented.
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Xu MD, Qi P, Du X. Long non-coding RNAs in colorectal cancer: implications for pathogenesis and clinical application. Mod Pathol 2014; 27:1310-20. [PMID: 24603586 DOI: 10.1038/modpathol.2014.33] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 12/14/2013] [Accepted: 12/17/2013] [Indexed: 01/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a class of newly identified non-coding RNA molecules that are emerging as key regulators of tumor initiation and development. Colorectal cancer (CRC) remains a major health problem worldwide, and there remains a need to further refine the current screening approaches as well as provide tailored diagnostic and therapeutic approaches. Multiple dysregulated lncRNAs participate in tumorigenesis through a variety of molecular mechanisms, and various regulatory factors frequently contribute to the aberrant expression of lncRNAs in CRC, thereby allowing malignant transformation. Additionally, the association of dysregulated lncRNAs with specific developmental stages and clinical outcomes indicates their potential as strong diagnostic and prognostic predictors as well as therapeutic targets. Here we provide a brief overview of the known functions of CRC-associated lncRNAs, describe some potential molecular mechanisms that underlie changes in lncRNA expression in CRC, and attempt to uncover their clinical and therapeutic potential.
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Affiliation(s)
- Mi-Die Xu
- 1] Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China [2] Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China [3] Institute of Pathology, Fudan University, Shanghai, China
| | - Peng Qi
- 1] Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China [2] Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China [3] Institute of Pathology, Fudan University, Shanghai, China
| | - Xiang Du
- 1] Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China [2] Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China [3] Institute of Pathology, Fudan University, Shanghai, China [4] Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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56
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Tani H, Onuma Y, Ito Y, Torimura M. Long non-coding RNAs as surrogate indicators for chemical stress responses in human-induced pluripotent stem cells. PLoS One 2014; 9:e106282. [PMID: 25171338 PMCID: PMC4149554 DOI: 10.1371/journal.pone.0106282] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/03/2014] [Indexed: 01/08/2023] Open
Abstract
In this study, we focused on two biological products as ideal tools for toxicological assessment: long non-coding RNAs (lncRNAs) and human-induced pluripotent stem cells (hiPSCs). lncRNAs are an important class of pervasive non-protein-coding transcripts involved in the molecular mechanisms associated with responses to cellular stresses. hiPSCs possess the capabilities of self-renewal and differentiation into multiple cell types, and they are free of the ethical issues associated with human embryonic stem cells. Here, we identified six novel lncRNAs (CDKN2B-AS1, MIR22HG, GABPB1-AS1, FLJ33630, LINC00152, and LINC0541471_v2) that respond to model chemical stresses (cycloheximide, hydrogen peroxide, cadmium, or arsenic) in hiPSCs. Our results indicated that the lncRNAs responded to general and specific chemical stresses. Compared with typical mRNAs such as p53-related mRNAs, the lncRNAs highly and rapidly responded to chemical stresses. We propose that these lncRNAs have the potential to be surrogate indicators of chemical stress responses in hiPSCs.
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Affiliation(s)
- Hidenori Tani
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1, Onogawa, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Yasuko Onuma
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
| | - Yuzuru Ito
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
| | - Masaki Torimura
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1, Onogawa, Tsukuba, Ibaraki, Japan
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57
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Kambara H, Niazi F, Kostadinova L, Moonka DK, Siegel CT, Post AB, Carnero E, Barriocanal M, Fortes P, Anthony DD, Valadkhan S. Negative regulation of the interferon response by an interferon-induced long non-coding RNA. Nucleic Acids Res 2014; 42:10668-80. [PMID: 25122750 PMCID: PMC4176326 DOI: 10.1093/nar/gku713] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play critical roles in diverse cellular processes; however, their involvement in many critical aspects of the immune response including the interferon (IFN) response remains poorly understood. To address this gap, we compared the global gene expression pattern of primary human hepatocytes before and at three time points after treatment with IFN-α. Among ∼200 IFN-induced lncRNAs, one transcript showed ∼100-fold induction. This RNA, which we named lncRNA-CMPK2, was a spliced, polyadenylated nuclear transcript that was induced by IFN in diverse cell types from human and mouse. Similar to protein-coding IFN-stimulated genes (ISGs), its induction was dependent on JAK-STAT signaling. Intriguingly, knockdown of lncRNA-CMPK2 resulted in a marked reduction in HCV replication in IFN-stimulated hepatocytes, suggesting that it could affect the antiviral role of IFN. We could show that lncRNA-CMPK2 knockdown resulted in upregulation of several protein-coding antiviral ISGs. The observed upregulation was caused by an increase in both basal and IFN-stimulated transcription, consistent with loss of transcriptional inhibition in knockdown cells. These results indicate that the IFN response involves a lncRNA-mediated negative regulatory mechanism. lncRNA-CMPK2 was strongly upregulated in a subset of HCV-infected human livers, suggesting a role in modulation of the IFN response in vivo.
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Affiliation(s)
- Hiroto Kambara
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Farshad Niazi
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Lenche Kostadinova
- Divisions of Infectious and Rheumatic Diseases, Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Dilip K Moonka
- Division of Gastroenterology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Christopher T Siegel
- Department of Surgery, University Hospitals Case Medical Center, Cleveland, OH 44106, USA
| | - Anthony B Post
- Department of Gastroenterology, University Hospitals Case Medical Center, Cleveland, OH 44106, USA
| | - Elena Carnero
- Department of Hepatology and Gene Therapy, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Marina Barriocanal
- Department of Hepatology and Gene Therapy, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Puri Fortes
- Department of Hepatology and Gene Therapy, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Donald D Anthony
- Divisions of Infectious and Rheumatic Diseases, Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Saba Valadkhan
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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58
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Mahboubi H, Stochaj U. Nucleoli and Stress Granules: Connecting Distant Relatives. Traffic 2014; 15:1179-93. [DOI: 10.1111/tra.12191] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Hicham Mahboubi
- Department of Physiology; McGill University; 3655 Promenade Sir William Osler Montreal Quebec H3G 1Y6 Canada
| | - Ursula Stochaj
- Department of Physiology; McGill University; 3655 Promenade Sir William Osler Montreal Quebec H3G 1Y6 Canada
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59
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Lin M, Zhao D, Hrabovsky A, Pedrosa E, Zheng D, Lachman HM. Heat shock alters the expression of schizophrenia and autism candidate genes in an induced pluripotent stem cell model of the human telencephalon. PLoS One 2014; 9:e94968. [PMID: 24736721 PMCID: PMC3988108 DOI: 10.1371/journal.pone.0094968] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/21/2014] [Indexed: 01/08/2023] Open
Abstract
Schizophrenia (SZ) and autism spectrum disorders (ASD) are highly heritable neuropsychiatric disorders, although environmental factors, such as maternal immune activation (MIA), play a role as well. Cytokines mediate the effects of MIA on neurogenesis and behavior in animal models. However, MIA stimulators can also induce a febrile reaction, which could have independent effects on neurogenesis through heat shock (HS)-regulated cellular stress pathways. However, this has not been well-studied. To help understand the role of fever in MIA, we used a recently described model of human brain development in which induced pluripotent stem cells (iPSCs) differentiate into 3-dimensional neuronal aggregates that resemble a first trimester telencephalon. RNA-seq was carried out on aggregates that were heat shocked at 39°C for 24 hours, along with their control partners maintained at 37°C. 186 genes showed significant differences in expression following HS (p<0.05), including known HS-inducible genes, as expected, as well as those coding for NGFR and a number of SZ and ASD candidates, including SMARCA2, DPP10, ARNT2, AHI1 and ZNF804A. The degree to which the expression of these genes decrease or increase during HS is similar to that found in copy loss and copy gain copy number variants (CNVs), although the effects of HS are likely to be transient. The dramatic effect on the expression of some SZ and ASD genes places HS, and perhaps other cellular stressors, into a common conceptual framework with disease-causing genetic variants. The findings also suggest that some candidate genes that are assumed to have a relatively limited impact on SZ and ASD pathogenesis based on a small number of positive genetic findings, such as SMARCA2 and ARNT2, may in fact have a much more substantial role in these disorders - as targets of common environmental stressors.
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Affiliation(s)
- Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Dejian Zhao
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Anastasia Hrabovsky
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (HML); (D. Zheng)
| | - Herbert M. Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (HML); (D. Zheng)
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60
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Amaral PP, Dinger ME, Mattick JS. Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective. Brief Funct Genomics 2013; 12:254-78. [PMID: 23709461 DOI: 10.1093/bfgp/elt016] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cells and organisms are subject to challenges and perturbations in their environment and physiology in all stages of life. The molecular response to such changes, including insulting conditions such as pathogen infections, involves coordinated modulation of gene expression programmes and has not only homeostatic but also ecological and evolutionary importance. Although attention has been primarily focused on signalling pathways and protein networks, non-coding RNAs (ncRNAs), which comprise a significant output of the genomes of prokaryotes and especially eukaryotes, are increasingly implicated in the molecular mechanisms of these responses. Long and short ncRNAs not only regulate development and cell physiology, they are also involved in disease states, including cancers, in host-pathogen interactions, and in a variety of stress responses. Indeed, regulatory RNAs are part of genetically encoded response networks and also underpin epigenetic processes, which are emerging as key mechanisms of adaptation and transgenerational inheritance. Here we present the growing evidence that ncRNAs are intrinsically involved in cellular and organismal adaptation processes, in both robustness and protection to stresses, as well as in mechanisms generating evolutionary change.
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61
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Humann FC, Tiberio GJ, Hartfelder K. Sequence and expression characteristics of long noncoding RNAs in honey bee caste development--potential novel regulators for transgressive ovary size. PLoS One 2013; 8:e78915. [PMID: 24205350 PMCID: PMC3814967 DOI: 10.1371/journal.pone.0078915] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 09/25/2013] [Indexed: 11/19/2022] Open
Abstract
Division of labor in social insect colonies relies on a strong reproductive bias that favors queens. Although the ecological and evolutionary success attained through caste systems is well sketched out in terms of ultimate causes, the molecular and cellular underpinnings driving the development of caste phenotypes are still far from understood. Recent genomics approaches on honey bee developmental biology revealed a set of genes that are differentially expressed genes in larval ovaries and associated with transgressive ovary size in queens and massive cell death in workers. Amongst these, two contigs called special attention, both being over 200 bp in size and lacking apparent coding potential. Herein, we obtained their full cDNA sequences. These and their secondary structure characteristics placed in evidence that they are bona fide long noncoding RNAs (lncRNA) differentially expressed in larval ovaries, thus named lncov1 and lncov2. Genomically, both map within a previously identified QTL on chromosome 11, associated with transgressive ovary size in honey bee workers. As lncov1 was over-expressed in worker ovaries we focused on this gene. Real-time qPCR analysis on larval worker ovaries evidenced an expression peak coinciding with the onset of autophagic cell death. Cellular localization analysis through fluorescence in situ hybridization revealed perinuclear spots resembling omega speckles known to regulate trafficking of RNA-binding proteins. With only four lncRNAs known so far in honey bees, two expressed in the ovaries, these findings open a novel perspective on regulatory factors acting in the fine tuning of developmental processes underlying phenotypic plasticity related to social life histories.
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Affiliation(s)
- Fernanda C. Humann
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Gustavo J. Tiberio
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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62
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Qureshi IA, Mehler MF. Long non-coding RNAs: novel targets for nervous system disease diagnosis and therapy. Neurotherapeutics 2013; 10:632-46. [PMID: 23817781 PMCID: PMC3805860 DOI: 10.1007/s13311-013-0199-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), a novel and important class of genes. Our knowledge of lncRNAs has grown exponentially since their discovery within the last decade. lncRNAs are expressed in a highly cell- and tissue-specific manner, and are particularly abundant within the nervous system. lncRNAs are subject to post-transcriptional processing and inter- and intra-cellular transport. lncRNAs act via a spectrum of molecular mechanisms leveraging their ability to engage in both sequence-specific and conformational interactions with diverse partners (DNA, RNA, and proteins). Because of their size, lncRNAs act in a modular fashion, bringing different macromolecules together within the three-dimensional context of the cell. lncRNAs thus coordinate the execution of transcriptional, post-transcriptional, and epigenetic processes and critical biological programs (growth and development, establishment of cell identity, and deployment of stress responses). Emerging data reveal that lncRNAs play vital roles in mediating the developmental complexity, cellular diversity, and activity-dependent plasticity that are hallmarks of brain. Corresponding studies implicate these factors in brain aging and the pathophysiology of brain disorders, through evolving paradigms including the following: (i) genetic variation in lncRNA genes causes disease and influences susceptibility; (ii) epigenetic deregulation of lncRNAs genes is associated with disease; (iii) genomic context links lncRNA genes to disease genes and pathways; and (iv) lncRNAs are otherwise interconnected with known pathogenic mechanisms. Hence, lncRNAs represent prime targets that can be exploited for diagnosing and treating nervous system diseases. Such clinical applications are in the early stages of development but are rapidly advancing because of existing expertise and technology platforms that are readily adaptable for these purposes.
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Affiliation(s)
- Irfan A. Qureshi
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, New York USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Room 401, Bronx, New York 10461 USA
| | - Mark F. Mehler
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, New York USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, New York USA
- />Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York USA
- />Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Room 401, Bronx, New York 10461 USA
- />Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, New York USA
- />Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York USA
- />Center for Epigenomics, Albert Einstein College of Medicine, Bronx, New York USA
- />Institute for Aging Research, Albert Einstein College of Medicine, Bronx, New York USA
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63
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Tani H, Torimura M. Identification of short-lived long non-coding RNAs as surrogate indicators for chemical stress response. Biochem Biophys Res Commun 2013; 439:547-51. [PMID: 24036268 DOI: 10.1016/j.bbrc.2013.09.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/02/2013] [Indexed: 11/30/2022]
Abstract
Abiotic and biotic stressors in human cells are often a result of sudden and/or frequent changes in environmental factors. The molecular response to stress involves elaborate modulation of gene expression and is of homeostatic, ecological, and evolutionary importance. Although attention has primarily focused on signaling pathways and protein networks, long non-coding RNAs (ncRNAs) are increasingly involved in the molecular mechanisms associated with responses to cellular stresses. We identified six novel short-lived long ncRNAs (MIR22HG, GABPB-AS1, LINC00152, IDI2-AS1, SNHG15, and FLJ33630) that responded to chemical stressors (cisplatin, cycloheximide, and mercury (II) oxide) in HeLa Tet-off cells. Our results indicate that short-lived long ncRNAs respond to general and specific chemical stressors. The expression levels of the short-lived long ncRNAs were elevated because of prolonged decay rates in response to chemical stressors and interruption of RNA degradation pathways. We propose that these long ncRNAs have the potential to be surrogate indicators of cellular stress responses.
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Affiliation(s)
- Hidenori Tani
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1, Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
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64
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Hahn Y. Evidence for the dissemination of cryptic non-coding RNAs transcribed from intronic and intergenic segments by retroposition. Bioinformatics 2013; 29:1593-9. [PMID: 23652427 DOI: 10.1093/bioinformatics/btt258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Insertion of DNA segments is one mechanism by which genomes evolve. The bulk of genomic segments are now known to be transcribed into long and short non-coding RNAs (ncRNAs), promoter-associated transcripts and enhancer-templated transcripts. These various cryptic ncRNAs are thought to be dispersed in the human and other genomes by retroposition. RESULTS In this study, I report clear evidence for dissemination of cryptic ncRNAs transcribed from intronic and intergenic segments by retroposition. I used highly stringent conditions to find recently retroposed ncRNAs that had a poly(A) tract and were flanked by target site duplication. I identified 73 instances of retroposition in the human, mouse, and rat genomes (12, 36 and 25 instances, respectively). The inserted segments, in some cases, served as a novel exon or promoter for the associated gene, resulting in novel transcript variants. Some disseminated sequences showed sequence conservation across animals, implying a possible regulatory role. My results indicate that retroposition is one of the mechanisms for dispersion of ncRNAs. I propose that these newly inserted segments may play a role in genome evolution by potentially functioning as novel exons, promoters or enhancers. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yoonsoo Hahn
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Korea.
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Tang JY, Lee JC, Chang YT, Hou MF, Huang HW, Liaw CC, Chang HW. Long noncoding RNAs-related diseases, cancers, and drugs. ScientificWorldJournal 2013; 2013:943539. [PMID: 23843741 PMCID: PMC3690748 DOI: 10.1155/2013/943539] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/20/2013] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNA (lncRNA) function is described in terms of related gene expressions, diseases, and cancers as well as their polymorphisms. Potential modulators of lncRNA function, including clinical drugs, natural products, and derivatives, are discussed, and bioinformatic resources are summarized. The improving knowledge of the lncRNA regulatory network has implications not only in gene expression, diseases, and cancers, but also in the development of lncRNA-based pharmacology.
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Affiliation(s)
- Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jin-Ching Lee
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yung-Ting Chang
- Doctor Degree Program in Marine Biotechnology, National Sun Yat-sen University/Academia Sinica, Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Hurng-Wern Huang
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chih-Chuang Liaw
- Doctor Degree Program in Marine Biotechnology, National Sun Yat-sen University/Academia Sinica, Kaohsiung, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
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Pathak RU, Mamillapalli A, Rangaraj N, Kumar RP, Vasanthi D, Mishra K, Mishra RK. AAGAG repeat RNA is an essential component of nuclear matrix in Drosophila. RNA Biol 2013; 10:564-71. [PMID: 23588056 DOI: 10.4161/rna.24326] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic nucleus is functionally as well as spatially compartmentalized and maintains dynamic organization of sub-nuclear bodies. This organization is supported by a non-chromatin nuclear structure called the nuclear matrix. Although the precise molecular composition and ultra-structure of the nuclear matrix is not known, proteins and RNA molecules are its major components and several nuclear matrix proteins have been identified. However, the nature of its RNA component is unknown. Here we show that in Drosophila melanogaster, transcripts from AAGAG repeats of several hundred nucleotide in length are critical constituents of the nuclear matrix. While both the strands of this repeat are transcribed and are nuclear matrix associated, the polypurine strand is predominantly detected in situ. We also show that AAGAG RNA is essential for viability. Our results reveal the molecular identity of a critical RNA component of the nuclear architecture and point to one of the utilities of the repetitive part of the genome that has accumulated in higher eukaryotes.
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Affiliation(s)
- Rashmi U Pathak
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
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